6Z5R | pdb_00006z5r

RC-LH1(16) complex from Rhodopseudomonas palustris

PDB DOI: https://doi.org/10.2210/pdb6Z5R/pdb
EM Map EMD-11080: EMDB EMDataResource

Classification: PHOTOSYNTHESIS
Organism(s): Rhodopseudomonas palustris CGA009
Mutation(s): No
Membrane Protein: Yes OPM PDBTM mpstruc

Deposited: 2020-05-27 Released: 2021-01-13
Deposition Author(s): Swainsbury, D.J.K., Qian, P., Hitchcock, A., Hunter, C.N.
Funding Organization(s): Biotechnology and Biological Sciences Research Council (BBSRC)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.80 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

Literature

Structures of Rhodopseudomonas palustris RC-LH1 complexes with open or closed quinone channels.

Swainsbury, D.J.K., Qian, P., Jackson, P.J., Faries, K.M., Niedzwiedzki, D.M., Martin, E.C., Farmer, D.A., Malone, L.A., Thompson, R.F., Ranson, N.A., Canniffe, D.P., Dickman, M.J., Holten, D., Kirmaier, C., Hitchcock, A., Hunter, C.N.

(2021) Sci Adv 7

PubMed: 33523887 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1126/sciadv.abe2631
Primary Citation Related Structures:
6Z5R, 6Z5S

PubMed Abstract:
The reaction-center light-harvesting complex 1 (RC-LH1) is the core photosynthetic component in purple phototrophic bacteria. We present two cryo-electron microscopy structures of RC-LH1 complexes from Rhodopseudomonas palustris A 2.65-Å resolution structure of the RC-LH1 ₁₄-W complex consists of an open 14-subunit LH1 ring surrounding the RC interrupted by protein-W, whereas the complex without protein-W at 2.80-Å resolution comprises an RC completely encircled by a closed, 16-subunit LH1 ring. Comparison of these structures provides insights into quinone dynamics within RC-LH1 complexes, including a previously unidentified conformational change upon quinone binding at the RC Q _B site, and the locations of accessory quinone binding sites that aid their delivery to the RC. The structurally unique protein-W prevents LH1 ring closure, creating a channel for accelerated quinone/quinol exchange.

Organizational Affiliation

Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield, S10 2TN, UK. d.swainsbury@sheffield.ac.uk c.n.hunter@sheffield.ac.uk.

Macromolecule Content

Total Structure Weight: 362.48 kDa
Atom Count: 25,048
Modeled Residue Count: 2,336
Deposited Residue Count: 2,439
Unique protein chains: 5

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Light-harvesting complex 1 alpha chain	A [auth C] BA [auth 3] C [auth E] DA [auth 5] E [auth G] A [auth C], BA [auth 3], C [auth E], DA [auth 5], E [auth G], FA [auth 7], G [auth J], HA [auth 9], I [auth N], N [auth R], P [auth T], R [auth V], T [auth P], V [auth Y], X [auth A], Z [auth 1]	48	Rhodopseudomonas palustris CGA009	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for Q6N9L4 (Rhodopseudomonas palustris (strain ATCC BAA-98 / CGA009)) Explore Q6N9L4 Go to UniProtKB: Q6N9L4
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q6N9L4
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Light-harvesting complex 1 beta chain	AA [auth 2] B [auth D] CA [auth 4] D [auth F] EA [auth 6] AA [auth 2], B [auth D], CA [auth 4], D [auth F], EA [auth 6], F [auth I], GA [auth 8], H [auth K], IA [auth 0], J [auth O], O [auth S], Q [auth U], S [auth X], U [auth Q], W [auth Z], Y [auth B]	52	Rhodopseudomonas palustris CGA009	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for Q6N9L5 (Rhodopseudomonas palustris (strain ATCC BAA-98 / CGA009)) Explore Q6N9L5 Go to UniProtKB: Q6N9L5
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q6N9L5
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Reference Sequence

