3WMM

Crystal structure of the LH1-RC complex from Thermochromatium tepidum in C2 form

PDB DOI: https://doi.org/10.2210/pdb3WMM/pdb

Classification: PHOTOSYNTHESIS
Organism(s): Thermochromatium tepidum
Mutation(s): No
Membrane Protein: Yes PDBTMMemProtMDmpstruc

Deposited: 2013-11-22 Released: 2014-04-09
Deposition Author(s): Niwa, S., Takeda, K., Wang-Otomo, Z.-Y., Miki, K.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.01 Å
R-Value Free: 0.337
R-Value Work: 0.314
R-Value Observed: 0.315

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Structure of the LH1-RC complex from Thermochromatium tepidum at 3.0 angstrom

Niwa, S., Yu, L.J., Takeda, K., Hirano, Y., Kawakami, T., Wang-Otomo, Z.Y., Miki, K.

(2014) Nature 508: 228-232

PubMed: 24670637 Search on PubMed
DOI: https://doi.org/10.1038/nature13197
Primary Citation of Related Structures:
3WMM, 4V8K

PubMed Abstract:
The light-harvesting core antenna (LH1) and the reaction centre (RC) of purple photosynthetic bacteria form a supramolecular complex (LH1-RC) to use sunlight energy in a highly efficient manner. Here we report the first near-atomic structure, to our knowledge, of a LH1-RC complex, namely that of a Ca(2+)-bound complex from Thermochromatium tepidum, which reveals detailed information on the arrangement and interactions of the protein subunits and the cofactors. The RC is surrounded by 16 heterodimers of the LH1 αβ-subunit that form a completely closed structure. The Ca(2+) ions are located at the periplasmic side of LH1. Thirty-two bacteriochlorophyll and 16 spirilloxanthin molecules in the LH1 ring form an elliptical assembly. The geometries of the pigment assembly involved in the absorption characteristics of the bacteriochlorophyll in LH1 and excitation energy transfer among the pigments are reported. In addition, possible ubiquinone channels in the closed LH1 complex are proposed based on the atomic structure.

Organizational Affiliation

1] Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan [2].

Macromolecule Content

Total Structure Weight: 392.58 kDa
Atom Count: 25,819
Modelled Residue Count: 2,774
Deposited Residue Count: 2,997
Unique protein chains: 6

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosynthetic reaction center C subunit	A [auth C]	404	Thermochromatium tepidum	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for D2Z0P5 (Thermochromatium tepidum) Explore D2Z0P5 Go to UniProtKB: D2Z0P5
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	D2Z0P5
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Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosynthetic reaction center L subunit	B [auth L]	281	Thermochromatium tepidum	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for D2Z0P3 (Thermochromatium tepidum) Explore D2Z0P3 Go to UniProtKB: D2Z0P3
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	D2Z0P3
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Reference Sequence

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Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosynthetic reaction center M subunit	C [auth M]	325	Thermochromatium tepidum	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for A8ASG6 (Thermochromatium tepidum) Explore A8ASG6 Go to UniProtKB: A8ASG6
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A8ASG6
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Reference Sequence

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Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosynthetic reaction center H subunit	D [auth H]	259	Thermochromatium tepidum	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for D2Z0P9 (Thermochromatium tepidum) Explore D2Z0P9 Go to UniProtKB: D2Z0P9
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	D2Z0P9
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Reference Sequence

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Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
LH1 alpha polypeptide	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	Thermochromatium tepidum	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for D2Z0P2 (Thermochromatium tepidum) Explore D2Z0P2 Go to UniProtKB: D2Z0P2
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	D2Z0P2
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Reference Sequence

