8WDU

Photosynthetic LH1-RC complex from the purple sulfur bacterium Allochromatium vinosum purified by sucrose density

PDB DOI: https://doi.org/10.2210/pdb8WDU/pdb
EM Map EMD-37465: EMDB EMDataResource

Classification: PHOTOSYNTHESIS
Organism(s): Allochromatium vinosum DSM 180
Mutation(s): No
Membrane Protein: Yes PDBTMMemProtMD

Deposited: 2023-09-16 Released: 2024-02-21
Deposition Author(s): Tani, K., Kanno, R., Harada, A., Kobayashi, A., Minamino, A., Nakamura, N., Ji, X.-C., Purba, E.R., Hall, M., Yu, L.-J., Madigan, M.T., Mizoguchi, A., Iwasaki, K., Humbel, B.M., Kimura, Y., Wang-Otomo, Z.-Y.
Funding Organization(s): Japan Agency for Medical Research and Development (AMED), Japan Society for the Promotion of Science (JSPS)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.24 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

High-resolution structure and biochemical properties of the LH1-RC photocomplex from the model purple sulfur bacterium, Allochromatium vinosum

Tani, K., Kanno, R., Harada, A., Kobayashi, Y., Minamino, A., Takenaka, S., Nakamura, N., Ji, X.C., Purba, E.R., Hall, M., Yu, L.J., Madigan, M.T., Mizoguchi, A., Iwasaki, K., Humbel, B.M., Kimura, Y., Wang-Otomo, Z.Y.

(2024) Commun Biol 7: 176

DOI: https://doi.org/10.1038/s42003-024-05863-w

Macromolecule Content

Total Structure Weight: 398.72 kDa
Atom Count: 26,274
Modelled Residue Count: 2,575
Deposited Residue Count: 2,833
Unique protein chains: 9