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| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
H subunit of photosynthetic reaction center complex	K [auth H]	255	Rhodopseudomonas palustris CGA009	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for A0A4Z9 (Rhodopseudomonas palustris (strain ATCC BAA-98 / CGA009)) Explore A0A4Z9 Go to UniProtKB: A0A4Z9
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A4Z9
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Reference Sequence

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| 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Reaction center protein L chain	L	277	Rhodopseudomonas palustris CGA009	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for O83005 (Rhodopseudomonas palustris (strain ATCC BAA-98 / CGA009)) Explore O83005 Go to UniProtKB: O83005
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O83005
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Reference Sequence

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| 3D Structure

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Reaction center protein M chain	M	307	Rhodopseudomonas palustris CGA009	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for A0A4Z7 (Rhodopseudomonas palustris (strain ATCC BAA-98 / CGA009)) Explore A0A4Z7 Go to UniProtKB: A0A4Z7
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A4Z7
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 10 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CDL (Subject of Investigation/LOI) Query on CDL Download:Ideal Coordinates CCD File SDF format, chain XA [auth G] SDF format, chain WB [auth L] SDF format, chain TA [auth G] SDF format, chain PA [auth E] SDF format, chain FC [auth M] SDF format, chain EC [auth M] MOL2 format, chain XA [auth G] MOL2 format, chain WB [auth L] MOL2 format, chain TA [auth G] MOL2 format, chain PA [auth E] MOL2 format, chain FC [auth M] MOL2 format, chain EC [auth M] mmCIF format, chain XA [auth G] mmCIF format, chain WB [auth L] mmCIF format, chain TA [auth G] mmCIF format, chain PA [auth E] mmCIF format, chain FC [auth M] mmCIF format, chain EC [auth M]	EC [auth M] FC [auth M] PA [auth E] TA [auth G] WB [auth L] EC [auth M], FC [auth M], PA [auth E], TA [auth G], WB [auth L], XA [auth G]	CARDIOLIPIN C₈₁ H₁₅₆ O₁₇ P₂ XVTUQDWPJJBEHJ-KZCWQMDCSA-L		Interactions Focus chain EC [auth M] Focus chain FC [auth M] Focus chain PA [auth E] Focus chain TA [auth G] Focus chain WB [auth L] Focus chain XA [auth G] Interactions & Density Focus chain EC [auth M] Focus chain FC [auth M] Focus chain PA [auth E] Focus chain TA [auth G] Focus chain WB [auth L] Focus chain XA [auth G]
BCL (Subject of Investigation/LOI) Query on BCL Download:Ideal Coordinates CCD File SDF format, chain YB [auth M] SDF format, chain XC [auth Q] SDF format, chain WD [auth 5] SDF format, chain WA [auth G] SDF format, chain VC [auth P] SDF format, chain VA [auth G] SDF format, chain UD [auth 5] SDF format, chain UB [auth L] SDF format, chain RD [auth 4] SDF format, chain RC [auth V] SDF format, chain RA [auth F] SDF format, chain QC [auth V] SDF format, chain PD [auth 3] SDF format, chain NC [auth U] SDF format, chain NB [auth L] SDF format, chain NA [auth E] SDF format, chain MC [auth T] SDF format, chain LD [auth 1] SDF format, chain KD [auth 1] SDF format, chain KA [auth C] SDF format, chain JC [auth R] SDF format, chain JA [auth C] SDF format, chain HE [auth 0] SDF format, chain HD [auth B] SDF format, chain HC [auth R] SDF format, chain HB [auth N] SDF format, chain GE [auth 9] SDF format, chain GB [auth N] SDF format, chain FD [auth A] SDF format, chain DB [auth J] SDF format, chain CE [auth 7] SDF format, chain BD [auth Y] SDF format, chain BB [auth J] SDF format, chain AE [auth 7] SDF format, chain AD [auth Y] SDF format, chain AC [auth M] MOL2 format, chain YB [auth M] MOL2 format, chain XC [auth Q] MOL2 format, chain WD [auth 5] MOL2 format, chain WA [auth G] MOL2 format, chain VC [auth P] MOL2 format, chain VA [auth G] MOL2 format, chain UD [auth 5] MOL2 format, chain UB [auth L] MOL2 format, chain RD [auth 4] MOL2 format, chain RC [auth V] MOL2 format, chain RA [auth F] MOL2 format, chain QC [auth V] MOL2 format, chain PD [auth 3] MOL2 format, chain NC [auth U] MOL2 format, chain NB [auth L] MOL2 format, chain NA [auth E] MOL2 format, chain MC [auth T] MOL2 format, chain LD [auth 1] MOL2 format, chain KD [auth 1] MOL2 format, chain KA [auth C] MOL2 format, chain JC [auth R] MOL2 format, chain JA [auth C] MOL2 format, chain HE [auth 0] MOL2 format, chain HD [auth B] MOL2 format, chain HC [auth R] MOL2 format, chain HB [auth N] MOL2 format, chain GE [auth 9] MOL2 format, chain GB [auth N] MOL2 format, chain FD [auth A] MOL2 format, chain DB [auth J] MOL2 format, chain CE [auth 7] MOL2 format, chain BD [auth Y] MOL2 format, chain BB [auth J] MOL2 format, chain AE [auth 7] MOL2 format, chain AD [auth Y] MOL2 format, chain AC [auth M] mmCIF format, chain YB [auth M] mmCIF format, chain XC [auth Q] mmCIF format, chain WD [auth 5] mmCIF format, chain WA [auth G] mmCIF format, chain VC [auth P] mmCIF format, chain VA [auth G] mmCIF format, chain UD [auth 5] mmCIF format, chain UB [auth L] mmCIF format, chain RD [auth 4] mmCIF format, chain RC [auth V] mmCIF format, chain RA [auth F] mmCIF format, chain QC [auth V] mmCIF format, chain PD [auth 3] mmCIF format, chain NC [auth U] mmCIF format, chain NB [auth L] mmCIF format, chain NA [auth E] mmCIF format, chain MC [auth T] mmCIF format, chain LD [auth 1] mmCIF format, chain KD [auth 1] mmCIF format, chain KA [auth C] mmCIF format, chain JC [auth R] mmCIF format, chain JA [auth C] mmCIF format, chain HE [auth 0] mmCIF format, chain HD [auth B] mmCIF format, chain HC [auth R] mmCIF format, chain HB [auth N] mmCIF format, chain GE [auth 9] mmCIF format, chain GB [auth N] mmCIF format, chain FD [auth A] mmCIF format, chain DB [auth J] mmCIF format, chain CE [auth 7] mmCIF format, chain BD [auth Y] mmCIF format, chain BB [auth J] mmCIF format, chain AE [auth 7] mmCIF format, chain AD [auth Y] mmCIF format, chain AC [auth M]	AC [auth M] AD [auth Y] AE [auth 7] BB [auth J] BD [auth Y] AC [auth M], AD [auth Y], AE [auth 7], BB [auth J], BD [auth Y], CE [auth 7], DB [auth J], FD [auth A], GB [auth N], GE [auth 9], HB [auth N], HC [auth R], HD [auth B], HE [auth 0], JA [auth C], JC [auth R], KA [auth C], KD [auth 1], LD [auth 1], MC [auth T], NA [auth E], NB [auth L], NC [auth U], PD [auth 3], QC [auth V], RA [auth F], RC [auth V], RD [auth 4], UB [auth L], UD [auth 5], VA [auth G], VC [auth P], WA [auth G], WD [auth 5], XC [auth Q], YB [auth M]	BACTERIOCHLOROPHYLL A C₅₅ H₇₄ Mg N₄ O₆ DSJXIQQMORJERS-AGGZHOMASA-M		Interactions Focus chain AC [auth M] Focus