6Z5S

RC-LH1(14)-W complex from Rhodopseudomonas palustris

DOI: 10.2210/pdb6Z5S/pdb
EMDataResource: EMD-11081

Classification: PHOTOSYNTHESIS
Organism(s): Rhodopseudomonas palustris CGA009
Mutation(s): No

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: 2.65 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

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

(2021) Sci Adv

Macromolecules

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(by identity cutoff) | Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Light harvesting complex 1 Protein W	W	102	Rhodopseudomonas palustris CGA009	Mutation(s): 0 Gene Names: RPA4402
Find proteins for Q6N1K3 (Rhodopseudomonas palustris (strain ATCC BAA-98 / CGA009)) Explore Q6N1K3 Go to UniProtKB: Q6N1K3
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Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Reaction center protein M chain	M	307	Rhodopseudomonas palustris CGA009	Mutation(s): 0 Gene Names: pufM, RPA1528
Find proteins for A0A4Z7 (Rhodopseudomonas palustris (strain ATCC BAA-98 / CGA009)) Explore A0A4Z7 Go to UniProtKB: A0A4Z7
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Reference Sequence

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Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Reaction center protein L chain	L	277	Rhodopseudomonas palustris CGA009	Mutation(s): 0 Gene Names: pufL, RPA1527
Find proteins for O83005 (Rhodopseudomonas palustris (strain ATCC BAA-98 / CGA009)) Explore O83005 Go to UniProtKB: O83005
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Reference Sequence

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Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
H subunit of photosynthetic reaction center complex	H	255	Rhodopseudomonas palustris CGA009	Mutation(s): 0 Gene Names: puhA, RPA1548
Find proteins for A0A4Z9 (Rhodopseudomonas palustris (strain ATCC BAA-98 / CGA009)) Explore A0A4Z9 Go to UniProtKB: A0A4Z9
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Reference Sequence

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Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Light-harvesting complex 1 alpha chain	1, 3, 5, A, C, E, G, J, N, P, R, T, V, Y	63	Rhodopseudomonas palustris CGA009	Mutation(s): 0 Gene Names: pufA, RPA1526
Find proteins for Q6N9L4 (Rhodopseudomonas palustris (strain ATCC BAA-98 / CGA009)) Explore Q6N9L4 Go to UniProtKB: Q6N9L4
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Reference Sequence

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Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
Light-harvesting complex 1 beta chain	2, 4, 6, B, D, F, I, K, O, Q, S, U, X, Z	65	Rhodopseudomonas palustris CGA009	Mutation(s): 0 Gene Names: pufB, RPA1525
Find proteins for Q6N9L5 (Rhodopseudomonas palustris (strain ATCC BAA-98 / CGA009)) Explore Q6N9L5 Go to UniProtKB: Q6N9L5
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Reference Sequence

