7XXF | pdb_00007xxf

Structure of photosynthetic LH1-RC super-complex of Rhodopila globiformis

PDB DOI: https://doi.org/10.2210/pdb7XXF/pdb
EM Map EMD-33501: EMDB EMDataResource

Classification: PHOTOSYNTHESIS
Organism(s): Rhodopila globiformis
Mutation(s): No
Membrane Protein: Yes OPM PDBTM MemProtMD

Deposited: 2022-05-30 Released: 2022-11-16
Deposition Author(s): Tani, K., Kanno, R., Kurosawa, K., Takaichi, S., Nagashima, K.V.P., Hall, M., Yu, L.-J., Kimura, Y., Madigan, M.T., Mizoguchi, A., Humbel, B.M., 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

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

An LH1-RC photocomplex from an extremophilic phototroph provides insight into origins of two photosynthesis proteins.

Tani, K., Kanno, R., Kurosawa, K., Takaichi, S., Nagashima, K.V.P., Hall, M., Yu, L.J., Kimura, Y., Madigan, M.T., Mizoguchi, A., Humbel, B.M., Wang-Otomo, Z.Y.

(2022) Commun Biol 5: 1197-1197

PubMed: 36344631 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1038/s42003-022-04174-2
Primary Citation Related Structures:
7XXF

PubMed Abstract:
Rhodopila globiformis is the most acidophilic of anaerobic purple phototrophs, growing optimally in culture at pH 5. Here we present a cryo-EM structure of the light-harvesting 1-reaction center (LH1-RC) complex from Rhodopila globiformis at 2.24 Å resolution. All purple bacterial cytochrome (Cyt, encoded by the gene pufC) subunit-associated RCs with known structures have their N-termini truncated. By contrast, the Rhodopila globiformis RC contains a full-length tetra-heme Cyt with its N-terminus embedded in the membrane forming an α-helix as the membrane anchor. Comparison of the N-terminal regions of the Cyt with PufX polypeptides widely distributed in Rhodobacter species reveals significant structural similarities, supporting a longstanding hypothesis that PufX is phylogenetically related to the N-terminus of the RC-bound Cyt subunit and that a common ancestor of phototrophic Proteobacteria contained a full-length tetra-heme Cyt subunit that evolved independently through partial deletions of its pufC gene. Eleven copies of a novel γ-like polypeptide were also identified in the bacteriochlorophyll a-containing Rhodopila globiformis LH1 complex; γ-polypeptides have previously been found only in the LH1 of bacteriochlorophyll b-containing species. These features are discussed in relation to their predicted functions of stabilizing the LH1 structure and regulating quinone transport under the warm acidic conditions.

Organizational Affiliation

Graduate School of Medicine, Mie University, Tsu, 514-8507, Japan. ktani@doc.medic.mie-u.ac.jp.

Macromolecule Content

Total Structure Weight: 481.88 kDa
Atom Count: 29,826
Modeled Residue Count: 3,004
Deposited Residue Count: 3,589
Unique protein chains: 7

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosynthetic reaction center cytochrome c subunit	A [auth C]	344	Rhodopila globiformis	Mutation(s): 0
UniProt
Find proteins for A0A2S6NEK5 (Rhodopila globiformis) Explore A0A2S6NEK5 Go to UniProtKB: A0A2S6NEK5
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A2S6NEK5
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Reaction center protein L chain	B [auth L]	275	Rhodopila globiformis	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for A0A2S6NEG7 (Rhodopila globiformis) Explore A0A2S6NEG7 Go to UniProtKB: A0A2S6NEG7
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A2S6NEG7
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Reference Sequence

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| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Reaction center protein M chain	C [auth M]	326	Rhodopila globiformis	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for A0A2S6NEP5 (Rhodopila globiformis) Explore A0A2S6NEP5 Go to UniProtKB: A0A2S6NEP5
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Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A2S6NEP5
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Reference Sequence

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| 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosynthetic reaction center H subunit	D [auth H]	258	Rhodopila globiformis	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for A0A2S6MZS1 (Rhodopila globiformis) Explore A0A2S6MZS1 Go to UniProtKB: A0A2S6MZS1
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A2S6MZS1
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Reference Sequence