chain AD [auth Y] Focus chain AE [auth 7] Focus chain BB [auth J] Focus chain BD [auth Y] Focus chain CE [auth 7] Focus chain DB [auth J] Focus chain FD [auth A] Focus chain GB [auth N] Focus chain GE [auth 9] Focus chain HB [auth N] Focus chain HC [auth R] Focus chain HD [auth B] Focus chain HE [auth 0] Focus chain JA [auth C] Focus chain JC [auth R] Focus chain KA [auth C] Focus chain KD [auth 1] Focus chain LD [auth 1] Focus chain MC [auth T] Focus chain NA [auth E] Focus chain NB [auth L] Focus chain NC [auth U] Focus chain PD [auth 3] Focus chain QC [auth V] Focus chain RA [auth F] Focus chain RC [auth V] Focus chain RD [auth 4] Focus chain UB [auth L] Focus chain UD [auth 5] Focus chain VA [auth G] Focus chain VC [auth P] Focus chain WA [auth G] Focus chain WD [auth 5] Focus chain XC [auth Q] Focus chain YB [auth M] Interactions & Density Focus chain AC [auth M] Focus chain AD [auth Y] Focus chain AE [auth 7] Focus chain BB [auth J] Focus chain BD [auth Y] Focus chain CE [auth 7] Focus chain DB [auth J] Focus chain FD [auth A] Focus chain GB [auth N] Focus chain GE [auth 9] Focus chain HB [auth N] Focus chain HC [auth R] Focus chain HD [auth B] Focus chain HE [auth 0] Focus chain JA [auth C] Focus chain JC [auth R] Focus chain KA [auth C] Focus chain KD [auth 1] Focus chain LD [auth 1] Focus chain MC [auth T] Focus chain NA [auth E] Focus chain NB [auth L] Focus chain NC [auth U] Focus chain PD [auth 3] Focus chain QC [auth V] Focus chain RA [auth F] Focus chain RC [auth V] Focus chain RD [auth 4] Focus chain UB [auth L] Focus chain UD [auth 5] Focus chain VA [auth G] Focus chain VC [auth P] Focus chain WA [auth G] Focus chain WD [auth 5] Focus chain XC [auth Q] Focus chain YB [auth M]
BPH (Subject of Investigation/LOI) Query on BPH Download:Ideal Coordinates CCD File SDF format, chain OB [auth L] SDF format, chain BC [auth M] MOL2 format, chain OB [auth L] MOL2 format, chain BC [auth M] mmCIF format, chain OB [auth L] mmCIF format, chain BC [auth M]	BC [auth M], OB [auth L]	BACTERIOPHEOPHYTIN A C₅₅ H₇₆ N₄ O₆ KWOZSBGNAHVCKG-SZQBJALDSA-N		Interactions Focus chain BC [auth M] Focus chain OB [auth L] Interactions & Density Focus chain BC [auth M] Focus chain OB [auth L]
U10 (Subject of Investigation/LOI) Query on U10 Download:Ideal Coordinates CCD File SDF format, chain VB [auth L] SDF format, chain TB [auth L] SDF format, chain PB [auth L] SDF format, chain GC [auth M] SDF format, chain CC [auth M] MOL2 format, chain VB [auth L] MOL2 format, chain TB [auth L] MOL2 format, chain PB [auth L] MOL2 format, chain GC [auth M] MOL2 format, chain CC [auth M] mmCIF format, chain VB [auth L] mmCIF format, chain TB [auth L] mmCIF format, chain PB [auth L] mmCIF format, chain GC [auth M] mmCIF format, chain CC [auth M]	CC [auth M], GC [auth M], PB [auth L], TB [auth L], VB [auth L]	UBIQUINONE-10 C₅₉ H₉₀ O₄ ACTIUHUUMQJHFO-UPTCCGCDSA-N		Interactions Focus chain CC [auth M] Focus chain GC [auth M] Focus chain PB [auth L] Focus chain TB [auth L] Focus chain VB [auth L] Interactions & Density Focus chain CC [auth M] Focus chain GC [auth M] Focus chain PB [auth L] Focus chain TB [auth L] Focus chain VB [auth L]
