7C9R | pdb_00007c9r

STRUCTURE OF PHOTOSYNTHETIC LH1-RC SUPER-COMPLEX OF THIORHODOVIBRIO STRAIN 970

PDB DOI: https://doi.org/10.2210/pdb7C9R/pdb
EM Map EMD-30314: EMDB EMDataResource

Classification: PHOTOSYNTHESIS
Organism(s): Thiorhodovibrio frisius
Mutation(s): No
Membrane Protein: Yes OPM PDBTM

Deposited: 2020-06-07 Released: 2020-10-07
Deposition Author(s): Tani, K., Kanno, R., Makino, Y., Hall, M., Takenouchi, M., Imanishi, M., Yu, L.-J., Overmann, J., Madigan, M.T., Kimura, Y., 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: 2.82 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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

Literature

Cryo-EM structure of a Ca 2+ -bound photosynthetic LH1-RC complex containing multiple alpha beta-polypeptides.

Tani, K., Kanno, R., Makino, Y., Hall, M., Takenouchi, M., Imanishi, M., Yu, L.J., Overmann, J., Madigan, M.T., Kimura, Y., Mizoguchi, A., Humbel, B.M., Wang-Otomo, Z.Y.

(2020) Nat Commun 11: 4955-4955

PubMed: 33009385 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1038/s41467-020-18748-3
Primary Citation Related Structures:
7C9R

PubMed Abstract:
The light-harvesting-reaction center complex (LH1-RC) from the purple phototrophic bacterium Thiorhodovibrio strain 970 exhibits an LH1 absorption maximum at 960 nm, the most red-shifted absorption for any bacteriochlorophyll (BChl) a-containing species. Here we present a cryo-EM structure of the strain 970 LH1-RC complex at 2.82 Å resolution. The LH1 forms a closed ring structure composed of sixteen pairs of the αβ-polypeptides. Sixteen Ca ions are present in the LH1 C-terminal domain and are coordinated by residues from the αβ-polypeptides that are hydrogen-bonded to BChl a. The Ca ²⁺-facilitated hydrogen-bonding network forms the structural basis of the unusual LH1 redshift. The structure also revealed the arrangement of multiple forms of α- and β-polypeptides in an individual LH1 ring. Such organization indicates a mechanism of interplay between the expression and assembly of the LH1 complex that is regulated through interactions with the RC subunits inside.

Organizational Affiliation

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

Macromolecule Content

Total Structure Weight: 442.27 kDa
Atom Count: 29,228
Modeled Residue Count: 3,009
Deposited Residue Count: 3,208
Unique protein chains: 10

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]	396	Thiorhodovibrio frisius	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for H8Z3S2 (Thiorhodovibrio frisius) Explore H8Z3S2 Go to UniProtKB: H8Z3S2
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	H8Z3S2
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Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
L subunit of the reaction center	B [auth L]	273	Thiorhodovibrio frisius	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for G1BIY6 (Thiorhodovibrio frisius) Explore G1BIY6 Go to UniProtKB: G1BIY6
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	G1BIY6
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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]	324	Thiorhodovibrio frisius	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for G1BIY7 (Thiorhodovibrio frisius) Explore G1BIY7 Go to UniProtKB: G1BIY7
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Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	G1BIY7
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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, subunit H, bacterial	D [auth H]	258	Thiorhodovibrio frisius	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for H8Z0X5 (Thiorhodovibrio frisius) Explore H8Z0X5 Go to UniProtKB: H8Z0X5
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	H8Z0X5
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Reference Sequence

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| 3D Structure

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Alpha subunit 1 of light-harvesting 1 complex	E [auth A] G [auth D] I [auth F] K [auth I] M [auth K] E [auth A], G [auth D], I [auth F], K [auth I], M [auth K], O	73	Thiorhodovibrio frisius	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for G1BIY5 (Thiorhodovibrio frisius) Explore G1BIY5 Go to UniProtKB: G1BIY5
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	G1BIY5
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Reference Sequence

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| 3D Structure

Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
Antenna complex alpha/beta subunit	DA [auth 4], F [auth B], P	46	Thiorhodovibrio frisius	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for G1BIY9 (Thiorhodovibrio frisius) Explore G1BIY9 Go to UniProtKB: G1BIY9
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Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	G1BIY9
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Reference Sequence