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| 3D Structure

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Light-harvesting protein	AA [auth 1] CA [auth 3] E [auth A] EA [auth 5] G [auth D] AA [auth 1], CA [auth 3], E [auth A], EA [auth 5], G [auth D], GA [auth 7], I [auth F], IA [auth 9], K [auth I], M [auth K], O, Q, S, U, W, Y	61	Rhodopila globiformis	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for A0A2S6NEK3 (Rhodopila globiformis) Explore A0A2S6NEK3 Go to UniProtKB: A0A2S6NEK3
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A2S6NEK3
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Reference Sequence

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| 3D Structure

Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
Light-harvesting protein	BA [auth 2] DA [auth 4] F [auth B] FA [auth 6] H [auth E] BA [auth 2], DA [auth 4], F [auth B], FA [auth 6], H [auth E], HA [auth 8], J [auth G], JA [auth 0], L [auth J], N, P, R, T, V, X, Z	73	Rhodopila globiformis	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for A0A2S6NEL9 (Rhodopila globiformis) Explore A0A2S6NEL9 Go to UniProtKB: A0A2S6NEL9
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A2S6NEL9
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
Light-harvesting protein LH1 Gamma-like	KA [auth a] LA [auth b] MA [auth c] NA [auth d] OA [auth e] KA [auth a], LA [auth b], MA [auth c], NA [auth d], OA [auth e], PA [auth f], QA [auth g], RA [auth h], SA [auth i], TA [auth j], UA [auth k]	22	Rhodopila globiformis	Mutation(s): 0