6PL (Subject of Investigation/LOI) Query on 6PL Download:Ideal Coordinates CCD File SDF format, chain ZC [auth Q] SDF format, chain YD [auth 6] SDF format, chain YA [auth I] SDF format, chain XB [auth M] SDF format, chain WC [auth P] SDF format, chain VD [auth 5] SDF format, chain TD [auth 4] SDF format, chain TC [auth X] SDF format, chain SA [auth F] SDF format, chain RB [auth L] SDF format, chain QB [auth L] SDF format, chain PC [auth U] SDF format, chain OD [auth 2] SDF format, chain OA [auth E] SDF format, chain MA [auth D] SDF format, chain LC [auth S] SDF format, chain LB [auth H] SDF format, chain KB [auth O] SDF format, chain JE [auth 0] SDF format, chain JD [auth B] SDF format, chain FB [auth K] SDF format, chain EE [auth 8] SDF format, chain ED [auth Z] SDF format, chain AB [auth I] MOL2 format, chain ZC [auth Q] MOL2 format, chain YD [auth 6] MOL2 format, chain YA [auth I] MOL2 format, chain XB [auth M] MOL2 format, chain WC [auth P] MOL2 format, chain VD [auth 5] MOL2 format, chain TD [auth 4] MOL2 format, chain TC [auth X] MOL2 format, chain SA [auth F] MOL2 format, chain RB [auth L] MOL2 format, chain QB [auth L] MOL2 format, chain PC [auth U] MOL2 format, chain OD [auth 2] MOL2 format, chain OA [auth E] MOL2 format, chain MA [auth D] MOL2 format, chain LC [auth S] MOL2 format, chain LB [auth H] MOL2 format, chain KB [auth O] MOL2 format, chain JE [auth 0] MOL2 format, chain JD [auth B] MOL2 format, chain FB [auth K] MOL2 format, chain EE [auth 8] MOL2 format, chain ED [auth Z] MOL2 format, chain AB [auth I] mmCIF format, chain ZC [auth Q] mmCIF format, chain YD [auth 6] mmCIF format, chain YA [auth I] mmCIF format, chain XB [auth M] mmCIF format, chain WC [auth P] mmCIF format, chain VD [auth 5] mmCIF format, chain TD [auth 4] mmCIF format, chain TC [auth X] mmCIF format, chain SA [auth F] mmCIF format, chain RB [auth L] mmCIF format, chain QB [auth L] mmCIF format, chain PC [auth U] mmCIF format, chain OD [auth 2] mmCIF format, chain OA [auth E] mmCIF format, chain MA [auth D] mmCIF format, chain LC [auth S] mmCIF format, chain LB [auth H] mmCIF format, chain KB [auth O] mmCIF format, chain JE [auth 0] mmCIF format, chain JD [auth B] mmCIF format, chain FB [auth K] mmCIF format, chain EE [auth 8] mmCIF format, chain ED [auth Z] mmCIF format, chain AB [auth I]	AB [auth I] ED [auth Z] EE [auth 8] FB [auth K] JD [auth B] AB [auth I], ED [auth Z], EE [auth 8], FB [auth K], JD [auth B], JE [auth 0], KB [auth O], LB [auth H], LC [auth S], MA [auth D], OA [auth E], OD [auth 2], PC [auth U], QB [auth L], RB [auth L], SA [auth F], TC [auth X], TD [auth 4], VD [auth 5], WC [auth P], XB [auth M], YA [auth I], YD [auth 6], ZC [auth Q]	(4S,7R)-4-HYDROXY-N,N,N-TRIMETHYL-9-OXO-7-[(PALMITOYLOXY)METHYL]-3,5,8-TRIOXA-4-PHOSPHAHEXACOSAN-1-AMINIUM 4-OXIDE C₄₂ H₈₅ N O₈ P PZNPLUBHRSSFHT-RRHRGVEJSA-O		Interactions Focus chain AB [auth I] Focus chain ED [auth Z] Focus chain EE [auth 8] Focus chain FB [auth K] Focus chain JD [auth B] Focus chain JE [auth 0] Focus chain KB [auth O] Focus chain LB [auth H] Focus chain LC [auth S] Focus chain MA [auth D] Focus chain OA [auth E] Focus chain OD [auth 2] Focus chain PC [auth U] Focus chain QB [auth L] Focus chain RB [auth L] Focus chain SA [auth F] Focus chain TC [auth X] Focus chain TD [auth 4] Focus chain VD [auth 5] Focus chain WC [auth P] Focus chain XB [auth M] Focus chain YA [auth I] Focus chain YD [auth 6] Focus chain ZC [auth Q] Interactions & Density Focus chain AB [auth I] Focus chain ED [auth Z] Focus chain EE [auth 8] Focus chain FB [auth K] Focus chain JD [auth B] Focus chain JE [auth 0] Focus chain KB [auth O] Focus chain LB [auth H] Focus chain LC [auth S] Focus chain MA [auth D] Focus chain OA [auth E] Focus chain OD [auth 2] Focus chain PC [auth U] Focus chain QB [auth L] Focus chain RB [auth L] Focus chain SA [auth F] Focus chain TC [auth X] Focus chain TD [auth 4] Focus chain VD [auth 5] Focus chain WC [auth P] Focus chain XB [auth M] Focus chain YA [auth I] Focus chain YD [auth 6] Focus chain ZC [auth Q]
