5GUP

Cryo-EM structure of mammalian respiratory supercomplex I1III2IV1

PDB DOI: https://doi.org/10.2210/pdb5GUP/pdb
EM Map EMD-9539: EMDB EMDataResource

Classification: ELECTRON TRANSPORT
Organism(s): Sus scrofa
Mutation(s): No
Membrane Protein: Yes OPMmpstruc

Deposited: 2016-08-30 Released: 2017-03-29
Deposition Author(s): Gu, J., Wu, M., Guo, R., Yang, M.
Funding Organization(s): Ministry of Science and Technology of China, National Outstanding Young Scholar Science Foundation, National Natural Science Foundation of China

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 4.00 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

Structure of Mammalian Respiratory Supercomplex I1III2IV1

Wu, M., Gu, J., Guo, R., Huang, Y., Yang, M.

(2016) Cell 167: 1598-1609.e10

PubMed: 27912063 Search on PubMed
DOI: https://doi.org/10.1016/j.cell.2016.11.012
Primary Citation of Related Structures:
5GUP

PubMed Abstract:
The mammalian respiratory chain complexes assemble into supercomplexes (SCs) and reside in the inner mitochondrial membrane to transfer electrons and establish the proton gradient for complex V to synthesize ATP. The precise arrangement of SCs is largely unknown. Here, we report a 4.0-Å cryo-electron microscopy (cryo-EM) structure of the major SC in porcine heart, the 1.7-MDa SCI ₁III ₂IV ₁. The complex III (CIII) dimer and complex IV (CIV) bind at the same side of the L-shaped complex I (CI). Several accessory or supernumerary subunits of CI, such as NDUFA11, NDUFB4, NDUFB8, and NDUFB9, directly contribute to the oligomerization of CI, CIII, and CIV. COX7C and COX7A of CIV attach CIV to the concave surface formed by CIII and the distal end of membrane arm of CI. The structure suggests a possible mechanism by which electrons are transferred from NADH to cytochrome c and provides a platform for future functional dissection of respiration.

Organizational Affiliation

Ministry of Education Key Laboratory of Protein Science, Tsinghua-Peking Joint Center for Life Sciences, Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China.

Macromolecule Content

Total Structure Weight: 1,818.75 kDa
Atom Count: 109,982
Modelled Residue Count: 13,920
Deposited Residue Count: 15,851
Unique protein chains: 67