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosynthetic reaction center cytochrome c subunit	A [auth C]	383	Allochromatium vinosum DSM 180	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for O82947 (Allochromatium vinosum (strain ATCC 17899 / DSM 180 / NBRC 103801 / NCIMB 10441 / D)) Explore O82947 Go to UniProtKB: O82947
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O82947
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Reaction center protein L chain	B [auth L]	278	Allochromatium vinosum DSM 180	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for P51762 (Allochromatium vinosum (strain ATCC 17899 / DSM 180 / NBRC 103801 / NCIMB 10441 / D)) Explore P51762 Go to UniProtKB: P51762
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P51762
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Reaction center protein M chain	C [auth M]	325	Allochromatium vinosum DSM 180	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for P51763 (Allochromatium vinosum (strain ATCC 17899 / DSM 180 / NBRC 103801 / NCIMB 10441 / D)) Explore P51763 Go to UniProtKB: P51763
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P51763
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 H subunit	D [auth H]	259	Allochromatium vinosum DSM 180	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for D3RPF6 (Allochromatium vinosum (strain ATCC 17899 / DSM 180 / NBRC 103801 / NCIMB 10441 / D)) Explore D3RPF6 Go to UniProtKB: D3RPF6
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	D3RPF6
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Antenna complex alpha/beta subunit	AA [auth 1] E [auth A] EA [auth 5] GA [auth 7] IA [auth 9] AA [auth 1], E [auth A], EA [auth 5], GA [auth 7], IA [auth 9], K [auth I], M [auth K], O, Q	44	Allochromatium vinosum DSM 180	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for D3RP69 (Allochromatium vinosum (strain ATCC 17899 / DSM 180 / NBRC 103801 / NCIMB 10441 / D)) Explore D3RP69 Go to UniProtKB: D3RP69
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	D3RP69
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	BA [auth 2] DA [auth 4] F [auth B] FA [auth 6] HA [auth 8] BA [auth 2], DA [auth 4], F [auth B], FA [auth 6], HA [auth 8], JA [auth 0], L [auth J], N, P, R	46	Allochromatium vinosum DSM 180	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for D3RP75 (Allochromatium vinosum (strain ATCC 17899 / DSM 180 / NBRC 103801 / NCIMB 10441 / D)) Explore D3RP75 Go to UniProtKB: D3RP75
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	D3RP75
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
Antenna complex alpha/beta subunit	G [auth D] I [auth F] S U W G [auth D], I [auth F], S, U, W, Y	64	Allochromatium vinosum DSM 180	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for D3RP74 (Allochromatium vinosum (strain ATCC 17899 / DSM 180 / NBRC 103801 / NCIMB 10441 / D)) Explore D3RP74 Go to UniProtKB: D3RP74
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	D3RP74
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details	Image
Antenna complex alpha/beta subunit	H [auth E] J [auth G] T V X H [auth E], J [auth G], T, V, X, Z	47	Allochromatium vinosum DSM 180	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for D3RP68 (Allochromatium vinosum (strain ATCC 17899 / DSM 180 / NBRC 103801 / NCIMB 10441 / D)) Explore D3RP68 Go to UniProtKB: D3RP68
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	D3RP68
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 9
Molecule	Chains	Sequence Length	Organism	Details	Image
Antenna complex alpha/beta subunit	CA [auth 3]	66	Allochromatium vinosum DSM 180	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for D3RP67 (Allochromatium vinosum (strain ATCC 17899 / DSM 180 / NBRC 103801 / NCIMB 10441 / D)) Explore D3RP67 Go to UniProtKB: D3RP67
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	D3RP67
