7DDQ

Structure of RC-LH1-PufX from Rhodobacter veldkampii

PDB DOI: https://doi.org/10.2210/pdb7DDQ/pdb
EM Map EMD-30656: EMDB EMDataResource

Classification: PHOTOSYNTHESIS
Organism(s): Phaeovulum veldkampii DSM 11550
Mutation(s): No
Membrane Protein: Yes OPMPDBTM

Deposited: 2020-10-29 Released: 2021-06-30
Deposition Author(s): Bracun, L., Yamagata, A., Shirouzu, M., Liu, L.N.
Funding Organization(s): Royal Society, Biotechnology and Biological Sciences Research Council (BBSRC), Japan Agency for Medical Research and Development (AMED), Japan Society for the Promotion of Science (JSPS)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.84 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 2.1 of the entry. See complete history.

Literature

Cryo-EM structure of the photosynthetic RC-LH1-PufX supercomplex at 2.8-angstrom resolution.

Bracun, L., Yamagata, A., Christianson, B.M., Terada, T., Canniffe, D.P., Shirouzu, M., Liu, L.N.

(2021) Sci Adv 7

PubMed: 34134992 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1126/sciadv.abf8864
Primary Citation of Related Structures:
7DDQ

PubMed Abstract:
The reaction center (RC)-light-harvesting complex 1 (LH1) supercomplex plays a pivotal role in bacterial photosynthesis. Many RC-LH1 complexes integrate an additional protein PufX that is key for bacterial growth and photosynthetic competence. Here, we present a cryo-electron microscopy structure of the RC-LH1-PufX supercomplex from Rhodobacter veldkampii at 2.8-Å resolution. The RC-LH1-PufX monomer contains an LH ring of 15 αβ-polypeptides with a 30-Å gap formed by PufX. PufX acts as a molecular "cross brace" to reinforce the RC-LH1 structure. The unusual PufX-mediated large opening in the LH1 ring and defined arrangement of proteins and cofactors provide the molecular basis for the assembly of a robust RC-LH1-PufX supercomplex and efficient quinone transport and electron transfer. These architectural features represent the natural strategies for anoxygenic photosynthesis and environmental adaptation.

Organizational Affiliation

Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK.

Macromolecule Content

Total Structure Weight: 335.12 kDa
Atom Count: 22,571
Modelled Residue Count: 2,354
Deposited Residue Count: 2,494
Unique protein chains: 6