Small Molecules

Ligands 11 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CDL Query on CDL Download:Ideal Coordinates CCD File SDF format, chain CC [auth H] SDF format, chain DC [auth A] SDF format, chain EE [auth 6] SDF format, chain HD [auth T] SDF format, chain NE [auth 0] SDF format, chain TD [auth 2] SDF format, chain VB [auth M] SDF format, chain WB [auth M] SDF format, chain HE [auth 6] MOL2 format, chain CC [auth H] MOL2 format, chain DC [auth A] MOL2 format, chain EE [auth 6] MOL2 format, chain HD [auth T] MOL2 format, chain NE [auth 0] MOL2 format, chain TD [auth 2] MOL2 format, chain VB [auth M] MOL2 format, chain WB [auth M] MOL2 format, chain HE [auth 6] mmCIF format, chain CC [auth H] mmCIF format, chain DC [auth A] mmCIF format, chain EE [auth 6] mmCIF format, chain HD [auth T] mmCIF format, chain NE [auth 0] mmCIF format, chain TD [auth 2] mmCIF format, chain VB [auth M] mmCIF format, chain WB [auth M] mmCIF format, chain HE [auth 6]	CC [auth H] DC [auth A] EE [auth 6] HD [auth T] HE [auth 6] CC [auth H], DC [auth A], EE [auth 6], HD [auth T], HE [auth 6], NE [auth 0], TD [auth 2], VB [auth M], WB [auth M]	CARDIOLIPIN C₈₁ H₁₅₆ O₁₇ P₂ XVTUQDWPJJBEHJ-KZCWQMDCSA-L		Interactions Focus chain CC [auth H] Focus chain DC [auth A] Focus chain EE [auth 6] Focus chain HD [auth T] Focus chain HE [auth 6] Focus chain NE [auth 0] Focus chain TD [auth 2] Focus chain VB [auth M] Focus chain WB [auth M] Interactions & Density Focus chain CC [auth H] Focus chain DC [auth A] Focus chain EE [auth 6] Focus chain HD [auth T] Focus chain HE [auth 6] Focus chain NE [auth 0] Focus chain TD [auth 2] Focus chain VB [auth M] Focus chain WB [auth M]
BCL (Subject of Investigation/LOI) Query on BCL Download:Ideal Coordinates CCD File SDF format, chain BD [auth Q] SDF format, chain BE [auth 5] SDF format, chain CB [auth L] SDF format, chain DD [auth R] SDF format, chain EC [auth A] SDF format, chain ED [auth S] SDF format, chain GC [auth B] SDF format, chain GD [auth T] SDF format, chain GE [auth 6] SDF format, chain ID [auth U] SDF format, chain JE [auth 7] SDF format, chain KB [auth L] SDF format, chain KD [auth V] SDF format, chain LC [auth E] SDF format, chain LD [auth W] SDF format, chain LE [auth 8] SDF format, chain MC [auth F] SDF format, chain ME [auth 9] SDF format, chain ND [auth X] SDF format, chain OC [auth G] SDF format, chain OD [auth Y] SDF format, chain OE [auth 0] SDF format, chain PD [auth Z] SDF format, chain QC [auth I] SDF format, chain RD [auth 1] SDF format, chain UC [auth K] SDF format, chain UD [auth 2] SDF format, chain WD [auth 3] SDF format, chain YC [auth O] SDF format, chain ZC [auth P] SDF format, chain ZD [auth 4] SDF format, chain XC [auth N] SDF format, chain SC [auth J] SDF format, chain RB [auth M] SDF format, chain QB [auth M] SDF format, chain IC [auth D] MOL2 format, chain BD [auth Q] MOL2 format, chain BE [auth 5] MOL2 format, chain CB [auth L] MOL2 format, chain DD [auth R] MOL2 format, chain EC [auth A] MOL2 format, chain ED [auth S] MOL2 format, chain GC [auth B] MOL2 format, chain GD [auth T] MOL2 format, chain GE [auth 6] MOL2 format, chain ID [auth U] MOL2 format, chain JE [auth 7] MOL2 format, chain KB [auth L] MOL2 format, chain KD [auth V] MOL2 format, chain LC [auth E] MOL2 format, chain LD [auth W] MOL2 format, chain LE [auth 8] MOL2 format, chain MC [auth F] MOL2 format, chain ME [auth 9] MOL2 format, chain ND [auth X] MOL2 format, chain OC [auth G] MOL2 format, chain OD [auth Y] MOL2 format, chain OE [auth 0] MOL2 format, chain PD [auth Z] MOL2 format, chain QC [auth I] MOL2 format, chain RD [auth 1] MOL2 format, chain UC [auth K] MOL2 format, chain UD [auth 2] MOL2 format, chain WD [auth 3] MOL2 format, chain YC [auth O] MOL2 