PGT (Subject of Investigation/LOI) Query on PGT Download:Ideal Coordinates CCD File SDF format, chain BE [auth 7] SDF format, chain FE [auth 9] MOL2 format, chain BE [auth 7] MOL2 format, chain FE [auth 9] mmCIF format, chain BE [auth 7] mmCIF format, chain FE [auth 9]	BE [auth 7], FE [auth 9]	(1S)-2-{[{[(2R)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL STEARATE C₄₀ H₇₉ O₁₀ P KBPVYRBBONZJHF-AMAPPZPBSA-N		Interactions Focus chain BE [auth 7] Focus chain FE [auth 9] Interactions & Density Focus chain BE [auth 7] Focus chain FE [auth 9]
CRT (Subject of Investigation/LOI) Query on CRT Download:Ideal Coordinates CCD File SDF format, chain ZD [auth 7] SDF format, chain ZA [auth I] SDF format, chain YC [auth Q] SDF format, chain UA [auth G] SDF format, chain SD [auth 4] SDF format, chain SC [auth X] SDF format, chain OC [auth U] SDF format, chain ND [auth 2] SDF format, chain LA [auth D] SDF format, chain KC [auth S] SDF format, chain JB [auth O] SDF format, chain IE [auth 0] SDF format, chain ID [auth B] SDF format, chain EB [auth K] SDF format, chain DE [auth 8] SDF format, chain DD [auth Z] MOL2 format, chain ZD [auth 7] MOL2 format, chain ZA [auth I] MOL2 format, chain YC [auth Q] MOL2 format, chain UA [auth G] MOL2 format, chain SD [auth 4] MOL2 format, chain SC [auth X] MOL2 format, chain OC [auth U] MOL2 format, chain ND [auth 2] MOL2 format, chain LA [auth D] MOL2 format, chain KC [auth S] MOL2 format, chain JB [auth O] MOL2 format, chain IE [auth 0] MOL2 format, chain ID [auth B] MOL2 format, chain EB [auth K] MOL2 format, chain DE [auth 8] MOL2 format, chain DD [auth Z] mmCIF format, chain ZD [auth 7] mmCIF format, chain ZA [auth I] mmCIF format, chain YC [auth Q] mmCIF format, chain UA [auth G] mmCIF format, chain SD [auth 4] mmCIF format, chain SC [auth X] mmCIF format, chain OC [auth U] mmCIF format, chain ND [auth 2] mmCIF format, chain LA [auth D] mmCIF format, chain KC [auth S] mmCIF format, chain JB [auth O] mmCIF format, chain IE [auth 0] mmCIF format, chain ID [auth B] mmCIF format, chain EB [auth K] mmCIF format, chain DE [auth 8] mmCIF format, chain DD [auth Z]	DD [auth Z] DE [auth 8] EB [auth K] ID [auth B] IE [auth 0] DD [auth Z], DE [auth 8], EB [auth K], ID [auth B], IE [auth 0], JB [auth O], KC [auth S], LA [auth D], ND [auth 2], OC [auth U], SC [auth X], SD [auth 4], UA [auth G], YC [auth Q], ZA [auth I], ZD [auth 7]	SPIRILLOXANTHIN C₄₂ H₆₀ O₂ VAZQBTJCYODOSV-RISZBRKMSA-N		Interactions Focus chain DD [auth Z] Focus chain DE [auth 8] Focus chain EB [auth K] Focus chain ID [auth B] Focus chain IE [auth 0] Focus chain JB [auth O] Focus chain KC [auth S] Focus chain LA [auth D] Focus chain ND [auth 2] Focus chain OC [auth U] Focus chain SC [auth X] Focus chain SD [auth 4] Focus chain UA [auth G] Focus chain YC [auth Q] Focus chain ZA [auth I] Focus chain ZD [auth 7] Interactions & Density Focus chain DD [auth Z] Focus chain DE [auth 8] Focus chain EB [auth K] Focus chain ID [auth B] Focus chain IE [auth 0] Focus chain JB [auth O] Focus chain KC [auth S] Focus chain LA [auth D] Focus chain ND [auth 2] Focus chain OC [auth U] Focus chain SC [auth X] Focus chain SD [auth 4] Focus chain UA [auth G] Focus chain YC [auth Q] Focus chain ZA [auth I] Focus chain ZD [auth 7]