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome c oxidase subunit 6C	A	73	Sus scrofa	Mutation(s): 0
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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial	B	464	Sus scrofa	Mutation(s): 0 EC: 7.1.1.2 Membrane Entity: Yes
UniProt
Find proteins for A0A4X1SZP7 (Sus scrofa) Explore A0A4X1SZP7 Go to UniProtKB: A0A4X1SZP7
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UniProt Group	A0A4X1SZP7
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Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
NADH dehydrogenase [ubiquinone] iron-sulfur protein 2, mitochondrial	C	463	Sus scrofa	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for F1S1A8 (Sus scrofa) Explore F1S1A8 Go to UniProtKB: F1S1A8
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UniProt Group	F1S1A8
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Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
NADH dehydrogenase [ubiquinone] iron-sulfur protein 3, mitochondrial	D	264	Sus scrofa	Mutation(s): 0
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Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
NADH dehydrogenase [ubiquinone] flavoprotein 2, mitochondrial	E	249	Sus scrofa	Mutation(s): 0
UniProt
Find proteins for F1SM98 (Sus scrofa) Explore F1SM98 Go to UniProtKB: F1SM98
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UniProt Group	F1SM98
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Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrial	F	123	Sus scrofa	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for F1S031 (Sus scrofa) Explore F1S031 Go to UniProtKB: F1S031
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UniProt Group	F1S031
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Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrial	G	727	Sus scrofa	Mutation(s): 0
UniProt
Find proteins for A0A4X1V1H9 (Sus scrofa) Explore A0A4X1V1H9 Go to UniProtKB: A0A4X1V1H9
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UniProt Group	A0A4X1V1H9
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Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details	Image
NADH dehydrogenase [ubiquinone] iron-sulfur protein 8, mitochondrial	H	212	Sus scrofa	Mutation(s): 0
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Entity ID: 9
Molecule	Chains	Sequence Length	Organism	Details	Image
NADH dehydrogenase [ubiquinone] iron-sulfur protein 7, mitochondrial	I	216	Sus scrofa	Mutation(s): 0
UniProt
Find proteins for A0A8D1TL60 (Sus scrofa) Explore A0A8D1TL60 Go to UniProtKB: A0A8D1TL60
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UniProt Group	A0A8D1TL60
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Entity ID: 10
Molecule	Chains	Sequence Length	Organism	Details	Image
NADH dehydrogenase [ubiquinone] iron-sulfur protein 4, mitochondrial	J	175	Sus scrofa	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for G8IFA6 (Sus scrofa) Explore G8IFA6 Go to UniProtKB: G8IFA6
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UniProt Group	G8IFA6
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Entity ID: 11
Molecule	Chains	Sequence Length	Organism	Details	Image
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12	K, R	145	Sus scrofa	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for F1SQP4 (Sus scrofa) Explore F1SQP4 Go to UniProtKB: F1SQP4
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Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	F1SQP4
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Entity ID: 12
Molecule	Chains	Sequence Length	Organism	Details	Image
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 9, mitochondrial	L	377	Sus scrofa	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for F1SL07 (Sus scrofa) Explore F1SL07 Go to UniProtKB: F1SL07
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UniProt Group	F1SL07
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Entity ID: 13
Molecule	Chains	Sequence Length	Organism	Details	Image
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 7	M	113	Sus scrofa	Mutation(s): 0
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Entity ID: 14
Molecule	Chains	Sequence Length	Organism	Details	Image
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 5	N	116	Sus scrofa	Mutation(s): 0
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Entity ID: 15
Molecule	Chains	Sequence Length	Organism	Details	Image
Acyl carrier protein, mitochondrial	O, X	156	Sus scrofa	Mutation(s): 0
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Entity ID: 16
Molecule	Chains	Sequence Length	Organism	Details	Image
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 2	P	99	Sus scrofa	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for F1RGE3 (Sus scrofa) Explore F1RGE3 Go to UniProtKB: F1RGE3
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UniProt Group	F1RGE3
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Entity ID: 17
Molecule	Chains	Sequence Length	Organism	Details	Image
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 6	Q	128	Sus scrofa	Mutation(s): 0
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Entity ID: 18
Molecule	Chains	Sequence Length	Organism	Details	Image