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| 3D Structure

Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
Antenna complex alpha/beta subunit	BA [auth 2] FA [auth 6] H [auth E] HA [auth 8] J [auth G] BA [auth 2], FA [auth 6], H [auth E], HA [auth 8], J [auth G], JA [auth 0], L [auth J], N, R, T, V, X, Z	46	Thiorhodovibrio frisius	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for G1BIY4 (Thiorhodovibrio frisius) Explore G1BIY4 Go to UniProtKB: G1BIY4
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Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	G1BIY4
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Reference Sequence

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| 3D Structure

Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details	Image
Antenna complex alpha/beta subunit	Q	81	Thiorhodovibrio frisius	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for H8Z3S4 (Thiorhodovibrio frisius) Explore H8Z3S4 Go to UniProtKB: H8Z3S4
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Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	H8Z3S4
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Reference Sequence

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| 3D Structure

Entity ID: 9
Molecule	Chains	Sequence Length	Organism	Details	Image
LHC domain-containing protein	AA [auth 1] CA [auth 3] EA [auth 5] GA [auth 7] S AA [auth 1], CA [auth 3], EA [auth 5], GA [auth 7], S, U, W, Y	77	Thiorhodovibrio frisius	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for H8Z3R9 (Thiorhodovibrio frisius) Explore H8Z3R9 Go to UniProtKB: H8Z3R9
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	H8Z3R9
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Reference Sequence

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| 3D Structure

Entity ID: 10
Molecule	Chains	Sequence Length	Organism	Details	Image
Alpha subunit 2 of light-harvesting 1 complex	IA [auth 9]	86	Thiorhodovibrio frisius	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for G1BIZ0 (Thiorhodovibrio frisius) Explore G1BIZ0 Go to UniProtKB: G1BIZ0
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	G1BIZ0
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Reference Sequence