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Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
LH1 beta polypeptide	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	47	Thermochromatium tepidum	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for D2Z0P1 (Thermochromatium tepidum) Explore D2Z0P1 Go to UniProtKB: D2Z0P1
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	D2Z0P1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 11 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
BCL Query on BCL Download Ideal Coordinates CCD File SDF format, chain AD [auth 1] SDF format, chain BD [auth 2] SDF format, chain CC [auth O] SDF format, chain DC [auth P] SDF format, chain ED [auth 3] SDF format, chain GC [auth Q] SDF format, chain GD [auth 4] SDF format, chain HB [auth A] SDF format, chain HC [auth R] SDF format, chain JD [auth 5] SDF format, chain KB [auth B] SDF format, chain KC [auth S] SDF format, chain KD [auth 6] SDF format, chain LC [auth T] SDF format, chain MD [auth 7] SDF format, chain NB [auth D] SDF format, chain ND [auth 7] SDF format, chain OB [auth E] SDF format, chain OC [auth U] SDF format, chain PA [auth L] SDF format, chain PC [auth V] SDF format, chain QB [auth F] SDF format, chain QD [auth 9] SDF format, chain RB [auth G] SDF format, chain RD [auth 0] SDF format, chain SC [auth W] SDF format, chain TA [auth L] SDF format, chain UA [auth M] SDF format, chain UB [auth I] SDF format, chain UC [auth X] SDF format, chain VA [auth M] SDF format, chain VB [auth I] SDF format, chain XC [auth Y] SDF format, chain YB [auth K] SDF format, chain YC [auth Z] SDF format, chain ZB [auth N] MOL2 format, chain AD [auth 1] MOL2 format, chain BD [auth 2] MOL2 format, chain CC [auth O] MOL2 format, chain DC [auth P] MOL2 format, chain ED [auth 3] MOL2 format, chain GC [auth Q] MOL2 format, chain GD [auth 4] MOL2 format, chain HB [auth A] MOL2 format, chain HC [auth R] MOL2 format, chain JD [auth 5] MOL2 format, chain KB [auth B] MOL2 format, chain KC [auth S] MOL2 format, chain KD [auth 6] MOL2 format, chain LC [auth T] MOL2 format, chain MD [auth 7] MOL2 format, chain NB [auth D] MOL2 format, chain ND [auth 7] MOL2 format, chain OB [auth E] MOL2 format, chain OC [auth U] MOL2 format, chain PA [auth L] MOL2 format, chain PC [auth V] MOL2 format, chain QB [auth F] MOL2 format, chain QD [auth 9] MOL2 format, chain RB [auth G] MOL2 format, chain RD [auth 0] MOL2 format, chain SC [auth W] MOL2 format, chain TA [auth L] MOL2 format, chain UA [auth M] MOL2 format, chain UB [auth I] MOL2 format, chain UC [auth X] MOL2 format, chain VA [auth M] MOL2 format, chain VB [auth I] MOL2 format, chain XC [auth Y] MOL2 format, chain YB [auth K] MOL2 format, chain YC [auth Z] MOL2 format, chain ZB [auth N]	AD [auth 1] BD [auth 2] CC [auth O] DC [auth P] ED [auth 3] AD [auth 1], BD [auth 2], CC [auth O], DC [auth P], ED [auth 3], GC [auth Q], GD [auth 4], HB [auth A], HC [auth R], JD [auth 5], KB [auth B], KC [auth S], KD [auth 6], LC [auth T], MD [auth 7], NB [auth D], ND [auth 7], OB [auth E], OC [auth U], PA [auth L], PC [auth V], QB [auth F], QD [auth 9], RB [auth G], RD [auth 0], SC [auth W], TA [auth L], UA [auth M], UB [auth I], UC [auth X], VA [auth M], VB [auth I], XC [auth Y], YB [auth K], YC [auth Z], ZB [auth N]	BACTERIOCHLOROPHYLL A C₅₅ H₇₄ Mg N₄ O₆ DSJXIQQMORJERS-AGGZHOMASA-M		Interactions Focus chain AD [auth 1] Focus chain BD [auth 2] Focus chain CC [auth O] Focus chain DC [auth P] Focus chain ED [auth 3] Focus chain GC [auth Q] Focus chain GD [auth 4] Focus chain HB [auth A] Focus chain HC [auth R] Focus chain JD [auth 5] Focus chain KB [auth B] Focus chain KC [auth S] Focus chain KD [auth 6] Focus