format, chain ZC [auth P] MOL2 format, chain ZD [auth 4] MOL2 format, chain XC [auth N] MOL2 format, chain SC [auth J] MOL2 format, chain RB [auth M] MOL2 format, chain QB [auth M] MOL2 format, chain IC [auth D] mmCIF format, chain BD [auth Q] mmCIF format, chain BE [auth 5] mmCIF format, chain CB [auth L] mmCIF format, chain DD [auth R] mmCIF format, chain EC [auth A] mmCIF format, chain ED [auth S] mmCIF format, chain GC [auth B] mmCIF format, chain GD [auth T] mmCIF format, chain GE [auth 6] mmCIF format, chain ID [auth U] mmCIF format, chain JE [auth 7] mmCIF format, chain KB [auth L] mmCIF format, chain KD [auth V] mmCIF format, chain LC [auth E] mmCIF format, chain LD [auth W] mmCIF format, chain LE [auth 8] mmCIF format, chain MC [auth F] mmCIF format, chain ME [auth 9] mmCIF format, chain ND [auth X] mmCIF format, chain OC [auth G] mmCIF format, chain OD [auth Y] mmCIF format, chain OE [auth 0] mmCIF format, chain PD [auth Z] mmCIF format, chain QC [auth I] mmCIF format, chain RD [auth 1] mmCIF format, chain UC [auth K] mmCIF format, chain UD [auth 2] mmCIF format, chain WD [auth 3] mmCIF format, chain YC [auth O] mmCIF format, chain ZC [auth P] mmCIF format, chain ZD [auth 4] mmCIF format, chain XC [auth N] mmCIF format, chain SC [auth J] mmCIF format, chain RB [auth M] mmCIF format, chain QB [auth M] mmCIF format, chain IC [auth D]	BD [auth Q] BE [auth 5] CB [auth L] DD [auth R] EC [auth A] BD [auth Q], BE [auth 5], CB [auth L], DD [auth R], EC [auth A], ED [auth S], GC [auth B], GD [auth T], GE [auth 6], IC [auth D], ID [auth U], JE [auth 7], KB [auth L], KD [auth V], LC [auth E], LD [auth W], LE [auth 8], MC [auth F], ME [auth 9], ND [auth X], OC [auth G], OD [auth Y], OE [auth 0], PD [auth Z], QB [auth M], QC [auth I], RB [auth M], RD [auth 1], SC [auth J], UC [auth K], UD [auth 2], WD [auth 3], XC [auth N], YC [auth O], ZC [auth P], ZD [auth 4]	BACTERIOCHLOROPHYLL A C₅₅ H₇₄ Mg N₄ O₆ DSJXIQQMORJERS-AGGZHOMASA-M		Interactions Focus chain BD [auth Q] Focus chain BE [auth 5] Focus chain CB [auth L] Focus chain DD [auth R] Focus chain EC [auth A] Focus chain ED [auth S] Focus chain GC [auth B] Focus chain GD [auth T] Focus chain GE [auth 6] Focus chain IC [auth D] Focus chain ID [auth U] Focus chain JE [auth 7] Focus chain KB [auth L] Focus chain KD [auth V] Focus chain LC [auth E] Focus chain LD [auth W] Focus chain LE [auth 8] Focus chain MC [auth F] Focus chain ME [auth 9] Focus chain ND [auth X] Focus chain OC [auth G] Focus chain OD [auth Y] Focus chain OE [auth 0] Focus chain PD [auth Z] Focus chain QB [auth M] Focus chain QC [auth I] Focus chain RB [auth M] Focus chain RD [auth 1] Focus chain SC [auth J] Focus chain UC [auth K] Focus chain UD [auth 2] Focus chain WD [auth 3] Focus chain XC [auth N] Focus chain YC [auth O] Focus chain ZC [auth P] Focus chain ZD [auth 4] Interactions & Density Focus chain BD [auth Q] Focus chain BE [auth 5] Focus chain CB [auth L] Focus chain DD [auth R] Focus chain EC [auth A] Focus chain ED [auth S] Focus chain GC [auth B] Focus chain GD [auth T] Focus chain GE [auth 6] Focus chain IC [auth D] Focus chain ID [auth U] Focus chain JE [auth 7] Focus chain KB [auth L] Focus chain KD [auth V] Focus chain LC [auth E] Focus chain LD [auth W] Focus chain LE [auth 8] Focus chain MC [auth F] Focus chain ME [auth 9] Focus chain ND [auth X] Focus chain OC [auth G] Focus chain OD [auth Y] Focus chain OE [auth 0] Focus chain PD [auth Z] Focus chain QB [auth M] Focus chain QC [auth I] Focus chain RB [auth M] Focus chain RD [auth 1] Focus chain SC [auth J] Focus chain UC [auth K] Focus chain UD [auth 2] Focus chain WD [auth 3] Focus chain XC [auth N] Focus chain YC [auth O] Focus chain ZC [auth P] Focus chain ZD [auth 4]