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 1	S	70	Sus scrofa	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for K7GR43 (Sus scrofa) Explore K7GR43 Go to UniProtKB: K7GR43
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UniProt Group	K7GR43
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Entity ID: 19
Molecule	Chains	Sequence Length	Organism	Details	Image
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 3	T	84	Sus scrofa	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for A0A4X1VPG4 (Sus scrofa) Explore A0A4X1VPG4 Go to UniProtKB: A0A4X1VPG4
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UniProt Group	A0A4X1VPG4
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Entity ID: 20
Molecule	Chains	Sequence Length	Organism	Details	Image
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 10, mitochondrial	U	357	Sus scrofa	Mutation(s): 0
UniProt
Find proteins for F1SIS9 (Sus scrofa) Explore F1SIS9 Go to UniProtKB: F1SIS9
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UniProt Group	F1SIS9
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Entity ID: 21
Molecule	Chains	Sequence Length	Organism	Details	Image
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 11	V	141	Sus scrofa	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for I3LGM4 (Sus scrofa) Explore I3LGM4 Go to UniProtKB: I3LGM4
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UniProt Group	I3LGM4
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Entity ID: 22
Molecule	Chains	Sequence Length	Organism	Details	Image
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13	W	144	Sus scrofa	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for A0A8D1NRT6 (Sus scrofa) Explore A0A8D1NRT6 Go to UniProtKB: A0A8D1NRT6
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UniProt Group	A0A8D1NRT6
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Entity ID: 23
Molecule	Chains	Sequence Length	Organism	Details	Image
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 2, mitochondrial	Y	105	Sus scrofa	Mutation(s): 0
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Entity ID: 24
Molecule	Chains	Sequence Length	Organism	Details	Image
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 3	Z	98	Sus scrofa	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for A0A4X1VBN1 (Sus scrofa) Explore A0A4X1VBN1 Go to UniProtKB: A0A4X1VBN1
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UniProt Group	A0A4X1VBN1
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Entity ID: 25
Molecule	Chains	Sequence Length	Organism	Details	Image
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 5, mitochondrial	AA [auth a]	189	Sus scrofa	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for F1SGC6 (Sus scrofa) Explore F1SGC6 Go to UniProtKB: F1SGC6
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UniProt Group	F1SGC6
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Entity ID: 26
Molecule	Chains	Sequence Length	Organism	Details	Image
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 6	BA [auth b]	128	Sus scrofa	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for Q2EN80 (Sus scrofa) Explore Q2EN80 Go to UniProtKB: Q2EN80
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UniProt Group	Q2EN80
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Entity ID: 27
Molecule	Chains	Sequence Length	Organism	Details	Image
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8, mitochondrial	CA [auth c]	186	Sus scrofa	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for F1RWL7 (Sus scrofa) Explore F1RWL7 Go to UniProtKB: F1RWL7
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UniProt Group	F1RWL7
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Entity ID: 28
Molecule	Chains	Sequence Length	Organism	Details	Image
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10	DA [auth d]	176	Sus scrofa	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for I3LDC3 (Sus scrofa) Explore I3LDC3 Go to UniProtKB: I3LDC3
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UniProt Group	I3LDC3
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Entity ID: 29
Molecule	Chains	Sequence Length	Organism	Details	Image
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 11, mitochondrial	EA [auth e]	154	Sus scrofa	Mutation(s): 0
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Entity ID: 30
Molecule	Chains	Sequence Length	Organism	Details	Image
NADH dehydrogenase [ubiquinone] 1 subunit C1, mitochondrial	FA [auth f]	76	Sus scrofa	Mutation(s): 0 Membrane Entity: Yes
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Find proteins for F1RRC9 (Sus scrofa) Explore F1RRC9 Go to UniProtKB: F1RRC9
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UniProt Group	F1RRC9
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Entity ID: 31
Molecule	Chains	Sequence Length	Organism	Details	Image
NADH dehydrogenase [ubiquinone] 1 subunit C2	GA [auth g]	122	Sus scrofa	Mutation(s): 0
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Entity ID: 32
Molecule	Chains	Sequence Length	Organism	Details	Image
NADH dehydrogenase [ubiquinone] iron-sulfur protein 5	HA [auth h]	106	Sus scrofa	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for F1SV23 (Sus scrofa) Explore F1SV23 Go to UniProtKB: F1SV23
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UniProt Group	F1SV23