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Antenna pigment protein alpha chain	A [auth o] C [auth t] E [auth r] EA [auth g] G [auth a] A [auth o], C [auth t], E [auth r], EA [auth g], G [auth a], GA [auth d], I [auth e], K [auth b], M [auth k], O [auth f], Q [auth u], T [auth s], V [auth n], X [auth i], Z [auth j]	57	Phaeovulum veldkampii DSM 11550	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for A0A2T4JIR4 (Phaeovulum veldkampii DSM 11550) Explore A0A2T4JIR4 Go to UniProtKB: A0A2T4JIR4
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A2T4JIR4
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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Antenna pigment protein beta chain	AA [auth I] B [auth N] D [auth S] F [auth O] FA [auth F] AA [auth I], B [auth N], D [auth S], F [auth O], FA [auth F], H [auth U], HA [auth B], J [auth D], L [auth A], N [auth J], P [auth E], R [auth T], U [auth R], W [auth K], Y [auth G]	48	Phaeovulum veldkampii DSM 11550	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for A0A2T4JIL7 (Phaeovulum veldkampii DSM 11550) Explore A0A2T4JIL7 Go to UniProtKB: A0A2T4JIL7
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A2T4JIL7
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Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
PufX	S [auth X]	83	Phaeovulum veldkampii DSM 11550	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for A0A2T4JIP3 (Phaeovulum veldkampii DSM 11550) Explore A0A2T4JIP3 Go to UniProtKB: A0A2T4JIP3
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A2T4JIP3
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Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosynthetic reaction center L subunit	BA [auth L]	276	Phaeovulum veldkampii DSM 11550	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for A0A2T4JIS6 (Phaeovulum veldkampii DSM 11550) Explore A0A2T4JIS6 Go to UniProtKB: A0A2T4JIS6
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A2T4JIS6
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Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Reaction center protein M chain	CA [auth M]	308	Phaeovulum veldkampii DSM 11550	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for A0A2T4JIN0 (Phaeovulum veldkampii DSM 11550) Explore A0A2T4JIN0 Go to UniProtKB: A0A2T4JIN0
Entity Groups
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UniProt Group	A0A2T4JIN0
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Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosynthetic reaction center subunit H	DA [auth H]	252	Phaeovulum veldkampii DSM 11550	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for A0A2T4JIP4 (Phaeovulum veldkampii DSM 11550) Explore A0A2T4JIP4 Go to UniProtKB: A0A2T4JIP4
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A2T4JIP4
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
BCL Query on BCL Download Ideal Coordinates CCD File SDF format, chain AB [auth A] SDF format, chain AC [auth M] SDF format, chain BB [auth k] SDF format, chain BC [auth M] SDF format, chain EB [auth E] SDF format, chain FB [auth u] SDF format, chain GB [auth u] SDF format, chain GC [auth M] SDF format, chain IA [auth o] SDF format, chain JB [auth s] SDF format, chain KA [auth N] SDF format, chain KB [auth R] SDF format, chain KC [auth g] SDF format, chain LA [auth t] SDF format, chain LB [auth n] SDF format, chain MB [auth K] SDF format, chain MC [auth F] SDF format, chain NA [auth t] SDF format, chain NB [auth i] SDF format, chain OA [auth S] SDF format, chain OB [auth G] SDF format, chain OC [auth F] SDF format, chain PA [auth r] SDF format, chain PC [auth d] SDF format, chain QB [auth j] SDF format, chain RB [auth j] SDF format, chain SA [auth O] SDF format, chain SB [auth I] SDF format, chain TA [auth