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 15 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CDL Query on CDL Download Ideal Coordinates CCD File SDF format, chain CB [auth L] SDF format, chain JB [auth M] SDF format, chain LB [auth M] SDF format, chain PB [auth H] SDF format, chain XB [auth D] MOL2 format, chain CB [auth L] MOL2 format, chain JB [auth M] MOL2 format, chain LB [auth M] MOL2 format, chain PB [auth H] MOL2 format, chain XB [auth D]	CB [auth L], JB [auth M], LB [auth M], PB [auth H], XB [auth D]	CARDIOLIPIN C₈₁ H₁₅₆ O₁₇ P₂ XVTUQDWPJJBEHJ-KZCWQMDCSA-L		Interactions Focus chain CB [auth L] Focus chain JB [auth M] Focus chain LB [auth M] Focus chain PB [auth H] Focus chain XB [auth D] Interactions & Density Focus chain CB [auth L] Focus chain JB [auth M] Focus chain LB [auth M] Focus chain PB [auth H] Focus chain XB [auth D]
BCL (Subject of Investigation/LOI) Query on BCL Download Ideal Coordinates CCD File SDF format, chain AD [auth R] SDF format, chain AE [auth 2] SDF format, chain BC [auth E] SDF format, chain CE [auth 3] SDF format, chain EB [auth M] SDF format, chain EC [auth F] SDF format, chain ED [auth S] SDF format, chain EE [auth 4] SDF format, chain FB [auth M] SDF format, chain GD [auth T] SDF format, chain HC [auth G] SDF format, chain IE [auth 5] SDF format, chain JC [auth I] SDF format, chain JD [auth U] SDF format, chain JE [auth 6] SDF format, chain LC [auth J] SDF format, chain LD [auth V] SDF format, chain LE [auth 7] SDF format, chain ND [auth W] SDF format, chain NE [auth 8] SDF format, chain PC [auth K] SDF format, chain QC [auth N] SDF format, chain QD [auth X] SDF format, chain QE [auth 9] SDF format, chain RE [auth 0] SDF format, chain SA [auth L] SDF format, chain SB [auth A] SDF format, chain SD [auth Y] SDF format, chain TC [auth O] SDF format, chain VB [auth B] SDF format, chain VC [auth P] SDF format, chain VD [auth Z] SDF format, chain YB [auth D] SDF format, chain YD [auth 1] SDF format, chain ZA [auth L] SDF format, chain ZC [auth Q] MOL2 format, chain AD [auth R] MOL2 format, chain AE [auth 2] MOL2 format, chain BC [auth E] MOL2 format, chain CE [auth 3] MOL2 format, chain EB [auth M] MOL2 format, chain EC [auth F] MOL2 format, chain ED [auth S] MOL2 format, chain EE [auth 4] MOL2 format, chain FB [auth M] MOL2 format, chain GD [auth T] MOL2 format, chain HC [auth G] MOL2 format, chain IE [auth 5] MOL2 format, chain JC [auth I] MOL2 format, chain JD [auth U] MOL2 format, chain JE [auth 6] MOL2 format, chain LC [auth J] MOL2 format, chain LD [auth V] MOL2 format, chain LE [auth 7] MOL2 format, chain ND [auth W] MOL2 format, chain NE [auth 8] MOL2 format, chain PC [auth K] MOL2 format, chain QC [auth N] MOL2 format, chain QD [auth X] MOL2 format, chain QE [auth 9] MOL2 format, chain RE [auth 0] MOL2 format, chain SA [auth L] MOL2 format, chain SB [auth A] MOL2 format, chain SD [auth Y] MOL2 format, chain TC [auth O] MOL2 format, chain VB [auth B] MOL2 format, chain VC [auth P] MOL2 format, chain VD [auth Z] MOL2 format, chain YB [auth D] MOL2 format, chain YD [auth 1] MOL2 format, chain ZA [auth L] MOL2 format, chain ZC [auth Q]	AD [auth R] AE [auth 2] BC [auth E] CE [auth 3] EB [auth M] AD [auth R], AE [auth 2], BC [auth E], CE [auth 3], EB [auth M], EC [auth F], ED [auth S], EE [auth 4], FB [auth M], GD [auth T], HC [auth G], IE [auth 5], JC [auth I], JD [auth U], JE [auth 6], LC [auth J], LD [auth V], LE [auth 7], ND [auth W], NE [auth 8], PC [auth K], QC [auth N], QD [auth X], QE [auth 9], RE [auth 0], SA [auth L], SB [auth A], SD [auth Y], TC [auth O], VB [auth B], VC [auth P], VD [auth Z], YB [auth D], YD [auth 1], ZA [auth L], ZC [auth Q]	BACTERIOCHLOROPHYLL A C₅₅ H₇₄ Mg N₄ O₆ DSJXIQQMORJERS-AGGZHOMASA-M		Interactions Focus chain AD [auth R] Focus chain AE [auth 2] Focus chain BC [auth E] Focus chain CE [auth 3] Focus chain EB [auth M] Focus chain EC [auth F] Focus chain ED [auth S] Focus chain EE [auth 4] Focus chain FB [auth M] Focus chain GD [auth T] Focus chain HC [auth G] Focus chain IE [auth 5] Focus chain JC [auth I] Focus chain JD [auth U] Focus chain JE [auth 6] Focus chain LC [auth J] Focus chain LD [auth V] Focus chain LE [auth 7] Focus chain ND [auth W] Focus chain NE [auth 8] Focus chain PC [auth K] Focus chain QC [auth N] Focus chain QD [auth