7OY8

Cryo-EM structure of the Rhodospirillum rubrum RC-LH1 complex

PDB DOI: https://doi.org/10.2210/pdb7OY8/pdb
EM Map EMD-13110: EMDB EMDataResource

Classification: STRUCTURAL PROTEIN
Organism(s): Rhodospirillum rubrum ATCC 11170
Mutation(s): No
Membrane Protein: Yes OPMPDBTMmpstruc

Deposited: 2021-06-23 Released: 2021-09-22
Deposition Author(s): Qian, P., Croll, T.I., Castro, H.P., Moriarty, N.W., sader, K., Hunter, C.N.
Funding Organization(s): Biotechnology and Biological Sciences Research Council (BBSRC), European Research Council (ERC), Wellcome Trust

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.50 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

Cryo-EM structure of the Rhodospirillum rubrum RC-LH1 complex at 2.5 angstrom.

Qian, P., Croll, T.I., Swainsbury, D.J.K., Castro-Hartmann, P., Moriarty, N.W., Sader, K., Hunter, C.N.

(2021) Biochem J 478: 3253-3263

PubMed: 34402504 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1042/BCJ20210511
Primary Citation of Related Structures:
7OY8

PubMed Abstract:
The reaction centre light-harvesting 1 (RC-LH1) complex is the core functional component of bacterial photosynthesis. We determined the cryo-electron microscopy (cryo-EM) structure of the RC-LH1 complex from Rhodospirillum rubrum at 2.5 Å resolution, which reveals a unique monomeric bacteriochlorophyll with a phospholipid ligand in the gap between the RC and LH1 complexes. The LH1 complex comprises a circular array of 16 αβ-polypeptide subunits that completely surrounds the RC, with a preferential binding site for a quinone, designated QP, on the inner face of the encircling LH1 complex. Quinols, initially generated at the RC QB site, are proposed to transiently occupy the QP site prior to traversing the LH1 barrier and diffusing to the cytochrome bc1 complex. Thus, the QP site, which is analogous to other such sites in recent cryo-EM structures of RC-LH1 complexes, likely reflects a general mechanism for exporting quinols from the RC-LH1 complex.

Organizational Affiliation

Materials and Structural Analysis, Thermo Fisher Scientific, Achtseweg Noord 5, 5651 GG Eindhoven, Netherlands.

Macromolecule Content

Total Structure Weight: 339.53 kDa
Atom Count: 22,902
Modelled Residue Count: 2,293
Deposited Residue Count: 2,515
Unique protein chains: 6