BPH Query on BPH Download:Ideal Coordinates CCD File SDF format, chain DB [auth L] SDF format, chain SB [auth M] MOL2 format, chain DB [auth L] MOL2 format, chain SB [auth M] mmCIF format, chain DB [auth L] mmCIF format, chain SB [auth M]	DB [auth L], SB [auth M]	BACTERIOPHEOPHYTIN A C₅₅ H₇₆ N₄ O₆ KWOZSBGNAHVCKG-SZQBJALDSA-N		Interactions Focus chain DB [auth L] Focus chain SB [auth M] Interactions & Density Focus chain DB [auth L] Focus chain SB [auth M]
U10 Query on U10 Download:Ideal Coordinates CCD File SDF format, chain HB [auth L] SDF format, chain IB [auth L] SDF format, chain IE [auth 7] SDF format, chain EB [auth L] MOL2 format, chain HB [auth L] MOL2 format, chain IB [auth L] MOL2 format, chain IE [auth 7] MOL2 format, chain EB [auth L] mmCIF format, chain HB [auth L] mmCIF format, chain IB [auth L] mmCIF format, chain IE [auth 7] mmCIF format, chain EB [auth L]	EB [auth L], HB [auth L], IB [auth L], IE [auth 7]	UBIQUINONE-10 C₅₉ H₉₀ O₄ ACTIUHUUMQJHFO-UPTCCGCDSA-N		Interactions Focus chain EB [auth L] Focus chain HB [auth L] Focus chain IB [auth L] Focus chain IE [auth 7] Interactions & Density Focus chain EB [auth L] Focus chain HB [auth L] Focus chain IB [auth L] Focus chain IE [auth 7]
MQ9 Query on MQ9 Download:Ideal Coordinates CCD File SDF format, chain TB [auth M] MOL2 format, chain TB [auth M] mmCIF format, chain TB [auth M]	TB [auth M]	MENAQUINONE-9 C₅₆ H₈₀ O₂ WCRXHNIUHQUASO-ABFXHILCSA-N		Interactions Focus chain TB [auth M] Interactions & Density Focus chain TB [auth M]
PGV Query on PGV Download:Ideal Coordinates CCD File SDF format, chain AB [auth C] SDF format, chain AC [auth H] SDF format, chain BB [auth C] SDF format, chain CE [auth 5] SDF format, chain DE [auth 5] SDF format, chain FB [auth L] SDF format, chain GB [auth L] SDF format, chain JC [auth D] SDF format, chain LB [auth L] SDF format, chain MB [auth L] SDF format, chain NB [auth L] SDF format, chain NC [auth F] SDF format, chain VC [auth K] SDF format, chain ZA [auth C] SDF format, chain ZB [auth M] SDF format, chain YB [auth M] SDF format, chain BC [auth H] SDF format, chain AE [auth 5] MOL2 format, chain AB [auth C] MOL2 format, chain AC [auth H] MOL2 format, chain BB [auth C] MOL2 format, chain CE [auth 5] MOL2 format, chain DE [auth 5] MOL2 format, chain FB [auth L] MOL2 format, chain GB [auth L] MOL2 format, chain JC [auth D] MOL2 format, chain LB [auth L] MOL2 format, chain MB [auth L] MOL2 format, chain NB [auth L] MOL2 format, chain NC [auth F] MOL2 format, chain VC [auth K] MOL2 format, chain ZA [auth C] MOL2 format, chain ZB [auth M] MOL2 format, chain YB [auth M] MOL2 format, chain BC [auth H] MOL2 format, chain AE [auth 5] mmCIF format, chain AB [auth C] mmCIF format, chain AC [auth H] mmCIF format, chain BB [auth C] mmCIF format, chain CE [auth 5] mmCIF format, chain DE [auth 5] mmCIF format, chain FB [auth L] mmCIF format, chain GB [auth L] mmCIF format, chain JC [auth D] mmCIF format, chain LB [auth L] mmCIF format, chain MB [auth L] mmCIF format, chain NB [auth L] mmCIF format, chain NC [auth F] mmCIF format, chain VC [auth K] mmCIF format, chain ZA [auth C] mmCIF format, chain ZB [auth M] mmCIF format, chain YB [auth M] mmCIF format, chain BC [auth H] mmCIF format, chain AE [auth 5]	AB [auth C] AC [auth H] AE [auth 5] BB [auth C] BC [auth H] AB [auth C], AC [auth H], AE [auth 5], BB [auth C], BC [auth H], CE [auth 5], DE [auth 5], FB [auth L], GB [auth L], JC [auth D], LB [auth L], MB [auth L], NB [auth L], NC [auth F], VC [auth K], YB [auth M], ZA [auth C], ZB [auth M]	(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 AB [auth C] Focus chain AC [auth H] Focus chain AE [auth 5] Focus chain BB [auth C] Focus chain BC [auth H] Focus chain CE [auth 5] Focus chain DE [auth 5] Focus chain FB [auth L] Focus