a] SDF format, chain UB [auth L] SDF format, chain VA [auth e] SDF format, chain XA [auth D] SDF format, chain YA [auth b] SDF format, chain ZA [auth b] MOL2 format, chain AB [auth A] MOL2 format, chain AC [auth M] MOL2 format, chain BB [auth k] MOL2 format, chain BC [auth M] MOL2 format, chain EB [auth E] MOL2 format, chain FB [auth u] MOL2 format, chain GB [auth u] MOL2 format, chain GC [auth M] MOL2 format, chain IA [auth o] MOL2 format, chain JB [auth s] MOL2 format, chain KA [auth N] MOL2 format, chain KB [auth R] MOL2 format, chain KC [auth g] MOL2 format, chain LA [auth t] MOL2 format, chain LB [auth n] MOL2 format, chain MB [auth K] MOL2 format, chain MC [auth F] MOL2 format, chain NA [auth t] MOL2 format, chain NB [auth i] MOL2 format, chain OA [auth S] MOL2 format, chain OB [auth G] MOL2 format, chain OC [auth F] MOL2 format, chain PA [auth r] MOL2 format, chain PC [auth d] MOL2 format, chain QB [auth j] MOL2 format, chain RB [auth j] MOL2 format, chain SA [auth O] MOL2 format, chain SB [auth I] MOL2 format, chain TA [auth a] MOL2 format, chain UB [auth L] MOL2 format, chain VA [auth e] MOL2 format, chain XA [auth D] MOL2 format, chain YA [auth b] MOL2 format, chain ZA [auth b] mmCIF format, chain AB [auth A] mmCIF format, chain AC [auth M] mmCIF format, chain BB [auth k] mmCIF format, chain BC [auth M] mmCIF format, chain EB [auth E] mmCIF format, chain FB [auth u] mmCIF format, chain GB [auth u] mmCIF format, chain GC [auth M] mmCIF format, chain IA [auth o] mmCIF format, chain JB [auth s] mmCIF format, chain KA [auth N] mmCIF format, chain KB [auth R] mmCIF format, chain KC [auth g] mmCIF format, chain LA [auth t] mmCIF format, chain LB [auth n] mmCIF format, chain MB [auth K] mmCIF format, chain MC [auth F] mmCIF format, chain NA [auth t] mmCIF format, chain NB [auth i] mmCIF format, chain OA [auth S] mmCIF format, chain OB [auth G] mmCIF format, chain OC [auth F] mmCIF format, chain PA [auth r] mmCIF format, chain PC [auth d] mmCIF format, chain QB [auth j] mmCIF format, chain RB [auth j] mmCIF format, chain SA [auth O] mmCIF format, chain SB [auth I] mmCIF format, chain TA [auth a] mmCIF format, chain UB [auth L] mmCIF format, chain VA [auth e] mmCIF format, chain XA [auth D] mmCIF format, chain YA [auth b] mmCIF format, chain ZA [auth b]	AB [auth A] AC [auth M] BB [auth k] BC [auth M] EB [auth E] AB [auth A], AC [auth M], BB [auth k], BC [auth M], EB [auth E], FB [auth u], GB [auth u], GC [auth M], IA [auth o], JB [auth s], KA [auth N], KB [auth R], KC [auth g], LA [auth t], LB [auth n], MB [auth K], MC [auth F], NA [auth t], NB [auth i], OA [auth S], OB [auth G], OC [auth F], PA [auth r], PC [auth d], QB [auth j], RB [auth j], SA [auth O], SB [auth I], TA [auth a], UB [auth L], VA [auth e], XA [auth D], YA [auth b], ZA [auth b]	BACTERIOCHLOROPHYLL A C₅₅ H₇₄ Mg N₄ O₆ DSJXIQQMORJERS-AGGZHOMASA-M		Interactions Focus chain AB [auth A] Focus chain AC [auth M] Focus chain BB [auth k] Focus chain BC [auth M] Focus chain EB [auth E] Focus chain FB [auth u] Focus chain GB [auth u] Focus chain GC [auth M] Focus chain IA [auth o] Focus chain JB [auth s] Focus chain KA [auth N] Focus chain KB [auth R] Focus chain KC [auth g] Focus chain LA [auth t] Focus chain LB [auth n] Focus chain MB [auth K] Focus chain MC [auth F] Focus chain NA [auth t] Focus chain NB [auth i] Focus chain OA [auth S] Focus chain OB [auth G] Focus chain OC [auth F] Focus chain PA [auth r] Focus chain PC [auth d] Focus chain QB [auth j] Focus chain RB [auth j] Focus chain SA [auth O] Focus chain SB [auth I] Focus chain TA [auth a] Focus chain UB [auth L] Focus chain VA [auth e] Focus chain XA [auth D] Focus chain YA [auth b] Focus chain ZA [auth b] Interactions & Density Focus chain AB [auth A] Focus chain AC [auth M] Focus chain BB [auth k] Focus chain BC [auth M] Focus chain EB [auth E] Focus chain FB [auth u] Focus chain GB [auth u] Focus chain GC [auth M] Focus chain IA [auth o] Focus chain JB [auth s] Focus chain KA [auth N] Focus chain KB [auth R] Focus chain KC [auth g] Focus chain LA [auth t] Focus chain LB [auth n] Focus chain MB [auth K] Focus chain MC [auth F] Focus chain NA [auth t] Focus chain NB [auth i] Focus chain OA [auth S] Focus chain OB [auth G] Focus chain OC [auth F] Focus chain PA [auth r] Focus chain PC [auth d] Focus chain QB [auth j] Focus chain RB [auth j] Focus chain SA [auth O] Focus chain SB [auth I] Focus chain TA [auth a] Focus chain UB [auth L] Focus chain VA [auth e] Focus chain XA [auth D] Focus chain YA [auth b] Focus chain ZA [auth b]
BPH Query on BPH Download Ideal Coordinates CCD File SDF format, chain CC [auth M] SDF format, chain VB [auth L] SDF format, chain ZB [auth L] MOL2 format, chain CC [auth M] MOL2 format, chain VB [auth L] MOL2 format, chain ZB [auth L] mmCIF format, chain CC [auth M] mmCIF format, chain VB [auth L] mmCIF format, chain ZB [auth L]	CC [auth M], VB [auth L], ZB [auth L]	BACTERIOPHEOPHYTIN A C₅₅ H₇₆ N₄ O₆ KWOZSBGNAHVCKG-SZQBJALDSA-N		Interactions Focus chain CC [auth M] Focus chain VB [auth L] Focus chain ZB [auth L] Interactions & Density Focus chain CC [auth M] Focus chain VB [auth L] Focus chain ZB [auth L]
U10 Query on U10 Download Ideal Coordinates CCD File SDF format, chain EC [auth M] SDF format, chain HC [auth M] SDF format, chain UA [auth a] SDF format, chain WB [auth L] SDF format, chain XB [auth L] SDF format, chain YB [auth L] MOL2 format, chain EC [auth M] MOL2 format, chain HC [auth M] MOL2 format, chain UA [auth a] MOL2 format, chain WB [auth L] MOL2 format, chain XB [auth L] MOL2 format, chain YB [auth L] mmCIF format, chain EC [auth M] mmCIF format, chain HC [auth M] mmCIF format, chain UA [auth a] mmCIF format, chain WB [auth L] mmCIF format, chain XB [auth L] mmCIF format, chain YB [auth L]	EC [auth M] HC [auth M] UA [auth a] WB [auth L] XB [auth L] EC [auth M], HC [auth M], UA [auth a], WB [auth L], XB [auth L], YB [auth L]	UBIQUINONE-10 C₅₉ H₉₀ O₄ ACTIUHUUMQJHFO-UPTCCGCDSA-N		Interactions Focus chain EC [auth M] Focus chain HC [auth M] Focus chain UA [auth a] Focus chain WB [auth L] Focus chain XB [auth L] Focus chain YB [auth L] Interactions & Density Focus chain EC [auth M] Focus chain HC [auth M] Focus chain UA [auth a] Focus chain WB [auth L] Focus chain XB [auth L] Focus chain YB [auth L]
3PE Query on 3PE Download Ideal Coordinates CCD File SDF format, chain IC [auth H] SDF format, chain JC [auth H] SDF format, chain QC [auth d] MOL2 format, chain IC [auth H] MOL2 format, chain JC [auth H] MOL2 format, chain QC [auth d] mmCIF format, chain IC [auth H] mmCIF format, chain JC [auth H] mmCIF format, chain QC [auth d]	IC [auth H], JC [auth H], QC [auth d]	1,2-Distearoyl-sn-glycerophosphoethanolamine C₄₁ H₈₂ N O₈ P LVNGJLRDBYCPGB-LDLOPFEMSA-N		Interactions Focus chain IC [auth H] Focus chain JC [auth H] Focus chain QC [auth d] Interactions & Density Focus chain IC [auth H] Focus chain JC [auth H] Focus chain QC [auth d]
SPO Query on SPO Download Ideal Coordinates CCD File SDF format, chain CB [auth k] SDF format, chain DB [auth E] SDF format, chain FC [auth M] SDF format, chain HB [auth X] SDF format, chain IB [auth s] SDF format, chain JA [auth N] SDF format, chain LC [auth g] SDF format, chain MA [auth t] SDF format, chain NC [auth F] SDF format, chain PB [auth j] SDF format, chain QA [auth r] SDF format, chain RA [auth r] SDF format, chain RC [auth B] SDF format, chain TB [auth I] SDF format, chain WA [auth D] MOL2 format, chain CB [auth k] MOL2 format, chain DB [auth E] MOL2 format, chain FC [auth M] MOL2 format, chain HB [auth X] MOL2 format, chain