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Light-harvesting protein B-870 beta chain	A [auth 1] AA [auth U] C [auth 3] CA [auth W] E [auth 5] A [auth 1], AA [auth U], C [auth 3], CA [auth W], E [auth 5], EA [auth Y], G [auth 7], GA [auth d], HA [auth m], I [auth 9], IA [auth n], P [auth I], R [auth K], V [auth O], W [auth Q], Y [auth S]	54	Rhodospirillum rubrum ATCC 11170	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for Q2RQ23 (Rhodospirillum rubrum (strain ATCC 11170 / ATH 1.1.1 / DSM 467 / LMG 4362 / NCIMB 8255 / S1)) Explore Q2RQ23 Go to UniProtKB: Q2RQ23
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q2RQ23
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Antenna complex, alpha/beta subunit	B [auth 2] BA [auth V] D [auth 4] DA [auth X] F [auth 6] B [auth 2], BA [auth V], D [auth 4], DA [auth X], F [auth 6], FA [auth Z], H [auth 8], J [auth A], K [auth D], L [auth E], M [auth F], N [auth G], Q [auth J], U [auth N], Z [auth T]	50	Rhodospirillum rubrum ATCC 11170	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for Q2RQ24 (Rhodospirillum rubrum (strain ATCC 11170 / ATH 1.1.1 / DSM 467 / LMG 4362 / NCIMB 8255 / S1)) Explore Q2RQ24 Go to UniProtKB: Q2RQ24
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q2RQ24
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosynthetic reaction center, H-chain	O [auth H]	257	Rhodospirillum rubrum ATCC 11170	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for Q2RWS4 (Rhodospirillum rubrum (strain ATCC 11170 / ATH 1.1.1 / DSM 467 / LMG 4362 / NCIMB 8255 / S1)) Explore Q2RWS4 Go to UniProtKB: Q2RWS4
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q2RWS4
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosynthetic reaction center L subunit	S [auth L]	276	Rhodospirillum rubrum ATCC 11170	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for Q2RQ25 (Rhodospirillum rubrum (strain ATCC 11170 / ATH 1.1.1 / DSM 467 / LMG 4362 / NCIMB 8255 / S1)) Explore Q2RQ25 Go to UniProtKB: Q2RQ25
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q2RQ25
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Reaction center protein M chain	T [auth M]	306	Rhodospirillum rubrum ATCC 11170	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for Q2RQ26 (Rhodospirillum rubrum (strain ATCC 11170 / ATH 1.1.1 / DSM 467 / LMG 4362 / NCIMB 8255 / S1)) Explore Q2RQ26 Go to UniProtKB: Q2RQ26
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q2RQ26
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
Antenna complex, alpha/beta subunit	X [auth R]	62	Rhodospirillum rubrum ATCC 11170	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for Q2RQ24 (Rhodospirillum rubrum (strain ATCC 11170 / ATH 1.1.1 / DSM 467 / LMG 4362 / NCIMB 8255 / S1)) Explore Q2RQ24 Go to UniProtKB: Q2RQ24
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q2RQ24
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 11 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CD4 Query on CD4 Download Ideal Coordinates CCD File SDF format, chain FB [auth H] SDF format, chain YB [auth M] MOL2 format, chain FB [auth H] MOL2 format, chain YB [auth M]	FB [auth H], YB [auth M]	(2R,5R,11R,14R)-5,8,11-trihydroxy-5,11-dioxido-17-oxo-2,14-bis(tetradecanoyloxy)-4,6,10,12,16-pentaoxa-5,11-diphosphatriacont-1-yl tetradecanoate C₆₅ H₁₂₆ O₁₇ P₂ SDCJNZZAOLRVCP-GTOSQJSUSA-N		Interactions Focus chain FB [auth H] Focus chain YB [auth M] Interactions & Density Focus chain FB [auth H] Focus chain YB [auth M]