chain GB [auth L] Focus chain JC [auth D] Focus chain LB [auth L] Focus chain MB [auth L] Focus chain NB [auth L] Focus chain NC [auth F] Focus chain VC [auth K] Focus chain YB [auth M] Focus chain ZA [auth C] Focus chain ZB [auth M] Interactions & Density Focus chain AB [auth C] Focus chain AC [auth H] Focus chain AE [auth 5] Focus chain BB [auth C] Focus chain BC [auth H] Focus chain CE [auth 5] Focus chain DE [auth 5] Focus chain FB [auth L] Focus chain GB [auth L] Focus chain JC [auth D] Focus chain LB [auth L] Focus chain MB [auth L] Focus chain NB [auth L] Focus chain NC [auth F] Focus chain VC [auth K] Focus chain YB [auth M] Focus chain ZA [auth C] Focus chain ZB [auth M]
PEE Query on PEE Download:Ideal Coordinates CCD File SDF format, chain XB [auth M] MOL2 format, chain XB [auth M] mmCIF format, chain XB [auth M]	XB [auth M]	1,2-dioleoyl-sn-glycero-3-phosphoethanolamine C₄₁ H₇₈ N O₈ P MWRBNPKJOOWZPW-NYVOMTAGSA-N		Interactions Focus chain XB [auth M] Interactions & Density Focus chain XB [auth M]
HEC Query on HEC Download:Ideal Coordinates CCD File SDF format, chain WA [auth C] SDF format, chain XA [auth C] SDF format, chain YA [auth C] SDF format, chain VA [auth C] MOL2 format, chain WA [auth C] MOL2 format, chain XA [auth C] MOL2 format, chain YA [auth C] MOL2 format, chain VA [auth C] mmCIF format, chain WA [auth C] mmCIF format, chain XA [auth C] mmCIF format, chain YA [auth C] mmCIF format, chain VA [auth C]	VA [auth C], WA [auth C], XA [auth C], YA [auth C]	HEME C C₃₄ H₃₄ Fe N₄ O₄ HXQIYSLZKNYNMH-LJNAALQVSA-N		Interactions Focus chain VA [auth C] Focus chain WA [auth C] Focus chain XA [auth C] Focus chain YA [auth C] Interactions & Density Focus chain VA [auth C] Focus chain WA [auth C] Focus chain XA [auth C] Focus chain YA [auth C]
I7D (Subject of Investigation/LOI) Query on I7D Download:Ideal Coordinates CCD File SDF format, chain AD [auth Q] SDF format, chain FC [auth A] SDF format, chain FD [auth T] SDF format, chain HC [auth D] SDF format, chain JD [auth V] SDF format, chain KC [auth E] SDF format, chain KE [auth 8] SDF format, chain MD [auth X] SDF format, chain PC [auth I] SDF format, chain QD [auth 1] SDF format, chain TC [auth K] SDF format, chain UB [auth M] SDF format, chain VD [auth 3] SDF format, chain WC [auth N] SDF format, chain YD [auth 4] SDF format, chain FE [auth 6] SDF format, chain CD [auth R] MOL2 format, chain AD [auth Q] MOL2 format, chain FC [auth A] MOL2 format, chain FD [auth T] MOL2 format, chain HC [auth D] MOL2 format, chain JD [auth V] MOL2 format, chain KC [auth E] MOL2 format, chain KE [auth 8] MOL2 format, chain MD [auth X] MOL2 format, chain PC [auth I] MOL2 format, chain QD [auth 1] MOL2 format, chain TC [auth K] MOL2 format, chain UB [auth M] MOL2 format, chain VD [auth 3] MOL2 format, chain WC [auth N] MOL2 format, chain YD [auth 4] MOL2 format, chain FE [auth 6] MOL2 format, chain CD [auth R] mmCIF format, chain AD [auth Q] mmCIF format, chain FC [auth A] mmCIF format, chain FD [auth T] mmCIF format, chain HC [auth D] mmCIF format, chain JD [auth V] mmCIF format, chain KC [auth E] mmCIF format, chain KE [auth 8] mmCIF format, chain MD [auth X] mmCIF format, chain PC [auth I] mmCIF format, chain QD [auth 1] mmCIF format, chain TC [auth K] mmCIF format, chain UB [auth M] mmCIF format, chain VD [auth 3] mmCIF format, chain WC [auth N] mmCIF format, chain YD [auth 4] mmCIF format, chain FE [auth 6] mmCIF format, chain CD [auth R]	AD [auth Q] CD [auth R] FC [auth A] FD [auth T] FE [auth 6] AD [auth Q], CD [auth R], FC [auth A], FD [auth T], FE [auth 6], HC [auth D], JD [auth V], KC [auth E], KE [auth 8], MD [auth X], PC [auth I], QD [auth 1], TC [auth K], UB [auth M], VD [auth 3], WC [auth N], YD [auth 4]	