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Entity ID: 33
Molecule	Chains	Sequence Length	Organism	Details	Image
NADH-ubiquinone oxidoreductase chain 2	IA [auth i]	347	Sus scrofa	Mutation(s): 0 EC: 7.1.1.2 Membrane Entity: Yes
UniProt
Find proteins for O79875 (Sus scrofa) Explore O79875 Go to UniProtKB: O79875
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UniProt Group	O79875
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Entity ID: 34
Molecule	Chains	Sequence Length	Organism	Details	Image
NADH-ubiquinone oxidoreductase chain 3	JA [auth j]	115	Sus scrofa	Mutation(s): 0 EC: 7.1.1.2 Membrane Entity: Yes
UniProt
Find proteins for O79880 (Sus scrofa) Explore O79880 Go to UniProtKB: O79880
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UniProt Group	O79880
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Entity ID: 35
Molecule	Chains	Sequence Length	Organism	Details	Image
NADH-ubiquinone oxidoreductase chain 4L	KA [auth k]	98	Sus scrofa	Mutation(s): 0 EC: 7.1.1.2 Membrane Entity: Yes
UniProt
Find proteins for P56632 (Sus scrofa) Explore P56632 Go to UniProtKB: P56632
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UniProt Group	P56632
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Entity ID: 36
Molecule	Chains	Sequence Length	Organism	Details	Image
NADH-ubiquinone oxidoreductase chain 5	LA [auth l]	606	Sus scrofa	Mutation(s): 0 EC: 7.1.1.2 Membrane Entity: Yes
UniProt
Find proteins for Q9TDR1 (Sus scrofa) Explore Q9TDR1 Go to UniProtKB: Q9TDR1
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UniProt Group	Q9TDR1
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Entity ID: 37
Molecule	Chains	Sequence Length	Organism	Details	Image
NADH-ubiquinone oxidoreductase chain 6	MA [auth m]	175	Sus scrofa	Mutation(s): 0 EC: 7.1.1.2 Membrane Entity: Yes
UniProt
Find proteins for O79882 (Sus scrofa) Explore O79882 Go to UniProtKB: O79882
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UniProt Group	O79882
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Entity ID: 38
Molecule	Chains	Sequence Length	Organism	Details	Image
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 1	NA [auth n]	58	Sus scrofa	Mutation(s): 0 Membrane Entity: Yes
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Find proteins for A0A8D2CGH8 (Sus scrofa) Explore A0A8D2CGH8 Go to UniProtKB: A0A8D2CGH8
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UniProt Group	A0A8D2CGH8
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Entity ID: 39
Molecule	Chains	Sequence Length	Organism	Details	Image
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 4	OA [auth o]	129	Sus scrofa	Mutation(s): 0
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Entity ID: 40
Molecule	Chains	Sequence Length	Organism	Details	Image
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9	PA [auth p]	179	Sus scrofa	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for K7GSE5 (Sus scrofa) Explore K7GSE5 Go to UniProtKB: K7GSE5
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UniProt Group	K7GSE5
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Entity ID: 41
Molecule	Chains	Sequence Length	Organism	Details	Image
NADH-ubiquinone oxidoreductase chain 4	QA [auth q]	459	Sus scrofa	Mutation(s): 0 EC: 7.1.1.2 Membrane Entity: Yes
UniProt
Find proteins for O79881 (Sus scrofa) Explore O79881 Go to UniProtKB: O79881
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UniProt Group	O79881
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Entity ID: 42
Molecule	Chains	Sequence Length	Organism	Details	Image
NADH-ubiquinone oxidoreductase chain 1	RA [auth r]	318	Sus scrofa	Mutation(s): 0 EC: 7.1.1.2 Membrane Entity: Yes
UniProt
Find proteins for O79874 (Sus scrofa) Explore O79874 Go to UniProtKB: O79874
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UniProt Group	O79874
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Entity ID: 43
Molecule	Chains	Sequence Length	Organism	Details	Image
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8	SA [auth s]	172	Sus scrofa	Mutation(s): 0
UniProt
Find proteins for F1SLR1 (Sus scrofa) Explore F1SLR1 Go to UniProtKB: F1SLR1
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UniProt Group	F1SLR1
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Entity ID: 44
Molecule	Chains	Sequence Length	Organism	Details	Image
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 7	TA [auth t]	137	Sus scrofa	Mutation(s): 0
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Entity ID: 45
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome b-c1 complex subunit 1, mitochondrial	FB [auth 5], UA [auth u]	480	Sus scrofa	Mutation(s): 0
UniProt
Find proteins for F1SKM0 (Sus scrofa) Explore F1SKM0 Go to UniProtKB: F1SKM0
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UniProt Group	F1SKM0
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Entity ID: 46
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome b-c1 complex subunit 2, mitochondrial	GB [auth 6], VA [auth v]	453	Sus scrofa	Mutation(s): 0
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Entity ID: 47
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome b	HB [auth 7], WA [auth w]	379	Sus scrofa	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for Q1HBG9 (Sus scrofa) Explore Q1HBG9 Go to UniProtKB: Q1HBG9