QAK (Subject of Investigation/LOI) Query on QAK 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]	(6~{R},10~{S},14~{R},19~{R},23~{S},24~{E},27~{S},28~{E})-2,6,10,14,19,23,27,31-octamethyldotriaconta-24,28-dien-2-ol C₄₀ H₇₈ O NKXXNXZGYNRQNV-BTRAWPHCSA-N		Interactions Focus chain DC [auth M] Interactions & Density Focus chain DC [auth M]
LMT (Subject of Investigation/LOI) Query on LMT Download:Ideal Coordinates CCD File SDF format, chain XD [auth 6] SDF format, chain UC [auth P] SDF format, chain SB [auth L] SDF format, chain QD [auth 4] SDF format, chain QA [auth F] SDF format, chain MD [auth 2] SDF format, chain MB [auth H] SDF format, chain IC [auth R] SDF format, chain IB [auth O] SDF format, chain GD [auth B] SDF format, chain CD [auth Z] SDF format, chain CB [auth J] MOL2 format, chain XD [auth 6] MOL2 format, chain UC [auth P] MOL2 format, chain SB [auth L] MOL2 format, chain QD [auth 4] MOL2 format, chain QA [auth F] MOL2 format, chain MD [auth 2] MOL2 format, chain MB [auth H] MOL2 format, chain IC [auth R] MOL2 format, chain IB [auth O] MOL2 format, chain GD [auth B] MOL2 format, chain CD [auth Z] MOL2 format, chain CB [auth J] mmCIF format, chain XD [auth 6] mmCIF format, chain UC [auth P] mmCIF format, chain SB [auth L] mmCIF format, chain QD [auth 4] mmCIF format, chain QA [auth F] mmCIF format, chain MD [auth 2] mmCIF format, chain MB [auth H] mmCIF format, chain IC [auth R] mmCIF format, chain IB [auth O] mmCIF format, chain GD [auth B] mmCIF format, chain CD [auth Z] mmCIF format, chain CB [auth J]	CB [auth J] CD [auth Z] GD [auth B] IB [auth O] IC [auth R] CB [auth J], CD [auth Z], GD [auth B], IB [auth O], IC [auth R], MB [auth H], MD [auth 2], QA [auth F], QD [auth 4], SB [auth L], UC [auth P], XD [auth 6]	DODECYL-BETA-D-MALTOSIDE C₂₄ H₄₆ O₁₁ NLEBIOOXCVAHBD-QKMCSOCLSA-N		Interactions Focus chain CB [auth J] Focus chain CD [auth Z] Focus chain GD [auth B] Focus chain IB [auth O] Focus chain IC [auth R] Focus chain MB [auth H] Focus chain MD [auth 2] Focus chain QA [auth F] Focus chain QD [auth 4] Focus chain SB [auth L] Focus chain UC [auth P] Focus chain XD [auth 6] Interactions & Density Focus chain CB [auth J] Focus chain CD [auth Z] Focus chain GD [auth B] Focus chain IB [auth O] Focus chain IC [auth R] Focus chain MB [auth H] Focus chain MD [auth 2] Focus chain QA [auth F] Focus chain QD [auth 4] Focus chain SB [auth L] Focus chain UC [auth P] Focus chain XD [auth 6]
FE (Subject of Investigation/LOI) Query on FE Download:Ideal Coordinates CCD File SDF format, chain ZB [auth M] MOL2 format, chain ZB [auth M] mmCIF format, chain ZB [auth M]	ZB [auth M]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N		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	A [auth C] BA [auth 3] C [auth E] DA [auth 5] E [auth G] A [auth C], BA [auth 3], C [auth E], DA [auth 5], E [auth G], FA [auth 7], G [auth J], HA [auth 9], I [auth N], N [auth R], P [auth T], R [auth V], T [auth P], V [auth Y], X [auth A], Z [auth 1]	L-PEPTIDE LINKING	C₆ H₁₁ N O₃ S		MET