Small Molecules

Ligands 14 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CDL Query on CDL Download:Ideal Coordinates CCD File SDF format, chain UD [auth Y] SDF format, chain GB [auth H] SDF format, chain DD [auth S] MOL2 format, chain UD [auth Y] MOL2 format, chain GB [auth H] MOL2 format, chain DD [auth S] mmCIF format, chain UD [auth Y] mmCIF format, chain GB [auth H] mmCIF format, chain DD [auth S]	DD [auth S], GB [auth H], UD [auth Y]	CARDIOLIPIN C₈₁ H₁₅₆ O₁₇ P₂ XVTUQDWPJJBEHJ-KZCWQMDCSA-L		Interactions Focus chain DD [auth S] Focus chain GB [auth H] Focus chain UD [auth Y] Interactions & Density Focus chain DD [auth S] Focus chain GB [auth H] Focus chain UD [auth Y]
BCL Query on BCL Download:Ideal Coordinates CCD File SDF format, chain ZC [auth Q] SDF format, chain YB [auth F] SDF format, chain WB [auth F] SDF format, chain VE [auth 7] SDF format, chain VD [auth Y] SDF format, chain VA [auth L] SDF format, chain UE [auth 7] SDF format, chain TD [auth Y] SDF format, chain TC [auth O] SDF format, chain SC [auth O] SDF format, chain SA [auth L] SDF format, chain RB [auth D] SDF format, chain QD [auth X] SDF format, chain QB [auth D] SDF format, chain PD [auth W] SDF format, chain OE [auth 5] SDF format, chain NE [auth 5] SDF format, chain NC [auth K] SDF format, chain MB [auth B] SDF format, chain KD [auth U] SDF format, chain KC [auth K] SDF format, chain JD [auth U] SDF format, chain IE [auth 3] SDF format, chain IB [auth A] SDF format, chain HE [auth 3] SDF format, chain GD [auth T] SDF format, chain FD [auth S] SDF format, chain EC [auth J] SDF format, chain DE [auth 2] SDF format, chain CF [auth 9] SDF format, chain CC [auth I] SDF format, chain BF [auth 9] SDF format, chain BB [auth M] SDF format, chain AE [auth 1] SDF format, chain AD [auth Q] SDF format, chain AB [auth M] MOL2 format, chain ZC [auth Q] MOL2 format, chain YB [auth F] MOL2 format, chain WB [auth F] MOL2 format, chain VE [auth 7] MOL2 format, chain VD [auth Y] MOL2 format, chain VA [auth L] MOL2 format, chain UE [auth 7] MOL2 format, chain TD [auth Y] MOL2 format, chain TC [auth O] MOL2 format, chain SC [auth O] MOL2 format, chain SA [auth L] MOL2 format, chain RB [auth D] MOL2 format, chain QD [auth X] MOL2 format, chain QB [auth D] MOL2 format, chain PD [auth W] MOL2 format, chain OE [auth 5] MOL2 format, chain NE [auth 5] MOL2 format, chain NC [auth K] MOL2 format, chain MB [auth B] MOL2 format, chain KD [auth U] MOL2 format, chain KC [auth K] MOL2 format, chain JD [auth U] MOL2 format, chain IE [auth 3] MOL2 format, chain IB [auth A] MOL2 format, chain HE [auth 3] MOL2 format, chain GD [auth T] MOL2 format, chain FD [auth S] MOL2 format, chain EC [auth J] MOL2 format, chain DE [auth 2] MOL2 format, chain CF [auth 9] MOL2 format, chain CC [auth I] MOL2 format, chain BF [auth 9] MOL2 format, chain BB [auth M] MOL2 format, chain AE [auth 1] MOL2 format, chain AD [auth Q] MOL2 format, chain AB [auth M] mmCIF format, chain ZC [auth Q] mmCIF format, chain YB [auth F] mmCIF format, chain WB [auth F] mmCIF format, chain VE [auth 7] mmCIF format, chain VD [auth Y] mmCIF format, chain VA [auth L] mmCIF format, chain UE [auth 7] mmCIF format, chain TD [auth Y] mmCIF format, chain TC [auth O] mmCIF format, chain SC [auth O] mmCIF format, chain SA [auth L] mmCIF format, chain RB [auth D] mmCIF format, chain QD [auth X] mmCIF format, chain QB [auth D] mmCIF format, chain PD [auth W] mmCIF format, chain OE [auth 5] mmCIF format, chain NE [auth 5] mmCIF format, chain NC [auth K] mmCIF format, chain MB [auth B] mmCIF format, chain KD [auth U] mmCIF format, chain KC [auth K] mmCIF format, chain JD [auth U] mmCIF format, chain IE [auth 3] mmCIF format, chain IB [auth A] mmCIF format, chain HE [auth 3] mmCIF format, chain GD [auth