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UniProt Group	Q1HBG9
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Entity ID: 48
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome c1, heme protein, mitochondrial	IB [auth 8], XA [auth x]	326	Sus scrofa	Mutation(s): 0
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Entity ID: 49
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome b-c1 complex subunit 7	JB [auth 9], YA [auth y]	111	Sus scrofa	Mutation(s): 0
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Entity ID: 50
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome b-c1 complex subunit 8	KB [auth Aa], ZA [auth z]	82	Sus scrofa	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for A0A4X1UYT9 (Sus scrofa) Explore A0A4X1UYT9 Go to UniProtKB: A0A4X1UYT9
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Entity ID: 51
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome b-c1 complex subunit 6, mitochondrial	AB [auth 0], LB [auth Ab]	91	Sus scrofa	Mutation(s): 0 Membrane Entity: Yes
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UniProt Group	F1S3W0
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Entity ID: 52
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome b-c1 complex subunit 9	BB [auth 1], MB [auth Ac]	64	Sus scrofa	Mutation(s): 0 Membrane Entity: Yes
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Find proteins for Q2EN79 (Sus scrofa) Explore Q2EN79 Go to UniProtKB: Q2EN79
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UniProt Group	Q2EN79
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Entity ID: 53
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome b-c1 complex subunit Rieske, mitochondrial	CB [auth 2], EB [auth 4]	274	Sus scrofa	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for F1RNZ1 (Sus scrofa) Explore F1RNZ1 Go to UniProtKB: F1RNZ1
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UniProt Group	F1RNZ1
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Entity ID: 54
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome b-c1 complex subunit 10	DB [auth 3], NB [auth Ad]	56	Sus scrofa	Mutation(s): 0 Membrane Entity: Yes
UniProt
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UniProt Group	F1SDI2
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Entity ID: 55
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome b-c1 complex subunit Rieske transit peptide, mitochondrial	OB [auth Ae], PB [auth Af]	78	Sus scrofa	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for F1RNZ1 (Sus scrofa) Explore F1RNZ1 Go to UniProtKB: F1RNZ1
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Entity ID: 56
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome c oxidase subunit 8B, mitochondrial	QB [auth Ag]	46	Sus scrofa	Mutation(s): 0
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Entity ID: 57
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome c oxidase subunit 7A1, mitochondrial	RB [auth Ah]	59	Sus scrofa	Mutation(s): 0
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Entity ID: 58
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome c oxidase subunit 7B, mitochondrial	SB [auth Ai]	56	Sus scrofa	Mutation(s): 0
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Entity ID: 59
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome c oxidase subunit 7C, mitochondrial	TB [auth Aj]	47	Sus scrofa	Mutation(s): 0
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Entity ID: 60
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome c oxidase subunit 1	UB [auth Ak]	514	Sus scrofa	Mutation(s): 0
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Entity ID: 61
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome c oxidase subunit 2	VB [auth Al]	227	Sus scrofa	Mutation(s): 0
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Entity ID: 62
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome c oxidase subunit 3	WB [auth Am]	261	Sus scrofa	Mutation(s): 0
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Entity ID: 63
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome c oxidase subunit 4 isoform 1, mitochondrial	XB [auth An]	147	Sus scrofa	Mutation(s): 0
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Entity ID: 64
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome c oxidase subunit 5A, mitochondrial	YB [auth Ao]	109	Sus scrofa	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for F1SJ34 (Sus scrofa) Explore F1SJ34 Go to UniProtKB: F1SJ34
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UniProt Group	F1SJ34
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Entity ID: 65
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome c oxidase subunit 5B, mitochondrial	ZB [auth Ap]	98	Sus scrofa	Mutation(s): 0
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Entity ID: 66
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome c oxidase subunit 6A, mitochondrial	AC [auth Aq]	84	Sus scrofa	Mutation(s): 0
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Entity ID: 67
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome c oxidase subunit 6B1	BC [auth Ar]	85	Sus scrofa	Mutation(s): 0
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Small Molecules