07D (Subject of Investigation/LOI) Query on 07D Download Ideal Coordinates CCD File SDF format, chain AB [auth F] SDF format, chain BB [auth G] SDF format, chain CB [auth H] SDF format, chain CC [auth N] SDF format, chain EC [auth O] SDF format, chain GC [auth Q] SDF format, chain HB [auth I] SDF format, chain HC [auth R] SDF format, chain IB [auth J] SDF format, chain JA [auth 1] SDF format, chain KC [auth S] SDF format, chain LA [auth 2] SDF format, chain LB [auth K] SDF format, chain LC [auth T] SDF format, chain MC [auth U] SDF format, chain NA [auth 3] SDF format, chain NC [auth V] SDF format, chain OA [auth 4] SDF format, chain OC [auth W] SDF format, chain PB [auth L] SDF format, chain PC [auth X] SDF format, chain QA [auth 5] SDF format, chain QB [auth L] SDF format, chain RA [auth 6] SDF format, chain RC [auth Y] SDF format, chain SC [auth Z] SDF format, chain TA [auth 7] SDF format, chain UA [auth 8] SDF format, chain UC [auth d] SDF format, chain VB [auth M] SDF format, chain WA [auth 9] SDF format, chain WB [auth M] SDF format, chain WC [auth m] SDF format, chain XA [auth A] SDF format, chain YA [auth D] SDF format, chain YC [auth n] SDF format, chain ZA [auth E] MOL2 format, chain AB [auth F] MOL2 format, chain BB [auth G] MOL2 format, chain CB [auth H] MOL2 format, chain CC [auth N] MOL2 format, chain EC [auth O] MOL2 format, chain GC [auth Q] MOL2 format, chain HB [auth I] MOL2 format, chain HC [auth R] MOL2 format, chain IB [auth J] MOL2 format, chain JA [auth 1] MOL2 format, chain KC [auth S] MOL2 format, chain LA [auth 2] MOL2 format, chain LB [auth K] MOL2 format, chain LC [auth T] MOL2 format, chain MC [auth U] MOL2 format, chain NA [auth 3] MOL2 format, chain NC [auth V] MOL2 format, chain OA [auth 4] MOL2 format, chain OC [auth W] MOL2 format, chain PB [auth L] MOL2 format, chain PC [auth X] MOL2 format, chain QA [auth 5] MOL2 format, chain QB [auth L] MOL2 format, chain RA [auth 6] MOL2 format, chain RC [auth Y] MOL2 format, chain SC [auth Z] MOL2 format, chain TA [auth 7] MOL2 format, chain UA [auth 8] MOL2 format, chain UC [auth d] MOL2 format, chain VB [auth M] MOL2 format, chain WA [auth 9] MOL2 format, chain WB [auth M] MOL2 format, chain WC [auth m] MOL2 format, chain XA [auth A] MOL2 format, chain YA [auth D] MOL2 format, chain YC [auth n] MOL2 format, chain ZA [auth E]	AB [auth F] BB [auth G] CB [auth H] CC [auth N] EC [auth O] AB [auth F], BB [auth G], CB [auth H], CC [auth N], EC [auth O], GC [auth Q], HB [auth I], HC [auth R], IB [auth J], JA [auth 1], KC [auth S], LA [auth 2], LB [auth K], LC [auth T], MC [auth U], NA [auth 3], NC [auth V], OA [auth 4], OC [auth W], PB [auth L], PC [auth X], QA [auth 5], QB [auth L], RA [auth 6], RC [auth Y], SC [auth Z], TA [auth 7], UA [auth 8], UC [auth d], VB [auth M], WA [auth 9], WB [auth M], WC [auth m], XA [auth A], YA [auth D], YC [auth n], ZA [auth E]	Trans-Geranyl BACTERIOCHLOROPHYLL A C₅₅ H₆₄ Mg N₄ O₆ ZBSZXIUSELHDGQ-POZHEDQMSA-M		Interactions Focus chain AB [auth F] Focus chain BB [auth G] Focus chain CB [auth H] Focus chain CC [auth N] Focus chain EC [auth O] Focus chain GC [auth Q] Focus chain HB [auth I] Focus chain HC [auth R] Focus chain IB [auth J] Focus chain JA [auth 1] Focus chain KC [auth S] Focus chain LA [auth 2] Focus chain LB [auth K] Focus chain LC [auth T] Focus chain MC [auth U] Focus chain NA [auth 3] Focus chain NC [auth V] Focus chain OA [auth 4] Focus chain OC [auth W] Focus chain PB [auth L] Focus chain PC [auth X] Focus chain QA [auth 5] Focus chain QB [auth L] Focus chain RA [auth 6] Focus chain RC [auth Y] Focus chain SC [auth Z] Focus chain TA [auth 7] Focus chain UA [auth 8] Focus chain UC [auth d] Focus chain VB [auth M] Focus