T] mmCIF format, chain FD [auth S] mmCIF format, chain EC [auth J] mmCIF format, chain DE [auth 2] mmCIF format, chain CF [auth 9] mmCIF format, chain CC [auth I] mmCIF format, chain BF [auth 9] mmCIF format, chain BB [auth M] mmCIF format, chain AE [auth 1] mmCIF format, chain AD [auth Q] mmCIF format, chain AB [auth M]	AB [auth M] AD [auth Q] AE [auth 1] BB [auth M] BF [auth 9] AB [auth M], AD [auth Q], AE [auth 1], BB [auth M], BF [auth 9], CC [auth I], CF [auth 9], DE [auth 2], EC [auth J], FD [auth S], GD [auth T], HE [auth 3], IB [auth A], IE [auth 3], JD [auth U], KC [auth K], KD [auth U], MB [auth B], NC [auth K], NE [auth 5], OE [auth 5], PD [auth W], QB [auth D], QD [auth X], RB [auth D], SA [auth L], SC [auth O], TC [auth O], TD [auth Y], UE [auth 7], VA [auth L], VD [auth Y], VE [auth 7], WB [auth F], YB [auth F], ZC [auth Q]	BACTERIOCHLOROPHYLL A C₅₅ H₇₄ Mg N₄ O₆ DSJXIQQMORJERS-AGGZHOMASA-M		Interactions Focus chain AB [auth M] Focus chain AD [auth Q] Focus chain AE [auth 1] Focus chain BB [auth M] Focus chain BF [auth 9] Focus chain CC [auth I] Focus chain CF [auth 9] Focus chain DE [auth 2] Focus chain EC [auth J] Focus chain FD [auth S] Focus chain GD [auth T] Focus chain HE [auth 3] Focus chain IB [auth A] Focus chain IE [auth 3] Focus chain JD [auth U] Focus chain KC [auth K] Focus chain KD [auth U] Focus chain MB [auth B] Focus chain NC [auth K] Focus chain NE [auth 5] Focus chain OE [auth 5] Focus chain PD [auth W] Focus chain QB [auth D] Focus chain QD [auth X] Focus chain RB [auth D] Focus chain SA [auth L] Focus chain SC [auth O] Focus chain TC [auth O] Focus chain TD [auth Y] Focus chain UE [auth 7] Focus chain VA [auth L] Focus chain VD [auth Y] Focus chain VE [auth 7] Focus chain WB [auth F] Focus chain YB [auth F] Focus chain ZC [auth Q] Interactions & Density Focus chain AB [auth M] Focus chain AD [auth Q] Focus chain AE [auth 1] Focus chain BB [auth M] Focus chain BF [auth 9] Focus chain CC [auth I] Focus chain CF [auth 9] Focus chain DE [auth 2] Focus chain EC [auth J] Focus chain FD [auth S] Focus chain GD [auth T] Focus chain HE [auth 3] Focus chain IB [auth A] Focus chain IE [auth 3] Focus chain JD [auth U] Focus chain KC [auth K] Focus chain KD [auth U] Focus chain MB [auth B] Focus chain NC [auth K] Focus chain NE [auth 5] Focus chain OE [auth 5] Focus chain PD [auth W] Focus chain QB [auth D] Focus chain QD [auth X] Focus chain RB [auth D] Focus chain SA [auth L] Focus chain SC [auth O] Focus chain TC [auth O] Focus chain TD [auth Y] Focus chain UE [auth 7] Focus chain VA [auth L] Focus chain VD [auth Y] Focus chain VE [auth 7] Focus chain WB [auth F] Focus chain YB [auth F] Focus chain ZC [auth Q]
BPH Query on BPH Download:Ideal Coordinates CCD File SDF format, chain TA [auth L] SDF format, chain CB [auth M] MOL2 format, chain TA [auth L] MOL2 format, chain CB [auth M] mmCIF format, chain TA [auth L] mmCIF format, chain CB [auth M]	CB [auth M], TA [auth L]	BACTERIOPHEOPHYTIN A C₅₅ H₇₆ N₄ O₆ KWOZSBGNAHVCKG-SZQBJALDSA-N		Interactions Focus chain CB [auth M] Focus chain TA [auth L] Interactions & Density Focus chain CB [auth M] Focus chain TA [auth L]
PGV Query on PGV Download:Ideal Coordinates CCD File SDF format, chain ZE [auth 9] SDF format, chain XC [auth Q] SDF format, chain XB [auth F] SDF format, chain WD [auth Y] SDF format, chain WA [auth L] SDF format, chain UB [auth F] SDF format, chain RA [auth C] SDF format, chain QC [auth O] SDF format, chain OB [auth D] SDF format, chain LE [auth 5] SDF format, chain LC [auth K] SDF format, chain HC [auth K] SDF format, chain HB [auth A] SDF format, chain GC [auth K] SDF format, chain FE [auth 3] SDF format, chain FB [auth H] SDF format, chain EB [auth M] SDF format, chain DC [auth I] SDF format, chain BE [auth 1] MOL2 