Ligands 14 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CDL Query on CDL Download Ideal Coordinates CCD File SDF format, chain FD [auth x] SDF format, chain GD [auth z] SDF format, chain MD [auth 5] SDF format, chain OC [auth V] SDF format, chain SD [auth 8] SDF format, chain UC [auth i] SDF format, chain UD [auth Aa] SDF format, chain WC [auth l] SDF format, chain YC [auth s] SDF format, chain ZC [auth u] MOL2 format, chain FD [auth x] MOL2 format, chain GD [auth z] MOL2 format, chain MD [auth 5] MOL2 format, chain OC [auth V] MOL2 format, chain SD [auth 8] MOL2 format, chain UC [auth i] MOL2 format, chain UD [auth Aa] MOL2 format, chain WC [auth l] MOL2 format, chain YC [auth s] MOL2 format, chain ZC [auth u] mmCIF format, chain FD [auth x] mmCIF format, chain GD [auth z] mmCIF format, chain MD [auth 5] mmCIF format, chain OC [auth V] mmCIF format, chain SD [auth 8] mmCIF format, chain UC [auth i] mmCIF format, chain UD [auth Aa] mmCIF format, chain WC [auth l] mmCIF format, chain YC [auth s] mmCIF format, chain ZC [auth u]	FD [auth x] GD [auth z] MD [auth 5] OC [auth V] SD [auth 8] FD [auth x], GD [auth z], MD [auth 5], OC [auth V], SD [auth 8], UC [auth i], UD [auth Aa], WC [auth l], YC [auth s], ZC [auth u]	CARDIOLIPIN C₈₁ H₁₅₆ O₁₇ P₂ XVTUQDWPJJBEHJ-KZCWQMDCSA-L		Interactions Focus chain FD [auth x] Focus chain GD [auth z] Focus chain MD [auth 5] Focus chain OC [auth V] Focus chain SD [auth 8] Focus chain UC [auth i] Focus chain UD [auth Aa] Focus chain WC [auth l] Focus chain YC [auth s] Focus chain ZC [auth u] Interactions & Density Focus chain FD [auth x] Focus chain GD [auth z] Focus chain MD [auth 5] Focus chain OC [auth V] Focus chain SD [auth 8] Focus chain UC [auth i] Focus chain UD [auth Aa] Focus chain WC [auth l] Focus chain YC [auth s] Focus chain ZC [auth u]
HEA Query on HEA Download Ideal Coordinates CCD File SDF format, chain VD [auth Ak] SDF format, chain WD [auth Ak] MOL2 format, chain VD [auth Ak] MOL2 format, chain WD [auth Ak] mmCIF format, chain VD [auth Ak] mmCIF format, chain WD [auth Ak]	VD [auth Ak], WD [auth Ak]	HEME-A C₄₉ H₅₆ Fe N₄ O₆ ZGGYGTCPXNDTRV-PRYGPKJJSA-L		Interactions Focus chain VD [auth Ak] Focus chain WD [auth Ak] Interactions & Density Focus chain VD [auth Ak] Focus chain WD [auth Ak]
PLX Query on PLX Download Ideal Coordinates CCD File SDF format, chain HD [auth 2] SDF format, chain KD [auth 4] SDF format, chain PC [auth V] SDF format, chain TC [auth i] SDF format, chain KC [auth H] MOL2 format, chain HD [auth 2] MOL2 format, chain KD [auth 4] MOL2 format, chain PC [auth V] MOL2 format, chain TC [auth i] MOL2 format, chain KC [auth H] mmCIF format, chain HD [auth 2] mmCIF format, chain KD [auth 4] mmCIF format, chain PC [auth V] mmCIF format, chain TC [auth i] mmCIF format, chain KC [auth H]	HD [auth 2], KC [auth H], KD [auth 4], PC [auth V], TC [auth i]	(9R,11S)-9-({[(1S)-1-HYDROXYHEXADECYL]OXY}METHYL)-2,2-DIMETHYL-5,7,10-TRIOXA-2LAMBDA~5~-AZA-6LAMBDA~5~-PHOSPHAOCTACOSANE-6,6,11-TRIOL C₄₂ H₈₉ N O₈ P YVNJQRQLQPWVSQ-IWSHAHEXSA-O		Interactions Focus chain HD [auth 2] Focus chain KC [auth H] Focus chain KD [auth 4] Focus chain PC [auth V] Focus chain TC [auth i] Interactions & Density Focus chain HD [auth 2] Focus chain KC [auth H] Focus chain KD [auth 4] Focus chain PC [auth V] Focus chain TC [auth i]
NDP Query on NDP Download Ideal Coordinates CCD File SDF format, chain MC [auth L] MOL2 format, chain MC [auth L] mmCIF format, chain MC [auth L]	MC [auth L]	NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C₂₁ H₃₀ N₇ O₁₇ P₃ ACFIXJIJDZMPPO-NNYOXOHSSA-N		Interactions Focus chain MC [auth L] Interactions & Density Focus chain MC [auth L]
