6KHJ

Supercomplex for electron transfer


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.00 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

Structural basis for electron transport mechanism of complex I-like photosynthetic NAD(P)H dehydrogenase.

Pan, X.Cao, D.Xie, F.Xu, F.Su, X.Mi, H.Zhang, X.Li, M.

(2020) Nat Commun 11: 610-610

  • DOI: https://doi.org/10.1038/s41467-020-14456-0
  • Primary Citation of Related Structures:  
    6KHI, 6KHJ

  • PubMed Abstract: 

    NAD(P)H dehydrogenase-like (NDH) complex NDH-1L of cyanobacteria plays a crucial role in cyclic electron flow (CEF) around photosystem I and respiration processes. NDH-1L couples the electron transport from ferredoxin (Fd) to plastoquinone (PQ) and proton pumping from cytoplasm to the lumen that drives the ATP production. NDH-1L-dependent CEF increases the ATP/NADPH ratio, and is therefore pivotal for oxygenic phototrophs to function under stress. Here we report two structures of NDH-1L from Thermosynechococcus elongatus BP-1, in complex with one Fd and an endogenous PQ, respectively. Our structures represent the complete model of cyanobacterial NDH-1L, revealing the binding manner of NDH-1L with Fd and PQ, as well as the structural elements crucial for proper functioning of the NDH-1L complex. Together, our data provides deep insights into the electron transport from Fd to PQ, and its coupling with proton translocation in NDH-1L.


  • Organizational Affiliation

    National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, PR China.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
NAD(P)H-quinone oxidoreductase subunit 1372Thermosynechococcus vestitus BP-1Mutation(s): 0 
EC: 7.1.1
Membrane Entity: Yes 
UniProt
Find proteins for Q8DL32 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1))
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UniProt GroupQ8DL32
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
NAD(P)H-quinone oxidoreductase subunit 2515Thermosynechococcus vestitus BP-1Mutation(s): 0 
EC: 7.1.1
Membrane Entity: Yes 
UniProt
Find proteins for Q8DMR6 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1))
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UniProt GroupQ8DMR6
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
NAD(P)H-quinone oxidoreductase subunit 3132Thermosynechococcus vestitus BP-1Mutation(s): 0 
EC: 7.1.1
Membrane Entity: Yes 
UniProt
Find proteins for Q8DJ02 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1))
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UniProt GroupQ8DJ02
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
NAD(P)H-quinone oxidoreductase chain 4 1529Thermosynechococcus vestitus BP-1Mutation(s): 0 
EC: 7.1.1
Membrane Entity: Yes 
UniProt
Find proteins for Q8DKY0 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1))
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UniProt GroupQ8DKY0
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
NAD(P)H-quinone oxidoreductase subunit 4L101Thermosynechococcus vestitus BP-1Mutation(s): 0 
EC: 7.1.1
Membrane Entity: Yes 
UniProt
Find proteins for Q8DL29 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1))
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UniProt GroupQ8DL29
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase subunit 5656Thermosynechococcus vestitus BP-1Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q8DKX9 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1))
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UniProt GroupQ8DKX9
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
NADH-quinone oxidoreductase subunit J200Thermosynechococcus vestitus BP-1Mutation(s): 0 
EC: 7.1.1
Membrane Entity: Yes 
UniProt
Find proteins for Q8DL30 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1))
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UniProt GroupQ8DL30
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
NAD(P)H-quinone oxidoreductase subunit H394Thermosynechococcus vestitus BP-1Mutation(s): 0 
EC: 7.1.1
Membrane Entity: Yes 
UniProt
Find proteins for Q8DJD9 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1))
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UniProt GroupQ8DJD9
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
NAD(P)H-quinone oxidoreductase subunit I196Thermosynechococcus vestitus BP-1Mutation(s): 0 
EC: 7.1.1
Membrane Entity: Yes 
UniProt
Find proteins for Q8DL31 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1))
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UniProt GroupQ8DL31
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
NAD(P)H-quinone oxidoreductase subunit J168Thermosynechococcus vestitus BP-1Mutation(s): 0 
EC: 7.1.1
Membrane Entity: Yes 
UniProt
Find proteins for Q8DJ01 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1))
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UniProt GroupQ8DJ01
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
NAD(P)H-quinone oxidoreductase subunit K237Thermosynechococcus vestitus BP-1Mutation(s): 0 
EC: 7.1.1
Membrane Entity: Yes 
UniProt
Find proteins for Q8DKZ4 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1))
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UniProt GroupQ8DKZ4
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
NAD(P)H-quinone oxidoreductase subunit L76Thermosynechococcus vestitus BP-1Mutation(s): 0 
EC: 7.1.1
Membrane Entity: Yes 
UniProt
Find proteins for Q8DKZ3 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1))
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UniProt GroupQ8DKZ3
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
NAD(P)H-quinone oxidoreductase subunit M111Thermosynechococcus vestitus BP-1Mutation(s): 0 
EC: 7.1.1
Membrane Entity: Yes 
UniProt
Find proteins for Q8DLN5 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1))
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UniProt GroupQ8DLN5
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
NAD(P)H-quinone oxidoreductase subunit N150Thermosynechococcus vestitus BP-1Mutation(s): 0 
EC: 7.1.1
Membrane Entity: Yes 
UniProt
Find proteins for Q8DJU2 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1))
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UniProt GroupQ8DJU2
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
NAD(P)H-quinone oxidoreductase subunit O70Thermosynechococcus vestitus BP-1Mutation(s): 0 
EC: 7.1.1
Membrane Entity: Yes 
UniProt
Find proteins for Q8DMU4 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1))
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UniProt GroupQ8DMU4
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
proton-translocating NADH-quinone dehydrogenase subunit P44Thermosynechococcus vestitus BP-1Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for V5V507 (Thermosynechococcus sp. NK55a)
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UniProt GroupV5V507
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
proton-translocating NADH-quinone dehydrogenase subunit Q45Thermosynechococcus vestitus BP-1Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for V5V791 (Thermosynechococcus sp. NK55a)
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UniProt GroupV5V791
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
Tlr0636 proteinR [auth S]110Thermosynechococcus vestitus BP-1Mutation(s): 0 
UniProt
Find proteins for Q8DL61 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1))
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UniProt GroupQ8DL61
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  • Reference Sequence
Small Molecules
Ligands 8 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
DGD (Subject of Investigation/LOI)
Query on DGD