(6~{E},8~{E},10~{E},12~{E},14~{E},16~{E},18~{E},20~{E},22~{E},24~{E},26~{E},28~{E})-2,31-dimethoxy-2,6,10,14,19,23,27,31-octamethyl-dotriaconta-6,8,10,12,14,16,18,20,22,24,26,28-dodecaen-5-one C₄₂ H₆₀ O₃ KSAQIRSWZGLSET-BOIKDPEESA-N		Interactions Focus chain AD [auth Q] Focus chain CD [auth R] Focus chain FC [auth A] Focus chain FD [auth T] Focus chain FE [auth 6] Focus chain HC [auth D] Focus chain JD [auth V] Focus chain KC [auth E] Focus chain KE [auth 8] Focus chain MD [auth X] Focus chain PC [auth I] Focus chain QD [auth 1] Focus chain TC [auth K] Focus chain UB [auth M] Focus chain VD [auth 3] Focus chain WC [auth N] Focus chain YD [auth 4] Interactions & Density Focus chain AD [auth Q] Focus chain CD [auth R] Focus chain FC [auth A] Focus chain FD [auth T] Focus chain FE [auth 6] Focus chain HC [auth D] Focus chain JD [auth V] Focus chain KC [auth E] Focus chain KE [auth 8] Focus chain MD [auth X] Focus chain PC [auth I] Focus chain QD [auth 1] Focus chain TC [auth K] Focus chain UB [auth M] Focus chain VD [auth 3] Focus chain WC [auth N] Focus chain YD [auth 4]
LMT Query on LMT Download:Ideal Coordinates CCD File SDF format, chain JB [auth L] SDF format, chain OB [auth L] SDF format, chain RC [auth I] SDF format, chain SD [auth 1] SDF format, chain XD [auth 3] MOL2 format, chain JB [auth L] MOL2 format, chain OB [auth L] MOL2 format, chain RC [auth I] MOL2 format, chain SD [auth 1] MOL2 format, chain XD [auth 3] mmCIF format, chain JB [auth L] mmCIF format, chain OB [auth L] mmCIF format, chain RC [auth I] mmCIF format, chain SD [auth 1] mmCIF format, chain XD [auth 3]	JB [auth L], OB [auth L], RC [auth I], SD [auth 1], XD [auth 3]	DODECYL-BETA-D-MALTOSIDE C₂₄ H₄₆ O₁₁ NLEBIOOXCVAHBD-QKMCSOCLSA-N		Interactions Focus chain JB [auth L] Focus chain OB [auth L] Focus chain RC [auth I] Focus chain SD [auth 1] Focus chain XD [auth 3] Interactions & Density Focus chain JB [auth L] Focus chain OB [auth L] Focus chain RC [auth I] Focus chain SD [auth 1] Focus chain XD [auth 3]
FE Query on FE Download:Ideal Coordinates CCD File SDF format, chain PB [auth M] MOL2 format, chain PB [auth M] mmCIF format, chain PB [auth M]	PB [auth M]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N		Interactions Focus chain PB [auth M] Interactions & Density Focus chain PB [auth M]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
FME Query on FME	AA [auth 1] CA [auth 3] E [auth A] EA [auth 5] G [auth D] AA [auth 1], CA [auth 3], E [auth A], EA [auth 5], G [auth D], GA [auth 7], I [auth F], IA [auth 9], K [auth I], M [auth K], O, Q, S, U, W, Y	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
MODEL REFINEMENT	PHENIX
RECONSTRUCTION	RELION	3.1

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2022-11-16

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: 2022-11-16
Type: Initial release
Version 1.1: 2022-11-23
Changes: Database references
Version 1.2: 2026-03-04
Changes: Data collection, Refinement description, Structure summary

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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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.

7XXF | pdb_00007xxf

Structure of photosynthetic LH1-RC super-complex of Rhodopila globiformis

Literature

An LH1-RC photocomplex from an extremophilic phototroph provides insight into origins of two photosynthesis proteins.

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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Entity ID: 6

UniProt

Entity Groups

Sequence Annotations

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Entity ID: 7

Small Molecules

Experimental Data & Validation

Experimental Data

Structure Validation

Entry History

Deposition Data

Revision History (Full details and data files)