format, chain ZE [auth 9] MOL2 format, chain XC [auth Q] MOL2 format, chain XB [auth F] MOL2 format, chain WD [auth Y] MOL2 format, chain WA [auth L] MOL2 format, chain UB [auth F] MOL2 format, chain RA [auth C] MOL2 format, chain QC [auth O] MOL2 format, chain OB [auth D] MOL2 format, chain LE [auth 5] MOL2 format, chain LC [auth K] MOL2 format, chain HC [auth K] MOL2 format, chain HB [auth A] MOL2 format, chain GC [auth K] MOL2 format, chain FE [auth 3] MOL2 format, chain FB [auth H] MOL2 format, chain EB [auth M] MOL2 format, chain DC [auth I] MOL2 format, chain BE [auth 1] mmCIF format, chain ZE [auth 9] mmCIF format, chain XC [auth Q] mmCIF format, chain XB [auth F] mmCIF format, chain WD [auth Y] mmCIF format, chain WA [auth L] mmCIF format, chain UB [auth F] mmCIF format, chain RA [auth C] mmCIF format, chain QC [auth O] mmCIF format, chain OB [auth D] mmCIF format, chain LE [auth 5] mmCIF format, chain LC [auth K] mmCIF format, chain HC [auth K] mmCIF format, chain HB [auth A] mmCIF format, chain GC [auth K] mmCIF format, chain FE [auth 3] mmCIF format, chain FB [auth H] mmCIF format, chain EB [auth M] mmCIF format, chain DC [auth I] mmCIF format, chain BE [auth 1]	BE [auth 1] DC [auth I] EB [auth M] FB [auth H] FE [auth 3] BE [auth 1], DC [auth I], EB [auth M], FB [auth H], FE [auth 3], GC [auth K], HB [auth A], HC [auth K], LC [auth K], LE [auth 5], OB [auth D], QC [auth O], RA [auth C], UB [auth F], WA [auth L], WD [auth Y], XB [auth F], XC [auth Q], ZE [auth 9]	(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 BE [auth 1] Focus chain DC [auth I] Focus chain EB [auth M] Focus chain FB [auth H] Focus chain FE [auth 3] Focus chain GC [auth K] Focus chain HB [auth A] Focus chain HC [auth K] Focus chain LC [auth K] Focus chain LE [auth 5] Focus chain OB [auth D] Focus chain QC [auth O] Focus chain RA [auth C] Focus chain UB [auth F] Focus chain WA [auth L] Focus chain WD [auth Y] Focus chain XB [auth F] Focus chain XC [auth Q] Focus chain ZE [auth 9] Interactions & Density Focus chain BE [auth 1] Focus chain DC [auth I] Focus chain EB [auth M] Focus chain FB [auth H] Focus chain FE [auth 3] Focus chain GC [auth K] Focus chain HB [auth A] Focus chain HC [auth K] Focus chain LC [auth K] Focus chain LE [auth 5] Focus chain OB [auth D] Focus chain QC [auth O] Focus chain RA [auth C] Focus chain UB [auth F] Focus chain WA [auth L] Focus chain WD [auth Y] Focus chain XB [auth F] Focus chain XC [auth Q] Focus chain ZE [auth 9]
UQ8 Query on UQ8 Download:Ideal Coordinates CCD File SDF format, chain XA [auth L] SDF format, chain UA [auth L] MOL2 format, chain XA [auth L] MOL2 format, chain UA [auth L] mmCIF format, chain XA [auth L] mmCIF format, chain UA [auth L]	UA [auth L], XA [auth L]	Ubiquinone-8 C₄₉ H₇₄ O₄ ICFIZJQGJAJRSU-SGHXUWJISA-N		Interactions Focus chain UA [auth L] Focus chain XA [auth L] Interactions & Density Focus chain UA [auth L] Focus chain XA [auth L]
MQ8 Query on MQ8 Download:Ideal Coordinates CCD File SDF format, chain DB [auth M] MOL2 format, chain DB [auth M] mmCIF format, chain DB [auth M]	DB [auth M]	MENAQUINONE 8 C₅₁ H₇₂ O₂ LXKDFTDVRVLXFY-ACMRXAIVSA-N		Interactions Focus chain DB [auth M] Interactions & Density Focus chain DB [auth M]
DGA Query on DGA Download:Ideal Coordinates CCD File SDF format, chain QA [auth C] MOL2 format, chain QA [auth C] mmCIF format, chain QA [auth C]	QA [auth C]	DIACYL GLYCEROL C₃₉ H₇₆ O₅ UHUSDOQQWJGJQS-QNGWXLTQSA-N		Interactions Focus chain QA [auth C] Interactions & Density Focus chain QA [auth C]
HEM Query on HEM Download:Ideal Coordinates CCD File SDF format, chain NA [auth C] SDF format, chain MA [auth C] SDF format, chain LA [auth C] SDF format, chain KA [auth C] MOL2 format, chain NA [auth C] MOL2 format, chain MA [auth C] MOL2 format, chain LA [auth C] MOL2 format, chain KA [auth C] mmCIF format, chain NA [auth C] mmCIF format, chain MA [auth C] mmCIF format, chain LA [auth C] mmCIF format, chain KA [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]