chain WA [auth 9] Focus chain WB [auth M] Focus chain WC [auth m] Focus chain XA [auth A] Focus chain YA [auth D] Focus chain YC [auth n] Focus chain ZA [auth E] Interactions & Density Focus chain AB [auth F] Focus chain BB [auth G] Focus chain CB [auth H] Focus chain CC [auth N] Focus chain EC [auth O] Focus chain GC [auth Q] Focus chain HB [auth I] Focus chain HC [auth R] Focus chain IB [auth J] Focus chain JA [auth 1] Focus chain KC [auth S] Focus chain LA [auth 2] Focus chain LB [auth K] Focus chain LC [auth T] Focus chain MC [auth U] Focus chain NA [auth 3] Focus chain NC [auth V] Focus chain OA [auth 4] Focus chain OC [auth W] Focus chain PB [auth L] Focus chain PC [auth X] Focus chain QA [auth 5] Focus chain QB [auth L] Focus chain RA [auth 6] Focus chain RC [auth Y] Focus chain SC [auth Z] Focus chain TA [auth 7] Focus chain UA [auth 8] Focus chain UC [auth d] Focus chain VB [auth M] Focus chain WA [auth 9] Focus chain WB [auth M] Focus chain WC [auth m] Focus chain XA [auth A] Focus chain YA [auth D] Focus chain YC [auth n] Focus chain ZA [auth E]
BPH (Subject of Investigation/LOI) Query on BPH Download Ideal Coordinates CCD File SDF format, chain MB [auth L] SDF format, chain TB [auth M] MOL2 format, chain MB [auth L] MOL2 format, chain TB [auth M]	MB [auth L], TB [auth M]	BACTERIOPHEOPHYTIN A C₅₅ H₇₆ N₄ O₆ KWOZSBGNAHVCKG-SZQBJALDSA-N		Interactions Focus chain MB [auth L] Focus chain TB [auth M] Interactions & Density Focus chain MB [auth L] Focus chain TB [auth M]
U10 (Subject of Investigation/LOI) Query on U10 Download Ideal Coordinates CCD File SDF format, chain OB [auth L] SDF format, chain RB [auth L] SDF format, chain UB [auth M] MOL2 format, chain OB [auth L] MOL2 format, chain RB [auth L] MOL2 format, chain UB [auth M]	OB [auth L], RB [auth L], UB [auth M]	UBIQUINONE-10 C₅₉ H₉₀ O₄ ACTIUHUUMQJHFO-UPTCCGCDSA-N		Interactions Focus chain OB [auth L] Focus chain RB [auth L] Focus chain UB [auth M] Interactions & Density Focus chain OB [auth L] Focus chain RB [auth L] Focus chain UB [auth M]
RQ0 (Subject of Investigation/LOI) Query on RQ0 Download Ideal Coordinates CCD File SDF format, chain NB [auth L] MOL2 format, chain NB [auth L]	NB [auth L]	2-azanyl-5-[(2~{E},6~{E},8~{E},10~{E},12~{E},14~{E},18~{E},22~{E},26~{E},30~{E},34~{E})-3,7,11,15,19,23,27,31,35,39-decamethyltetraconta-2,6,8,10,12,14,18,22,26,30,34,38-dodecaenyl]-3-methoxy-6-methyl-cyclohexa-2,5-diene-1,4-dione C₅₈ H₈₅ N O₃ WXESXKLCRFKYIR-NBYUNPNPSA-N		Interactions Focus chain NB [auth L] Interactions & Density Focus chain NB [auth L]
PGW Query on PGW Download Ideal Coordinates CCD File SDF format, chain DB [auth H] SDF format, chain EB [auth H] MOL2 format, chain DB [auth H] MOL2 format, chain EB [auth H]	DB [auth H], EB [auth H]	(1R)-2-{[(S)-{[(2S)-2,3-dihydroxypropyl]oxy}(hydroxy)phosphoryl]oxy}-1-[(hexadecanoyloxy)methyl]ethyl (9Z)-octadec-9-enoate C₄₀ H₇₇ O₁₀ P PAZGBAOHGQRCBP-HGWHEPCSSA-N		Interactions Focus chain DB [auth H] Focus chain EB [auth H] Interactions & Density Focus chain DB [auth H] Focus chain EB [auth H]
CRT Query on CRT Download Ideal Coordinates CCD File SDF format, chain BC [auth N] SDF format, chain DC [auth O] SDF format, chain FC [auth Q] SDF format, chain GB [auth I] SDF format, chain JB [auth J] SDF format, chain JC [auth S] SDF format, chain KA [auth 1] SDF format, chain KB [auth K] SDF format, chain MA [auth 3] SDF format, chain PA [auth 5] SDF format, chain QC [auth Y] SDF format, chain SA [auth 7] SDF format, chain TC [auth d] SDF format, chain VA [auth 9] SDF format, chain VC [auth m] SDF format, chain XB [auth M] SDF