PEE Query on PEE Download Ideal Coordinates CCD File SDF format, chain AD [auth u] SDF format, chain ID [auth 2] SDF format, chain PD [auth 7] SDF format, chain QC [auth W] SDF format, chain SC [auth i] SDF format, chain VC [auth l] SDF format, chain XC [auth q] SDF format, chain DD [auth w] SDF format, chain ND [auth 5] SDF format, chain OD [auth 7] MOL2 format, chain AD [auth u] MOL2 format, chain ID [auth 2] MOL2 format, chain PD [auth 7] MOL2 format, chain QC [auth W] MOL2 format, chain SC [auth i] MOL2 format, chain VC [auth l] MOL2 format, chain XC [auth q] MOL2 format, chain DD [auth w] MOL2 format, chain ND [auth 5] MOL2 format, chain OD [auth 7] mmCIF format, chain AD [auth u] mmCIF format, chain ID [auth 2] mmCIF format, chain PD [auth 7] mmCIF format, chain QC [auth W] mmCIF format, chain SC [auth i] mmCIF format, chain VC [auth l] mmCIF format, chain XC [auth q] mmCIF format, chain DD [auth w] mmCIF format, chain ND [auth 5] mmCIF format, chain OD [auth 7]	AD [auth u] DD [auth w] ID [auth 2] ND [auth 5] OD [auth 7] AD [auth u], DD [auth w], ID [auth 2], ND [auth 5], OD [auth 7], PD [auth 7], QC [auth W], SC [auth i], VC [auth l], XC [auth q]	1,2-dioleoyl-sn-glycero-3-phosphoethanolamine C₄₁ H₇₈ N O₈ P MWRBNPKJOOWZPW-NYVOMTAGSA-N		Interactions Focus chain AD [auth u] Focus chain DD [auth w] Focus chain ID [auth 2] Focus chain ND [auth 5] Focus chain OD [auth 7] Focus chain PD [auth 7] Focus chain QC [auth W] Focus chain SC [auth i] Focus chain VC [auth l] Focus chain XC [auth q] Interactions & Density Focus chain AD [auth u] Focus chain DD [auth w] Focus chain ID [auth 2] Focus chain ND [auth 5] Focus chain OD [auth 7] Focus chain PD [auth 7] Focus chain QC [auth W] Focus chain SC [auth i] Focus chain VC [auth l] Focus chain XC [auth q]
HEC Query on HEC Download Ideal Coordinates CCD File SDF format, chain ED [auth x] SDF format, chain TD [auth 8] MOL2 format, chain ED [auth x] MOL2 format, chain TD [auth 8] mmCIF format, chain ED [auth x] mmCIF format, chain TD [auth 8]	ED [auth x], TD [auth 8]	HEME C C₃₄ H₃₄ Fe N₄ O₄ HXQIYSLZKNYNMH-LJNAALQVSA-N		Interactions Focus chain ED [auth x] Focus chain TD [auth 8] Interactions & Density Focus chain ED [auth x] Focus chain TD [auth 8]
HEM Query on HEM Download Ideal Coordinates CCD File SDF format, chain BD [auth w] SDF format, chain CD [auth w] SDF format, chain QD [auth 7] SDF format, chain RD [auth 7] MOL2 format, chain BD [auth w] MOL2 format, chain CD [auth w] MOL2 format, chain QD [auth 7] MOL2 format, chain RD [auth 7] mmCIF format, chain BD [auth w] mmCIF format, chain CD [auth w] mmCIF format, chain QD [auth 7] mmCIF format, chain RD [auth 7]	BD [auth w], CD [auth w], QD [auth 7], RD [auth 7]	PROTOPORPHYRIN IX CONTAINING FE C₃₄ H₃₂ Fe N₄ O₄ KABFMIBPWCXCRK-RGGAHWMASA-L		Interactions Focus chain BD [auth w] Focus chain CD [auth w] Focus chain QD [auth 7] Focus chain RD [auth 7] Interactions & Density Focus chain BD [auth w] Focus chain CD [auth w] Focus chain QD [auth 7] Focus chain RD [auth 7]
ZMP Query on ZMP Download Ideal Coordinates CCD File SDF format, chain NC [auth Q] SDF format, chain RC [auth X] MOL2 format, chain NC [auth Q] MOL2 format, chain RC [auth X] mmCIF format, chain NC [auth Q] mmCIF format, chain RC [auth X]	NC [auth Q], RC [auth X]	S-[2-({N-[(2S)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alanyl}amino)ethyl] tetradecanethioate C₂₅ H₄₉ N₂ O₈ P S HDTINWYIVVMRIN-HSZRJFAPSA-N		Interactions Focus chain NC [auth Q] Focus chain RC [auth X] Interactions & Density Focus chain NC [auth Q] Focus chain RC [auth X]
FMN Query on FMN Download Ideal Coordinates CCD File SDF format, chain DC [auth B] MOL2 format, chain DC [auth B] mmCIF format, chain DC [auth B]	DC [auth B]	FLAVIN MONONUCLEOTIDE C₁₇ H₂₁ N₄ O₉ P FVTCRASFADXXNN-SCRDCRAPSA-N		Interactions Focus chain DC [auth B] Interactions & Density Focus chain DC [auth B]