H4X Query on H4X Download:Ideal Coordinates CCD File SDF format, chain ZB [auth G] SDF format, chain XD [auth Z] SDF format, chain WE [auth 7] SDF format, chain VC [auth P] SDF format, chain UC [auth O] SDF format, chain SB [auth E] SDF format, chain RE [auth 6] SDF format, chain PE [auth 5] SDF format, chain PC [auth O] SDF format, chain MD [auth V] SDF format, chain MC [auth K] SDF format, chain LD [auth U] SDF format, chain KB [auth B] SDF format, chain JE [auth 4] SDF format, chain IC [auth K] SDF format, chain CE [auth 2] SDF format, chain BD [auth Q] MOL2 format, chain ZB [auth G] MOL2 format, chain XD [auth Z] MOL2 format, chain WE [auth 7] MOL2 format, chain VC [auth P] MOL2 format, chain UC [auth O] MOL2 format, chain SB [auth E] MOL2 format, chain RE [auth 6] MOL2 format, chain PE [auth 5] MOL2 format, chain PC [auth O] MOL2 format, chain MD [auth V] MOL2 format, chain MC [auth K] MOL2 format, chain LD [auth U] MOL2 format, chain KB [auth B] MOL2 format, chain JE [auth 4] MOL2 format, chain IC [auth K] MOL2 format, chain CE [auth 2] MOL2 format, chain BD [auth Q] mmCIF format, chain ZB [auth G] mmCIF format, chain XD [auth Z] mmCIF format, chain WE [auth 7] mmCIF format, chain VC [auth P] mmCIF format, chain UC [auth O] mmCIF format, chain SB [auth E] mmCIF format, chain RE [auth 6] mmCIF format, chain PE [auth 5] mmCIF format, chain PC [auth O] mmCIF format, chain MD [auth V] mmCIF format, chain MC [auth K] mmCIF format, chain LD [auth U] mmCIF format, chain KB [auth B] mmCIF format, chain JE [auth 4] mmCIF format, chain IC [auth K] mmCIF format, chain CE [auth 2] mmCIF format, chain BD [auth Q]	BD [auth Q] CE [auth 2] IC [auth K] JE [auth 4] KB [auth B] BD [auth Q], CE [auth 2], IC [auth K], JE [auth 4], KB [auth B], LD [auth U], MC [auth K], MD [auth V], PC [auth O], PE [auth 5], RE [auth 6], SB [auth E], UC [auth O], VC [auth P], WE [auth 7], XD [auth Z], ZB [auth G]	(6~{E},8~{E},10~{E},12~{E},14~{E},16~{E},18~{E},20~{E},22~{E},24~{E},26~{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-undecaene C₄₂ H₆₄ O₂ LCTIOHZQWXQPIB-VYCPWLLESA-N		Interactions Focus chain BD [auth Q] Focus chain CE [auth 2] Focus chain IC [auth K] Focus chain JE [auth 4] Focus chain KB [auth B] Focus chain LD [auth U] Focus chain MC [auth K] Focus chain MD [auth V] Focus chain PC [auth O] Focus chain PE [auth 5] Focus chain RE [auth 6] Focus chain SB [auth E] Focus chain UC [auth O] Focus chain VC [auth P] Focus chain WE [auth 7] Focus chain XD [auth Z] Focus chain ZB [auth G] Interactions & Density Focus chain BD [auth Q] Focus chain CE [auth 2] Focus chain IC [auth K] Focus chain JE [auth 4] Focus chain KB [auth B] Focus chain LD [auth U] Focus chain MC [auth K] Focus chain MD [auth V] Focus chain PC [auth O] Focus chain PE [auth 5] Focus chain RE [auth 6] Focus chain SB [auth E] Focus chain UC [auth O] Focus chain VC [auth P] Focus chain WE [auth 7] Focus chain XD [auth Z] Focus chain ZB [auth G]
LMT Query on LMT Download:Ideal Coordinates CCD File SDF format, chain YE [auth 8] SDF format, chain YD [auth Z] SDF format, chain XE [auth 8] SDF format, chain WC [auth P] SDF format, chain TB [auth E] SDF format, chain SE [auth 6] SDF format, chain RD [auth X] SDF format, chain OC [auth N] SDF format, chain ND [auth V] SDF format, chain NB [auth B] SDF format, chain LB [auth B] SDF format, chain KE [auth 4] SDF format, chain HD [auth T] SDF format, chain FC [auth J] SDF format, chain EE [auth 2] SDF format, chain DF [auth 0] SDF format, chain CD [auth R] SDF format, chain AC [auth G] MOL2 