format, chain XC [auth n] MOL2 format, chain BC [auth N] MOL2 format, chain DC [auth O] MOL2 format, chain FC [auth Q] MOL2 format, chain GB [auth I] MOL2 format, chain JB [auth J] MOL2 format, chain JC [auth S] MOL2 format, chain KA [auth 1] MOL2 format, chain KB [auth K] MOL2 format, chain MA [auth 3] MOL2 format, chain PA [auth 5] MOL2 format, chain QC [auth Y] MOL2 format, chain SA [auth 7] MOL2 format, chain TC [auth d] MOL2 format, chain VA [auth 9] MOL2 format, chain VC [auth m] MOL2 format, chain XB [auth M] MOL2 format, chain XC [auth n]	BC [auth N] DC [auth O] FC [auth Q] GB [auth I] JB [auth J] BC [auth N], DC [auth O], FC [auth Q], GB [auth I], JB [auth J], JC [auth S], KA [auth 1], KB [auth K], MA [auth 3], PA [auth 5], QC [auth Y], SA [auth 7], TC [auth d], VA [auth 9], VC [auth m], XB [auth M], XC [auth n]	SPIRILLOXANTHIN C₄₂ H₆₀ O₂ VAZQBTJCYODOSV-RISZBRKMSA-N		Interactions Focus chain BC [auth N] Focus chain DC [auth O] Focus chain FC [auth Q] Focus chain GB [auth I] Focus chain JB [auth J] Focus chain JC [auth S] Focus chain KA [auth 1] Focus chain KB [auth K] Focus chain MA [auth 3] Focus chain PA [auth 5] Focus chain QC [auth Y] Focus chain SA [auth 7] Focus chain TC [auth d] Focus chain VA [auth 9] Focus chain VC [auth m] Focus chain XB [auth M] Focus chain XC [auth n] Interactions & Density Focus chain BC [auth N] Focus chain DC [auth O] Focus chain FC [auth Q] Focus chain GB [auth I] Focus chain JB [auth J] Focus chain JC [auth S] Focus chain KA [auth 1] Focus chain KB [auth K] Focus chain MA [auth 3] Focus chain PA [auth 5] Focus chain QC [auth Y] Focus chain SA [auth 7] Focus chain TC [auth d] Focus chain VA [auth 9] Focus chain VC [auth m] Focus chain XB [auth M] Focus chain XC [auth n]
LMT Query on LMT Download Ideal Coordinates CCD File SDF format, chain IC [auth R] MOL2 format, chain IC [auth R]	IC [auth R]	DODECYL-BETA-D-MALTOSIDE C₂₄ H₄₆ O₁₁ NLEBIOOXCVAHBD-QKMCSOCLSA-N		Interactions Focus chain IC [auth R] Interactions & Density Focus chain IC [auth R]
PO4 Query on PO4 Download Ideal Coordinates CCD File SDF format, chain AC [auth M] MOL2 format, chain AC [auth M]	AC [auth M]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain AC [auth M] Interactions & Density Focus chain AC [auth M]
FE Query on FE Download Ideal Coordinates CCD File SDF format, chain SB [auth M] MOL2 format, chain SB [auth M]	SB [auth M]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N		Interactions Focus chain SB [auth M] Interactions & Density Focus chain SB [auth M]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain ZB [auth M] MOL2 format, chain ZB [auth M]	ZB [auth M]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain ZB [auth M] Interactions & Density Focus chain ZB [auth M]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
FME Query on FME	B [auth 2] BA [auth V] D [auth 4] DA [auth X] F [auth 6] B [auth 2], BA [auth V], D [auth 4], DA [auth X], F [auth 6], FA [auth Z], H [auth 8], J [auth A], K [auth D], L [auth E], M [auth F], N [auth G], Q [auth J], U [auth N], Z [auth T]	L-PEPTIDE LINKING	C₆ H₁₁ N O₃ S		MET

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 2.50 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
RECONSTRUCTION	RELION	3.1
MODEL REFINEMENT	PHENIX

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2021-09-22

Deposition Author(s):

Funding Organization	Location	Grant Number
Biotechnology and Biological Sciences Research Council (BBSRC)	United Kingdom	BB/M000265/1
European Research Council (ERC)	European Union	Synergy Award 854126
Wellcome Trust	United Kingdom	209407/Z/17/Z