X] Focus chain QE [auth 9] Focus chain RE [auth 0] Focus chain SA [auth L] Focus chain SB [auth A] Focus chain SD [auth Y] Focus chain TC [auth O] Focus chain VB [auth B] Focus chain VC [auth P] Focus chain VD [auth Z] Focus chain YB [auth D] Focus chain YD [auth 1] Focus chain ZA [auth L] Focus chain ZC [auth Q] Interactions & Density Focus chain AD [auth R] Focus chain AE [auth 2] Focus chain BC [auth E] Focus chain CE [auth 3] Focus chain EB [auth M] Focus chain EC [auth F] Focus chain ED [auth S] Focus chain EE [auth 4] Focus chain FB [auth M] Focus chain GD [auth T] Focus chain HC [auth G] Focus chain IE [auth 5] Focus chain JC [auth I] Focus chain JD [auth U] Focus chain JE [auth 6] Focus chain LC [auth J] Focus chain LD [auth V] Focus chain LE [auth 7] Focus chain ND [auth W] Focus chain NE [auth 8] Focus chain PC [auth K] Focus chain QC [auth N] Focus chain QD [auth X] Focus chain QE [auth 9] Focus chain RE [auth 0] Focus chain SA [auth L] Focus chain SB [auth A] Focus chain SD [auth Y] Focus chain TC [auth O] Focus chain VB [auth B] Focus chain VC [auth P] Focus chain VD [auth Z] Focus chain YB [auth D] Focus chain YD [auth 1] Focus chain ZA [auth L] Focus chain ZC [auth Q]
BPH Query on BPH Download Ideal Coordinates CCD File SDF format, chain GB [auth M] SDF format, chain TA [auth L] MOL2 format, chain GB [auth M] MOL2 format, chain TA [auth L]	GB [auth M], TA [auth L]	BACTERIOPHEOPHYTIN A C₅₅ H₇₆ N₄ O₆ KWOZSBGNAHVCKG-SZQBJALDSA-N		Interactions Focus chain GB [auth M] Focus chain TA [auth L] Interactions & Density Focus chain GB [auth M] Focus chain TA [auth L]
PGV Query on PGV Download Ideal Coordinates CCD File SDF format, chain BB [auth L] SDF format, chain DC [auth F] SDF format, chain KB [auth M] SDF format, chain OB [auth H] SDF format, chain RA [auth C] SDF format, chain RB [auth A] SDF format, chain TB [auth A] SDF format, chain WA [auth L] SDF format, chain XA [auth L] SDF format, chain XD [auth 1] SDF format, chain YC [auth Q] MOL2 format, chain BB [auth L] MOL2 format, chain DC [auth F] MOL2 format, chain KB [auth M] MOL2 format, chain OB [auth H] MOL2 format, chain RA [auth C] MOL2 format, chain RB [auth A] MOL2 format, chain TB [auth A] MOL2 format, chain WA [auth L] MOL2 format, chain XA [auth L] MOL2 format, chain XD [auth 1] MOL2 format, chain YC [auth Q]	BB [auth L] DC [auth F] KB [auth M] OB [auth H] RA [auth C] BB [auth L], DC [auth F], KB [auth M], OB [auth H], RA [auth C], RB [auth A], TB [auth A], WA [auth L], XA [auth L], XD [auth 1], YC [auth Q]	(1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE C₄₀ H₇₇ O₁₀ P ADYWCMPUNIVOEA-GPJPVTGXSA-N		Interactions Focus chain BB [auth L] Focus chain DC [auth F] Focus chain KB [auth M] Focus chain OB [auth H] Focus chain RA [auth C] Focus chain RB [auth A] Focus chain TB [auth A] Focus chain WA [auth L] Focus chain XA [auth L] Focus chain XD [auth 1] Focus chain YC [auth Q] Interactions & Density Focus chain BB [auth L] Focus chain DC [auth F] Focus chain KB [auth M] Focus chain OB [auth H] Focus chain RA [auth C] Focus chain RB [auth A] Focus chain TB [auth A] Focus chain WA [auth L] Focus chain XA [auth L] Focus chain XD [auth 1] Focus chain YC [auth Q]
UQ8 Query on UQ8 Download Ideal Coordinates CCD File SDF format, chain AB [auth L] SDF format, chain UA [auth L] SDF format, chain VA [auth L] MOL2 format, chain AB [auth L] MOL2 format, chain UA [auth L] MOL2 format, chain VA [auth L]	AB [auth L], UA [auth L], VA [auth L]	Ubiquinone-8 C₄₉ H₇₄ O₄ ICFIZJQGJAJRSU-SGHXUWJISA-N		Interactions Focus chain AB [auth L] Focus chain UA [auth L] Focus chain VA [auth L] Interactions & Density Focus chain AB [auth L] Focus chain UA [auth L] Focus chain VA [auth L]
MQ8 Query on MQ8 Download Ideal Coordinates CCD File SDF format, chain HB [auth M] MOL2 format, chain HB [auth M]	HB [auth M]	MENAQUINONE 8 C₅₁ H₇₂ O₂ LXKDFTDVRVLXFY-ACMRXAIVSA-N		Interactions Focus chain HB [auth M] Interactions & Density Focus chain HB [auth M]