format, chain YE [auth 8] MOL2 format, chain YD [auth Z] MOL2 format, chain XE [auth 8] MOL2 format, chain WC [auth P] MOL2 format, chain TB [auth E] MOL2 format, chain SE [auth 6] MOL2 format, chain RD [auth X] MOL2 format, chain OC [auth N] MOL2 format, chain ND [auth V] MOL2 format, chain NB [auth B] MOL2 format, chain LB [auth B] MOL2 format, chain KE [auth 4] MOL2 format, chain HD [auth T] MOL2 format, chain FC [auth J] MOL2 format, chain EE [auth 2] MOL2 format, chain DF [auth 0] MOL2 format, chain CD [auth R] MOL2 format, chain AC [auth G] mmCIF format, chain YE [auth 8] mmCIF format, chain YD [auth Z] mmCIF format, chain XE [auth 8] mmCIF format, chain WC [auth P] mmCIF format, chain TB [auth E] mmCIF format, chain SE [auth 6] mmCIF format, chain RD [auth X] mmCIF format, chain OC [auth N] mmCIF format, chain ND [auth V] mmCIF format, chain NB [auth B] mmCIF format, chain LB [auth B] mmCIF format, chain KE [auth 4] mmCIF format, chain HD [auth T] mmCIF format, chain FC [auth J] mmCIF format, chain EE [auth 2] mmCIF format, chain DF [auth 0] mmCIF format, chain CD [auth R] mmCIF format, chain AC [auth G]	AC [auth G] CD [auth R] DF [auth 0] EE [auth 2] FC [auth J] AC [auth G], CD [auth R], DF [auth 0], EE [auth 2], FC [auth J], HD [auth T], KE [auth 4], LB [auth B], NB [auth B], ND [auth V], OC [auth N], RD [auth X], SE [auth 6], TB [auth E], WC [auth P], XE [auth 8], YD [auth Z], YE [auth 8]	DODECYL-BETA-D-MALTOSIDE C₂₄ H₄₆ O₁₁ NLEBIOOXCVAHBD-QKMCSOCLSA-N		Interactions Focus chain AC [auth G] Focus chain CD [auth R] Focus chain DF [auth 0] Focus chain EE [auth 2] Focus chain FC [auth J] Focus chain HD [auth T] Focus chain KE [auth 4] Focus chain LB [auth B] Focus chain NB [auth B] Focus chain ND [auth V] Focus chain OC [auth N] Focus chain RD [auth X] Focus chain SE [auth 6] Focus chain TB [auth E] Focus chain WC [auth P] Focus chain XE [auth 8] Focus chain YD [auth Z] Focus chain YE [auth 8] Interactions & Density Focus chain AC [auth G] Focus chain CD [auth R] Focus chain DF [auth 0] Focus chain EE [auth 2] Focus chain FC [auth J] Focus chain HD [auth T] Focus chain KE [auth 4] Focus chain LB [auth B] Focus chain NB [auth B] Focus chain ND [auth V] Focus chain OC [auth N] Focus chain RD [auth X] Focus chain SE [auth 6] Focus chain TB [auth E] Focus chain WC [auth P] Focus chain XE [auth 8] Focus chain YD [auth Z] Focus chain YE [auth 8]
8K6 Query on 8K6 Download:Ideal Coordinates CCD File SDF format, chain YA [auth L] SDF format, chain QE [auth 5] MOL2 format, chain YA [auth L] MOL2 format, chain QE [auth 5] mmCIF format, chain YA [auth L] mmCIF format, chain QE [auth 5]	QE [auth 5], YA [auth L]	Octadecane C₁₈ H₃₈ RZJRJXONCZWCBN-UHFFFAOYSA-N		Interactions Focus chain QE [auth 5] Focus chain YA [auth L] Interactions & Density Focus chain QE [auth 5] Focus chain YA [auth L]
FE Query on FE Download:Ideal Coordinates CCD File SDF format, chain ZA [auth M] MOL2 format, chain ZA [auth M] mmCIF format, chain ZA [auth M]	ZA [auth M]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N		Interactions Focus chain ZA [auth M] Interactions & Density Focus chain ZA [auth M]
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain ZD [auth 1] SDF format, chain YC [auth Q] SDF format, chain VB [auth F] SDF format, chain TE [auth 7] SDF format, chain SD [auth Y] SDF format, chain RC [auth O] SDF format, chain PB [auth D] SDF format, chain PA [auth C] SDF format, chain OD [auth W] SDF format, chain ME [auth 5] SDF format, chain JC [auth K] SDF format, chain JB [auth A] SDF format, chain ID [auth U] SDF format, chain GE [auth 3] SDF format, chain ED [auth S] SDF format, chain BC [auth I] SDF format, chain AF [auth 9] MOL2 format, chain ZD [auth 1] MOL2 format, chain YC [auth Q] MOL2 format, chain VB [auth