Small Molecules

Ligands 10 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CDL Query on CDL Download Ideal Coordinates CCD File SDF format, chain GD [G] SDF format, chain HB [3] SDF format, chain JD [G] SDF format, chain LA [M] SDF format, chain SA [L] SDF format, chain WA [H] MOL2 format, chain GD [G] MOL2 format, chain HB [3] MOL2 format, chain JD [G] MOL2 format, chain LA [M] MOL2 format, chain SA [L] MOL2 format, chain WA [H]	3, G, H, L, M	CARDIOLIPIN C₈₁ H₁₅₆ O₁₇ P₂ XVTUQDWPJJBEHJ-KZCWQMDCSA-L		Ligand Interaction
BCL Query on BCL Download Ideal Coordinates CCD File SDF format, chain BD [J] SDF format, chain CD [J] SDF format, chain DB [5] SDF format, chain DC [C] SDF format, chain EB [5] SDF format, chain GB [3] SDF format, chain HA [M] SDF format, chain HC [D] SDF format, chain HD [G] SDF format, chain ID [G] SDF format, chain JB [4] SDF format, chain LB [Y] SDF format, chain LC [R] SDF format, chain MA [M] SDF format, chain MB [Y] SDF format, chain MC [R] SDF format, chain OD [E] SDF format, chain PA [L] SDF format, chain PB [V] SDF format, chain PD [E] SDF format, chain QA [L] SDF format, chain QB [V] SDF format, chain QC [P] SDF format, chain SC [P] SDF format, chain UB [T] SDF format, chain VB [T] SDF format, chain WC [N] SDF format, chain XA [1] SDF format, chain XC [N] SDF format, chain YB [A] SDF format, chain ZA [2] SDF format, chain ZB [A] MOL2 format, chain BD [J] MOL2 format, chain CD [J] MOL2 format, chain DB [5] MOL2 format, chain DC [C] MOL2 format, chain EB [5] MOL2 format, chain GB [3] MOL2 format, chain HA [M] MOL2 format, chain HC [D] MOL2 format, chain HD [G] MOL2 format, chain ID [G] MOL2 format, chain JB [4] MOL2 format, chain LB [Y] MOL2 format, chain LC [R] MOL2 format, chain MA [M] MOL2 format, chain MB [Y] MOL2 format, chain MC [R] MOL2 format, chain OD [E] MOL2 format, chain PA [L] MOL2 format, chain PB [V] MOL2 format, chain PD [E] MOL2 format, chain QA [L] MOL2 format, chain QB [V] MOL2 format, chain QC [P] MOL2 format, chain SC [P] MOL2 format, chain UB [T] MOL2 format, chain VB [T] MOL2 format, chain WC [N] MOL2 format, chain XA [1] MOL2 format, chain XC [N] MOL2 format, chain YB [A] MOL2 format, chain ZA [2] MOL2 format, chain ZB [A]	1, 2, 3, 4, 5, A, C, D, E, G, J, L, M, N, P, R, T, V, Y	BACTERIOCHLOROPHYLL A C₅₅ H₇₄ Mg N₄ O₆ DSJXIQQMORJERS-RUUWGSCADZ		Ligand Interaction
BPH Query on BPH Download Ideal Coordinates CCD File SDF format, chain IA [M] SDF format, chain RA [L] MOL2 format, chain IA [M] MOL2 format, chain RA [L]	L, M	BACTERIOPHEOPHYTIN A C₅₅ H₇₆ N₄ O₆ KWOZSBGNAHVCKG-SZQBJALDSA-N		Ligand Interaction
U10 Query on U10 Download Ideal Coordinates CCD File SDF format, chain JA [M] SDF format, chain UA [L] SDF format, chain YA [1] MOL2 format, chain JA [M] MOL2 format, chain UA [L] MOL2 format, chain YA [1]	1, L, M	UBIQUINONE-10 C₅₉ H₉₀ O₄ ACTIUHUUMQJHFO-UPTCCGCDSA-N		Ligand Interaction
6PL Query on 6PL Download Ideal Coordinates CCD File SDF format, chain KA [M] SDF format, chain ND [E] SDF format, chain VA [H] MOL2 format, chain KA [M] MOL2 format, chain ND [E] MOL2 format, chain VA [H]	E, H, M	(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		Ligand Interaction
PGT Query on PGT Download Ideal Coordinates CCD File SDF format, chain RC [P] MOL2 format, chain RC [P]	P	(1S)-2-{[{[(2R)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL STEARATE C₄₀ H₇₉ O₁₀ P KBPVYRBBONZJHF-AMAPPZPBSA-N		Ligand Interaction
CRT Query on CRT Download Ideal Coordinates CCD File SDF format, chain AB [2] SDF format, chain CC [B] SDF format, chain FD [K] SDF format, chain IB [3] SDF format, chain IC [D] SDF format, chain JC [R] SDF format, chain MD [I] SDF format, chain NB [Z] SDF format, chain PC [S] SDF format, chain SB [X] SDF format, chain SD [F] SDF format, chain VC [Q] SDF format, chain ZC [O] MOL2 format, chain AB [2] MOL2 format, chain CC [B] MOL2 format, chain FD [K] MOL2 format, chain IB [3] MOL2 format, chain IC [D] MOL2 format, chain JC [R] MOL2 format, chain MD [I] MOL2 format, chain NB [Z] MOL2 format, chain PC [S] MOL2 format, chain SB [X] MOL2 format, chain SD [F] MOL2 format, chain VC [Q] MOL2 format, chain ZC [O]	2, 3, B, D, F, I, K, O, Q, R, S, X, Z	SPIRILLOXANTHIN C₄₂ H₆₀ O₂ VAZQBTJCYODOSV-RISZBRKMSA-N		Ligand Interaction
QAK Query on QAK Download Ideal Coordinates CCD File SDF format, chain GA [M] MOL2 format, chain GA [M]	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		Ligand Interaction
LMT Query on LMT Download Ideal Coordinates CCD File SDF format, chain AC [B] SDF format, chain AD [J] SDF format, chain BB [2] SDF format, chain BC [B] SDF format, chain CB [2] SDF format, chain DD [K] SDF format, chain EC [D] SDF format, chain ED [K] SDF format, chain FB [6] SDF format, chain FC [D] SDF format, chain GC [D] SDF format, chain KB [4] SDF format, chain KC [R] SDF format, chain KD [I] SDF format, chain LD [I] SDF format, chain NC [S] SDF format, chain OA [M] SDF format, chain OB [Z] SDF format, chain OC [S] SDF format, chain QD [F] SDF format, chain RB [X] SDF format, chain RD [F] SDF format, chain TA [L] SDF format, chain TB [X] SDF format, chain TC [Q] SDF format, chain UC [Q] SDF format, chain WB [U] SDF format, chain XB [U] SDF format, chain YC [O] MOL2 format, chain AC [B] MOL2 format, chain AD [J] MOL2 format, chain BB [2] MOL2 format, chain BC [B] MOL2 format, chain CB [2] MOL2 format, chain DD [K] MOL2 format, chain EC [D] MOL2 format, chain ED [K] MOL2 format, chain FB [6] MOL2 format, chain FC [D] MOL2 format, chain GC [D] MOL2 format, chain KB [4] MOL2 format, chain KC [R] MOL2 format, chain KD [I] MOL2 format, chain LD [I] MOL2 format, chain NC [S] MOL2 format, chain OA [M] MOL2 format, chain OB [Z] MOL2 format, chain OC [S] MOL2 format, chain QD [F] MOL2 format, chain RB [X] MOL2 format, chain RD [F] MOL2 format, chain TA [L] MOL2 format, chain TB [X] MOL2 format, chain TC [Q] MOL2 format, chain UC [Q] MOL2 format, chain WB [U] MOL2 format, chain XB [U] MOL2 format, chain YC [O]	2, 4, 6, B, D, F, I, J, K, L, M, O, Q, R, S, U, X, Z	DODECYL-BETA-D-MALTOSIDE C₂₄ H₄₆ O₁₁ NLEBIOOXCVAHBD-QKMCSOCLSA-N		Ligand Interaction
FE Query on FE Download Ideal Coordinates CCD File SDF format, chain NA [M] MOL2 format, chain NA [M]	M	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N		Ligand Interaction