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 2.80 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
RECONSTRUCTION	RELION	3.0
MODEL REFINEMENT	PHENIX	1.16

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2021-01-13

Deposition Author(s):

Funding Organization	Location	Grant Number
Biotechnology and Biological Sciences Research Council (BBSRC)	United Kingdom	BB/M000265/1

Revision History (Full details and data files)

Version 1.0: 2021-01-13
Type: Initial release
Version 1.1: 2021-02-10
Changes: Database references
Version 1.2: 2024-10-23
Changes: Data collection, Database references, Structure summary
Version 1.3: 2026-09-02
Type: Remediation
Reason: Metalloprotein remediation
Changes: Data collection, Derived calculations, Structure summary

6Z5R | pdb_00006z5r

RC-LH1(16) complex from Rhodopseudomonas palustris

Literature

Structures of Rhodopseudomonas palustris RC-LH1 complexes with open or closed quinone channels.

Biological Assembly 1

Macromolecules

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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Entity ID: 2

UniProt

Entity Groups

Sequence Annotations

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Entity ID: 3

UniProt

Entity Groups

Sequence Annotations

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Entity ID: 4

UniProt

Entity Groups

Sequence Annotations

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Entity ID: 5

UniProt

Entity Groups

Sequence Annotations

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Small Molecules

Experimental Data & Validation

Experimental Data

Structure Validation

Entry History

Deposition Data

Revision History (Full details and data files)