IB [auth s] MOL2 format, chain JA [auth N] MOL2 format, chain LC [auth g] MOL2 format, chain MA [auth t] MOL2 format, chain NC [auth F] MOL2 format, chain PB [auth j] MOL2 format, chain QA [auth r] MOL2 format, chain RA [auth r] MOL2 format, chain RC [auth B] MOL2 format, chain TB [auth I] MOL2 format, chain WA [auth D] mmCIF format, chain CB [auth k] mmCIF format, chain DB [auth E] mmCIF format, chain FC [auth M] mmCIF format, chain HB [auth X] mmCIF format, chain IB [auth s] mmCIF format, chain JA [auth N] mmCIF format, chain LC [auth g] mmCIF format, chain MA [auth t] mmCIF format, chain NC [auth F] mmCIF format, chain PB [auth j] mmCIF format, chain QA [auth r] mmCIF format, chain RA [auth r] mmCIF format, chain RC [auth B] mmCIF format, chain TB [auth I] mmCIF format, chain WA [auth D]	CB [auth k] DB [auth E] FC [auth M] HB [auth X] IB [auth s] CB [auth k], DB [auth E], FC [auth M], HB [auth X], IB [auth s], JA [auth N], LC [auth g], MA [auth t], NC [auth F], PB [auth j], QA [auth r], RA [auth r], RC [auth B], TB [auth I], WA [auth D]	SPHEROIDENE C₄₁ H₆₀ O FJOCMTHZSURUFA-KXCOHNEYSA-N		Interactions Focus chain CB [auth k] Focus chain DB [auth E] Focus chain FC [auth M] Focus chain HB [auth X] Focus chain IB [auth s] Focus chain JA [auth N] Focus chain LC [auth g] Focus chain MA [auth t] Focus chain NC [auth F] Focus chain PB [auth j] Focus chain QA [auth r] Focus chain RA [auth r] Focus chain RC [auth B] Focus chain TB [auth I] Focus chain WA [auth D] Interactions & Density Focus chain CB [auth k] Focus chain DB [auth E] Focus chain FC [auth M] Focus chain HB [auth X] Focus chain IB [auth s] Focus chain JA [auth N] Focus chain LC [auth g] Focus chain MA [auth t] Focus chain NC [auth F] Focus chain PB [auth j] Focus chain QA [auth r] Focus chain RA [auth r] Focus chain RC [auth B] Focus chain TB [auth I] Focus chain WA [auth D]
FE Query on FE Download Ideal Coordinates CCD File SDF format, chain DC [auth M] MOL2 format, chain DC [auth M] mmCIF format, chain DC [auth M]	DC [auth M]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N		Interactions Focus chain DC [auth M] Interactions & Density Focus chain DC [auth M]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 2.84 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

Structure Validation

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Entry History & Funding Information

Deposition Data

Released Date: 2021-06-30

Deposition Author(s):

Funding Organization	Location	Grant Number
Royal Society	United Kingdom	180030
Biotechnology and Biological Sciences Research Council (BBSRC)	United Kingdom	R003890
Japan Agency for Medical Research and Development (AMED)	Japan	JP20am0101082
Japan Agency for Medical Research and Development (AMED)	Japan	JP20am0101115
Japan Society for the Promotion of Science (JSPS)	Japan	JP 19H03162

Revision History (Full details and data files)

Version 1.0: 2021-06-30
Type: Initial release
Version 2.0: 2021-07-07
Changes: Advisory, Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary
Version 2.1: 2024-03-27
Changes: Data collection, Database references

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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7DDQ

Structure of RC-LH1-PufX from Rhodobacter veldkampii

Cryo-EM structure of the photosynthetic RC-LH1-PufX supercomplex at 2.8-angstrom resolution.

Entity ID: 1

UniProt

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Entity ID: 2

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Entity ID: 3

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Entity ID: 4

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Entity ID: 5

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Entity ID: 6

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