HEM Query on HEM Download Ideal Coordinates CCD File SDF format, chain KA [auth C] SDF format, chain LA [auth C] SDF format, chain MA [auth C] SDF format, chain NA [auth C] MOL2 format, chain KA [auth C] MOL2 format, chain LA [auth C] MOL2 format, chain MA [auth C] MOL2 format, chain NA [auth C]	KA [auth C], LA [auth C], MA [auth C], NA [auth C]	PROTOPORPHYRIN IX CONTAINING FE C₃₄ H₃₂ Fe N₄ O₄ KABFMIBPWCXCRK-RGGAHWMASA-L		Interactions Focus chain KA [auth C] Focus chain LA [auth C] Focus chain MA [auth C] Focus chain NA [auth C] Interactions & Density Focus chain KA [auth C] Focus chain LA [auth C] Focus chain MA [auth C] Focus chain NA [auth C]
CRT Query on CRT Download Ideal Coordinates CCD File SDF format, chain BD [auth R] SDF format, chain BE [auth 2] SDF format, chain CC [auth E] SDF format, chain FE [auth 4] SDF format, chain HD [auth T] SDF format, chain IB [auth M] SDF format, chain IC [auth G] SDF format, chain KE [auth 6] SDF format, chain MC [auth J] SDF format, chain MD [auth V] SDF format, chain PE [auth 9] SDF format, chain RC [auth N] SDF format, chain RD [auth Y] SDF format, chain SE [auth 0] SDF format, chain WB [auth B] SDF format, chain WC [auth P] SDF format, chain WD [auth Z] MOL2 format, chain BD [auth R] MOL2 format, chain BE [auth 2] MOL2 format, chain CC [auth E] MOL2 format, chain FE [auth 4] MOL2 format, chain HD [auth T] MOL2 format, chain IB [auth M] MOL2 format, chain IC [auth G] MOL2 format, chain KE [auth 6] MOL2 format, chain MC [auth J] MOL2 format, chain MD [auth V] MOL2 format, chain PE [auth 9] MOL2 format, chain RC [auth N] MOL2 format, chain RD [auth Y] MOL2 format, chain SE [auth 0] MOL2 format, chain WB [auth B] MOL2 format, chain WC [auth P] MOL2 format, chain WD [auth Z]	BD [auth R] BE [auth 2] CC [auth E] FE [auth 4] HD [auth T] BD [auth R], BE [auth 2], CC [auth E], FE [auth 4], HD [auth T], IB [auth M], IC [auth G], KE [auth 6], MC [auth J], MD [auth V], PE [auth 9], RC [auth N], RD [auth Y], SE [auth 0], WB [auth B], WC [auth P], WD [auth Z]	SPIRILLOXANTHIN C₄₂ H₆₀ O₂ VAZQBTJCYODOSV-RISZBRKMSA-N		Interactions Focus chain BD [auth R] Focus chain BE [auth 2] Focus chain CC [auth E] Focus chain FE [auth 4] Focus chain HD [auth T] Focus chain IB [auth M] Focus chain IC [auth G] Focus chain KE [auth 6] Focus chain MC [auth J] Focus chain MD [auth V] Focus chain PE [auth 9] Focus chain RC [auth N] Focus chain RD [auth Y] Focus chain SE [auth 0] Focus chain WB [auth B] Focus chain WC [auth P] Focus chain WD [auth Z] Interactions & Density Focus chain BD [auth R] Focus chain BE [auth 2] Focus chain CC [auth E] Focus chain FE [auth 4] Focus chain HD [auth T] Focus chain IB [auth M] Focus chain IC [auth G] Focus chain KE [auth 6] Focus chain MC [auth J] Focus chain MD [auth V] Focus chain PE [auth 9] Focus chain RC [auth N] Focus chain RD [auth Y] Focus chain SE [auth 0] Focus chain WB [auth B] Focus chain WC [auth P] Focus chain WD [auth Z]
Z41 Query on Z41 Download Ideal Coordinates CCD File SDF format, chain PA [auth C] MOL2 format, chain PA [auth C]	PA [auth C]	(2S)-3-hydroxypropane-1,2-diyl dihexadecanoate C₃₅ H₆₈ O₅ JEJLGIQLPYYGEE-XIFFEERXSA-N		Interactions Focus chain PA [auth C] Interactions & Density Focus chain PA [auth C]
LMT Query on LMT Download Ideal Coordinates CCD File SDF format, chain AC [auth E] SDF format, chain CD [auth R] SDF format, chain DD [auth S] SDF format, chain DE [auth 4] SDF format, chain GC [auth G] SDF format, chain GE [auth 4] SDF format, chain HE [auth 5] SDF format, chain ID [auth T] SDF format, chain KC [auth J] SDF format, chain MB [auth M] SDF format, chain ME [auth 8] SDF format, chain NB [auth M] SDF format, chain NC [auth J] SDF format, chain OE [auth 8] SDF format, chain PD [auth X] SDF format, chain QB [auth H] SDF format, chain UB [auth B] SDF format, chain UC [auth P] SDF format, chain UD [auth Z] SDF format, chain XC [auth P] SDF format, chain YA [auth L] SDF format, chain ZD [auth 2] MOL2 format, chain AC [auth E] MOL2 format, chain CD [auth R] MOL2 format, chain DD [auth S] MOL2 format, chain DE [auth 4] MOL2 format, chain GC [auth G] MOL2 format, chain GE [auth 4] MOL2 format, chain HE [auth 5] MOL2 format, chain ID [auth T] MOL2 format, chain KC [auth J] MOL2 format, chain MB [auth M] MOL2 format, chain ME [auth 8] MOL2 format, chain NB [auth M] MOL2 format, chain NC [auth J] MOL2 format, chain OE [auth 8] MOL2 format, chain PD [auth X] MOL2 format, chain QB [auth H] MOL2 format, chain UB [auth B] MOL2 format, chain UC [auth P] MOL2 format, chain UD [auth Z] MOL2 format, chain XC [auth P] MOL2 format, chain YA [auth L] MOL2 format, chain ZD [auth 2]	AC [auth E] CD [auth R] DD [auth S] DE [auth 4] GC [auth G] AC [auth E], CD [auth R], DD [auth S], DE [auth 4], GC [auth G], GE [auth 4], HE [auth 5], ID [auth T], KC [auth J], MB [auth M], ME [auth 8], NB [auth M], NC [auth J], OE [auth 8], PD [auth X], QB [auth H], UB [auth B], UC [auth P], UD [auth Z], XC [auth P], YA [auth L], ZD [auth 2]	DODECYL-BETA-D-MALTOSIDE C₂₄ H₄₆ O₁₁ NLEBIOOXCVAHBD-QKMCSOCLSA-N		Interactions Focus chain AC [auth E] Focus chain CD [auth R] Focus chain DD [auth S] Focus chain DE [auth 4] Focus chain GC [auth G] Focus chain GE [auth 4] Focus chain HE [auth 5] Focus chain ID [auth T] Focus chain KC [auth J] Focus chain MB [auth M] Focus chain ME [auth 8] Focus chain NB [auth M] Focus chain NC [auth J] Focus chain OE [auth 8] Focus chain PD [auth X] Focus chain QB [auth H] Focus chain UB [auth B] Focus chain UC [auth P] Focus chain UD [auth Z] Focus chain XC [auth P] Focus chain YA [auth L] Focus chain ZD [auth 2] Interactions & Density Focus chain AC [auth E] Focus chain CD [auth R] Focus chain DD [auth S] Focus chain DE [auth 4] Focus chain GC [auth G] Focus chain GE [auth 4] Focus chain HE [auth 5] Focus chain ID [auth T] Focus chain KC [auth J] Focus chain MB [auth M] Focus chain ME [auth 8] Focus chain NB [auth M] Focus chain NC [auth J] Focus chain OE [auth 8] Focus chain PD [auth X] Focus chain QB [auth H] Focus chain UB [auth B] Focus chain UC [auth P] Focus chain UD [auth Z] Focus chain XC [auth P] Focus chain YA [auth L] Focus chain ZD [auth 2]
PLM Query on PLM Download Ideal Coordinates CCD File SDF format, chain QA [auth C] MOL2 format, chain QA [auth C]	QA [auth C]	PALMITIC ACID C₁₆ H₃₂ O₂ IPCSVZSSVZVIGE-UHFFFAOYSA-N		Interactions Focus chain QA [auth C] Interactions & Density Focus chain QA [auth C]
LDA Query on LDA Download Ideal Coordinates CCD File SDF format, chain OC [auth K] SDF format, chain SC [auth O] MOL2 format, chain OC [auth K] MOL2 format, chain SC [auth O]	OC [auth K], SC [auth O]	LAURYL DIMETHYLAMINE-N-OXIDE C₁₄ H₃₁ N O SYELZBGXAIXKHU-UHFFFAOYSA-N		Interactions Focus chain OC [auth K] Focus chain SC [auth O] Interactions & Density Focus chain OC [auth K] Focus chain SC [auth O]
FE Query on FE Download Ideal Coordinates CCD File SDF format, chain DB [auth M] MOL2 format, chain DB [auth M]	DB [auth M]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N		Interactions Focus chain DB [auth M] Interactions & Density Focus chain DB [auth M]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain FC [auth F] SDF format, chain FD [auth S] SDF format, chain KD [auth U] SDF format, chain OD [auth W] SDF format, chain TD [auth Y] SDF format, chain ZB [auth D] MOL2 format, chain FC [auth F] MOL2 format, chain FD [auth S] MOL2 format, chain KD [auth U] MOL2 format, chain OD [auth W] MOL2 format, chain TD [auth Y] MOL2 format, chain ZB [auth D]	FC [auth F] FD [auth S] KD [auth U] OD [auth W] TD [auth Y] FC [auth F], FD [auth S], KD [auth U], OD [auth W], TD [auth Y], ZB [auth D]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain FC [auth F] Focus chain FD [auth S] Focus chain KD [auth U] Focus chain OD [auth W] Focus chain TD [auth Y] Focus chain ZB [auth D] Interactions & Density Focus chain FC [auth F] Focus chain FD [auth S] Focus chain KD [auth U] Focus chain OD [auth W] Focus chain TD [auth Y] Focus chain ZB [auth D]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain OA [auth C] MOL2 format, chain OA [auth C]	OA [auth C]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain OA [auth C] Interactions & Density Focus chain OA [auth C]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
FME Query on FME	D [auth H]	L-PEPTIDE LINKING	C₆ H₁₁ N O₃ S		MET