Download Ideal Coordinates CCD File 
S [auth A],
T [auth A]
DIGALACTOSYL DIACYL GLYCEROL (DGDG)
C51 H96 O15
LDQFLSUQYHBXSX-HXXRYREZSA-N
SQD (Subject of Investigation/LOI)
Query on SQD

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LA [auth N],
V [auth B],
W [auth C]
1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL
C41 H78 O12 S
RVUUQPKXGDTQPG-JUDHQOGESA-N
LMG (Subject of Investigation/LOI)
Query on LMG

Download Ideal Coordinates CCD File 
CA [auth F],
EA [auth F]
1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
C45 H86 O10
DCLTVZLYPPIIID-CVELTQQQSA-N
PL9 (Subject of Investigation/LOI)
Query on PL9

Download Ideal Coordinates CCD File 
U [auth A]2,3-DIMETHYL-5-(3,7,11,15,19,23,27,31,35-NONAMETHYL-2,6,10,14,18,22,26,30,34-HEXATRIACONTANONAENYL-2,5-CYCLOHEXADIENE-1,4-DIONE-2,3-DIMETHYL-5-SOLANESYL-1,4-BENZOQUINONE
C53 H80 O2
FKUYMLZIRPABFK-UHFFFAOYSA-N
LHG (Subject of Investigation/LOI)
Query on LHG

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DA [auth F]
FA [auth F]
GA [auth F]
HA [auth I]
X [auth C]
DA [auth F],
FA [auth F],
GA [auth F],
HA [auth I],
X [auth C],
Y [auth D]
1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
C38 H75 O10 P
BIABMEZBCHDPBV-MPQUPPDSSA-N
BCR (Subject of Investigation/LOI)
Query on BCR

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BA [auth F],
Z [auth D]
BETA-CAROTENE
C40 H56
OENHQHLEOONYIE-JLTXGRSLSA-N
LMT
Query on LMT

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AA [auth D]DODECYL-BETA-D-MALTOSIDE
C24 H46 O11
NLEBIOOXCVAHBD-QKMCSOCLSA-N
SF4 (Subject of Investigation/LOI)
Query on SF4

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IA [auth I],
JA [auth I],
KA [auth K]
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Ministry of Science and Technology (China)China2017YFA0503702
Ministry of Science and Technology (China)China2017YFA0504700
Ministry of Science and Technology (China)China2016YFA0502900
Chinese Academy of SciencesChinaXDB08020302
Chinese Academy of SciencesChinaXDB08030204
Chinese Academy of SciencesChinaXDB27020106
Chinese Academy of SciencesChinaQYZDB-SSW-SMC005
National Natural Science Foundation of ChinaChina31770778
National Natural Science Foundation of ChinaChina31600609

Revision History  (Full details and data files)

  • Version 1.0: 2020-02-12
    Type: Initial release
  • Version 1.1: 2024-03-27
    Changes: Data collection, Database references