chain LC [auth T] Focus chain MD [auth 7] Focus chain NB [auth D] Focus chain ND [auth 7] Focus chain OB [auth E] Focus chain OC [auth U] Focus chain PA [auth L] Focus chain PC [auth V] Focus chain QB [auth F] Focus chain QD [auth 9] Focus chain RB [auth G] Focus chain RD [auth 0] Focus chain SC [auth W] Focus chain TA [auth L] Focus chain UA [auth M] Focus chain UB [auth I] Focus chain UC [auth X] Focus chain VA [auth M] Focus chain VB [auth I] Focus chain XC [auth Y] Focus chain YB [auth K] Focus chain YC [auth Z] Focus chain ZB [auth N] Interactions & Density Focus chain AD [auth 1] Focus chain BD [auth 2] Focus chain CC [auth O] Focus chain DC [auth P] Focus chain ED [auth 3] Focus chain GC [auth Q] Focus chain GD [auth 4] Focus chain HB [auth A] Focus chain HC [auth R] Focus chain JD [auth 5] Focus chain KB [auth B] Focus chain KC [auth S] Focus chain KD [auth 6] Focus chain LC [auth T] Focus chain MD [auth 7] Focus chain NB [auth D] Focus chain ND [auth 7] Focus chain OB [auth E] Focus chain OC [auth U] Focus chain PA [auth L] Focus chain PC [auth V] Focus chain QB [auth F] Focus chain QD [auth 9] Focus chain RB [auth G] Focus chain RD [auth 0] Focus chain SC [auth W] Focus chain TA [auth L] Focus chain UA [auth M] Focus chain UB [auth I] Focus chain UC [auth X] Focus chain VA [auth M] Focus chain VB [auth I] Focus chain XC [auth Y] Focus chain YB [auth K] Focus chain YC [auth Z] Focus chain ZB [auth N]
BPH Query on BPH Download Ideal Coordinates CCD File SDF format, chain QA [auth L] SDF format, chain WA [auth M] MOL2 format, chain QA [auth L] MOL2 format, chain WA [auth M]	QA [auth L], WA [auth M]	BACTERIOPHEOPHYTIN A C₅₅ H₇₆ N₄ O₆ KWOZSBGNAHVCKG-SZQBJALDSA-N		Interactions Focus chain QA [auth L] Focus chain WA [auth M] Interactions & Density Focus chain QA [auth L] Focus chain WA [auth M]
PGW Query on PGW Download Ideal Coordinates CCD File SDF format, chain AB [auth M] SDF format, chain DB [auth H] MOL2 format, chain AB [auth M] MOL2 format, chain DB [auth H]	AB [auth M], DB [auth H]	(1R)-2-{[(S)-{[(2S)-2,3-dihydroxypropyl]oxy}(hydroxy)phosphoryl]oxy}-1-[(hexadecanoyloxy)methyl]ethyl (9Z)-octadec-9-enoate C₄₀ H₇₇ O₁₀ P PAZGBAOHGQRCBP-HGWHEPCSSA-N		Interactions Focus chain AB [auth M] Focus chain DB [auth H] Interactions & Density Focus chain AB [auth M] Focus chain DB [auth H]
UQ8 Query on UQ8 Download Ideal Coordinates CCD File SDF format, chain RA [auth L] MOL2 format, chain RA [auth L]	RA [auth L]	Ubiquinone-8 C₄₉ H₇₄ O₄ ICFIZJQGJAJRSU-SGHXUWJISA-N		Interactions Focus chain RA [auth L] Interactions & Density Focus chain RA [auth L]
MQ8 Query on MQ8 Download Ideal Coordinates CCD File SDF format, chain YA [auth M] MOL2 format, chain YA [auth M]	YA [auth M]	MENAQUINONE 8 C₅₁ H₇₂ O₂ LXKDFTDVRVLXFY-ACMRXAIVSA-N		Interactions Focus chain YA [auth M] Interactions & Density Focus chain YA [auth M]
PEF Query on PEF Download Ideal Coordinates CCD File SDF format, chain CB [auth H] MOL2 format, chain CB [auth H]	CB [auth H]	DI-PALMITOYL-3-SN-PHOSPHATIDYLETHANOLAMINE C₃₇ H₇₄ N O₈ P SLKDGVPOSSLUAI-PGUFJCEWSA-N		Interactions Focus chain CB [auth H] Interactions & Density Focus chain CB [auth H]