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 2.24 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: 2024-02-21

Deposition Author(s):

Funding Organization	Location	Grant Number
Japan Agency for Medical Research and Development (AMED)	Japan	JP21am0101118
Japan Agency for Medical Research and Development (AMED)	Japan	JP21am0101116
Japan Society for the Promotion of Science (JSPS)	Japan	JP16H04174
Japan Society for the Promotion of Science (JSPS)	Japan	JP18H05153
Japan Society for the Promotion of Science (JSPS)	Japan	20H05086
Japan Society for the Promotion of Science (JSPS)	Japan	20H02856

Revision History (Full details and data files)

Version 1.0: 2024-02-21
Type: Initial release

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.

Prepare Data

Validate Data

Deposit Data

Help and Resources

8WDU

Photosynthetic LH1-RC complex from the purple sulfur bacterium Allochromatium vinosum purified by sucrose density

High-resolution structure and biochemical properties of the LH1-RC photocomplex from the model purple sulfur bacterium, Allochromatium vinosum

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

Entity ID: 2

UniProt

Entity Groups

Sequence Annotations

Entity ID: 3

UniProt

Entity Groups

Sequence Annotations

Entity ID: 4

UniProt

Entity Groups

Sequence Annotations

Entity ID: 5

UniProt

Entity Groups

Sequence Annotations

Entity ID: 6

UniProt

Entity Groups

Sequence Annotations

Entity ID: 7

UniProt

Entity Groups

Sequence Annotations

Entity ID: 8

UniProt

Entity Groups

Sequence Annotations

Entity ID: 9

UniProt

Entity Groups

Sequence Annotations

Experimental Data

Structure Validation

Deposition Data

Revision History (Full details and data files)