F] MOL2 format, chain TE [auth 7] MOL2 format, chain SD [auth Y] MOL2 format, chain RC [auth O] MOL2 format, chain PB [auth D] MOL2 format, chain PA [auth C] MOL2 format, chain OD [auth W] MOL2 format, chain ME [auth 5] MOL2 format, chain JC [auth K] MOL2 format, chain JB [auth A] MOL2 format, chain ID [auth U] MOL2 format, chain GE [auth 3] MOL2 format, chain ED [auth S] MOL2 format, chain BC [auth I] MOL2 format, chain AF [auth 9] mmCIF format, chain ZD [auth 1] mmCIF format, chain YC [auth Q] mmCIF format, chain VB [auth F] mmCIF format, chain TE [auth 7] mmCIF format, chain SD [auth Y] mmCIF format, chain RC [auth O] mmCIF format, chain PB [auth D] mmCIF format, chain PA [auth C] mmCIF format, chain OD [auth W] mmCIF format, chain ME [auth 5] mmCIF format, chain JC [auth K] mmCIF format, chain JB [auth A] mmCIF format, chain ID [auth U] mmCIF format, chain GE [auth 3] mmCIF format, chain ED [auth S] mmCIF format, chain BC [auth I] mmCIF format, chain AF [auth 9]	AF [auth 9] BC [auth I] ED [auth S] GE [auth 3] ID [auth U] AF [auth 9], BC [auth I], ED [auth S], GE [auth 3], ID [auth U], JB [auth A], JC [auth K], ME [auth 5], OD [auth W], PA [auth C], PB [auth D], RC [auth O], SD [auth Y], TE [auth 7], VB [auth F], YC [auth Q], ZD [auth 1]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain AF [auth 9] Focus chain BC [auth I] Focus chain ED [auth S] Focus chain GE [auth 3] Focus chain ID [auth U] Focus chain JB [auth A] Focus chain JC [auth K] Focus chain ME [auth 5] Focus chain OD [auth W] Focus chain PA [auth C] Focus chain PB [auth D] Focus chain RC [auth O] Focus chain SD [auth Y] Focus chain TE [auth 7] Focus chain VB [auth F] Focus chain YC [auth Q] Focus chain ZD [auth 1] Interactions & Density Focus chain AF [auth 9] Focus chain BC [auth I] Focus chain ED [auth S] Focus chain GE [auth 3] Focus chain ID [auth U] Focus chain JB [auth A] Focus chain JC [auth K] Focus chain ME [auth 5] Focus chain OD [auth W] Focus chain PA [auth C] Focus chain PB [auth D] Focus chain RC [auth O] Focus chain SD [auth Y] Focus chain TE [auth 7] Focus chain VB [auth F] Focus chain YC [auth Q] Focus chain ZD [auth 1]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain OA [auth C] MOL2 format, chain OA [auth C] mmCIF 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]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 2.82 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX
MODEL REFINEMENT	REFMAC
RECONSTRUCTION	RELION

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2020-10-07

Deposition Author(s):

Funding Organization	Location	Grant Number
Japan Agency for Medical Research and Development (AMED)	Japan	JP20am0101118
Japan Agency for Medical Research and Development (AMED)	Japan	JP20am0101116
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: 2020-10-07
Type: Initial release
Version 1.1: 2020-10-14
Changes: Database references
Version 1.2: 2025-04-09
Changes: Data collection, Database references, Refinement description, Structure summary
Version 1.3: 2025-09-17
Changes: Advisory, Data collection, Derived calculations

RCSB PDB is hosted by

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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.

7C9R | pdb_00007c9r

STRUCTURE OF PHOTOSYNTHETIC LH1-RC SUPER-COMPLEX OF THIORHODOVIBRIO STRAIN 970

Literature

Cryo-EM structure of a Ca 2+ -bound photosynthetic LH1-RC complex containing multiple alpha beta-polypeptides.

Biological Assembly 1

Macromolecules

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

Entity ID: 10

UniProt

Entity Groups

Sequence Annotations

Small Molecules

Experimental Data & Validation

Experimental Data

Structure Validation

Entry History

Deposition Data

Revision History (Full details and data files)