SF4 Query on SF4 Download Ideal Coordinates CCD File SDF format, chain CC [auth B] SDF format, chain GC [auth G] SDF format, chain IC [auth H] SDF format, chain JC [auth H] SDF format, chain LC [auth I] SDF format, chain FC [auth G] MOL2 format, chain CC [auth B] MOL2 format, chain GC [auth G] MOL2 format, chain IC [auth H] MOL2 format, chain JC [auth H] MOL2 format, chain LC [auth I] MOL2 format, chain FC [auth G] mmCIF format, chain CC [auth B] mmCIF format, chain GC [auth G] mmCIF format, chain IC [auth H] mmCIF format, chain JC [auth H] mmCIF format, chain LC [auth I] mmCIF format, chain FC [auth G]	CC [auth B] FC [auth G] GC [auth G] IC [auth H] JC [auth H] CC [auth B], FC [auth G], GC [auth G], IC [auth H], JC [auth H], LC [auth I]	IRON/SULFUR CLUSTER Fe₄ S₄ LJBDFODJNLIPKO-UHFFFAOYSA-N		Interactions Focus chain CC [auth B] Focus chain FC [auth G] Focus chain GC [auth G] Focus chain IC [auth H] Focus chain JC [auth H] Focus chain LC [auth I] Interactions & Density Focus chain CC [auth B] Focus chain FC [auth G] Focus chain GC [auth G] Focus chain IC [auth H] Focus chain JC [auth H] Focus chain LC [auth I]
FES Query on FES Download Ideal Coordinates CCD File SDF format, chain EC [auth E] SDF format, chain HC [auth G] SDF format, chain JD [auth 2] SDF format, chain LD [auth 4] MOL2 format, chain EC [auth E] MOL2 format, chain HC [auth G] MOL2 format, chain JD [auth 2] MOL2 format, chain LD [auth 4] mmCIF format, chain EC [auth E] mmCIF format, chain HC [auth G] mmCIF format, chain JD [auth 2] mmCIF format, chain LD [auth 4]	EC [auth E], HC [auth G], JD [auth 2], LD [auth 4]	FE2/S2 (INORGANIC) CLUSTER Fe₂ S₂ NIXDOXVAJZFRNF-UHFFFAOYSA-N		Interactions Focus chain EC [auth E] Focus chain HC [auth G] Focus chain JD [auth 2] Focus chain LD [auth 4] Interactions & Density Focus chain EC [auth E] Focus chain HC [auth G] Focus chain JD [auth 2] Focus chain LD [auth 4]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain BE [auth Ap] MOL2 format, chain BE [auth Ap] mmCIF format, chain BE [auth Ap]	BE [auth Ap]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain BE [auth Ap] Interactions & Density Focus chain BE [auth Ap]
CU Query on CU Download Ideal Coordinates CCD File SDF format, chain XD [auth Ak] SDF format, chain ZD [auth Al] SDF format, chain AE [auth Al] MOL2 format, chain XD [auth Ak] MOL2 format, chain ZD [auth Al] MOL2 format, chain AE [auth Al] mmCIF format, chain XD [auth Ak] mmCIF format, chain ZD [auth Al] mmCIF format, chain AE [auth Al]	AE [auth Al], XD [auth Ak], ZD [auth Al]	COPPER (II) ION Cu JPVYNHNXODAKFH-UHFFFAOYSA-N		Interactions Focus chain AE [auth Al] Focus chain XD [auth Ak] Focus chain ZD [auth Al] Interactions & Density Focus chain AE [auth Al] Focus chain XD [auth Ak] Focus chain ZD [auth Al]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain YD [auth Ak] MOL2 format, chain YD [auth Ak] mmCIF format, chain YD [auth Ak]	YD [auth Ak]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain YD [auth Ak] Interactions & Density Focus chain YD [auth Ak]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 4.00 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
RECONSTRUCTION	RELION	1.4
MODEL REFINEMENT	PHENIX	1.9

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2017-03-29

Deposition Author(s):

Funding Organization	Location	Grant Number
Ministry of Science and Technology of China	China	2016YFA0501100 and 2012CB911101
National Outstanding Young Scholar Science Foundation	China	--
National Natural Science Foundation of China	China	3162500065, 31030020 and 31170679

Revision History (Full details and data files)

Version 1.0: 2017-03-29
Type: Initial release
Version 1.1: 2019-11-06
Changes: Data collection, Other

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.

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Help and Resources

5GUP

Cryo-EM structure of mammalian respiratory supercomplex I1III2IV1

Structure of Mammalian Respiratory Supercomplex I1III2IV1

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