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 AC [auth N] SDF format, chain CD [auth 2] SDF format, chain EC [auth P] SDF format, chain FD [auth 3] SDF format, chain GB [auth A] SDF format, chain HD [auth 4] SDF format, chain IB [auth A] SDF format, chain IC [auth R] SDF format, chain LB [auth B] SDF format, chain MC [auth T] SDF format, chain OD [auth 8] SDF format, chain QC [auth V] SDF format, chain SB [auth G] SDF format, chain TC [auth W] SDF format, chain VC [auth X] SDF format, chain WB [auth J] SDF format, chain ZA [auth M] MOL2 format, chain AC [auth N] MOL2 format, chain CD [auth 2] MOL2 format, chain EC [auth P] MOL2 format, chain FD [auth 3] MOL2 format, chain GB [auth A] MOL2 format, chain HD [auth 4] MOL2 format, chain IB [auth A] MOL2 format, chain IC [auth R] MOL2 format, chain LB [auth B] MOL2 format, chain MC [auth T] MOL2 format, chain OD [auth 8] MOL2 format, chain QC [auth V] MOL2 format, chain SB [auth G] MOL2 format, chain TC [auth W] MOL2 format, chain VC [auth X] MOL2 format, chain WB [auth J] MOL2 format, chain ZA [auth M]	AC [auth N] CD [auth 2] EC [auth P] FD [auth 3] GB [auth A] AC [auth N], CD [auth 2], EC [auth P], FD [auth 3], GB [auth A], HD [auth 4], IB [auth A], IC [auth R], LB [auth B], MC [auth T], OD [auth 8], QC [auth V], SB [auth G], TC [auth W], VC [auth X], WB [auth J], ZA [auth M]	SPIRILLOXANTHIN C₄₂ H₆₀ O₂ VAZQBTJCYODOSV-RISZBRKMSA-N		Interactions Focus chain AC [auth N] Focus chain CD [auth 2] Focus chain EC [auth P] Focus chain FD [auth 3] Focus chain GB [auth A] Focus chain HD [auth 4] Focus chain IB [auth A] Focus chain IC [auth R] Focus chain LB [auth B] Focus chain MC [auth T] Focus chain OD [auth 8] Focus chain QC [auth V] Focus chain SB [auth G] Focus chain TC [auth W] Focus chain VC [auth X] Focus chain WB [auth J] Focus chain ZA [auth M] Interactions & Density Focus chain AC [auth N] Focus chain CD [auth 2] Focus chain EC [auth P] Focus chain FD [auth 3] Focus chain GB [auth A] Focus chain HD [auth 4] Focus chain IB [auth A] Focus chain IC [auth R] Focus chain LB [auth B] Focus chain MC [auth T] Focus chain OD [auth 8] Focus chain QC [auth V] Focus chain SB [auth G] Focus chain TC [auth W] Focus chain VC [auth X] Focus chain WB [auth J] Focus chain ZA [auth M]
PO4 Query on PO4 Download Ideal Coordinates CCD File SDF format, chain BB [auth M] SDF format, chain EB [auth H] SDF format, chain FB [auth H] SDF format, chain SA [auth L] MOL2 format, chain BB [auth M] MOL2 format, chain EB [auth H] MOL2 format, chain FB [auth H] MOL2 format, chain SA [auth L]	BB [auth M], EB [auth H], FB [auth H], SA [auth L]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain BB [auth M] Focus chain EB [auth H] Focus chain FB [auth H] Focus chain SA [auth L] Interactions & Density Focus chain BB [auth M] Focus chain EB [auth H] Focus chain FB [auth H] Focus chain SA [auth L]
FE Query on FE Download Ideal Coordinates CCD File SDF format, chain XA [auth M] MOL2 format, chain XA [auth M]	XA [auth M]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N		Interactions Focus chain XA [auth M] Interactions & Density Focus chain XA [auth M]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain BC [auth O] SDF format, chain DD [auth 3] SDF format, chain FC [auth Q] SDF format, chain ID [auth 5] SDF format, chain JB [auth A] SDF format, chain JC [auth S] SDF format, chain LD [auth 7] SDF format, chain MB [auth D] SDF format, chain NC [auth U] SDF format, chain OA [auth C] SDF format, chain PB [auth F] SDF format, chain PD [auth 9] SDF format, chain RC [auth W] SDF format, chain TB [auth I] SDF format, chain WC [auth Y] SDF format, chain XB [auth K] SDF format, chain ZC [auth 1] MOL2 format, chain BC [auth O] MOL2 format, chain DD [auth 3] MOL2 format, chain FC [auth Q] MOL2 format, chain ID [auth 5] MOL2 format, chain JB [auth A] MOL2 format, chain JC [auth S] MOL2 format, chain LD [auth 7] MOL2 format, chain MB [auth D] MOL2 format, chain NC [auth U] MOL2 format, chain OA [auth C] MOL2 format, chain PB [auth F] MOL2 format, chain PD [auth 9] MOL2 format, chain RC [auth W] MOL2 format, chain TB [auth I] MOL2 format, chain WC [auth Y] MOL2 format, chain XB [auth K] MOL2 format, chain ZC [auth 1]	BC [auth O] DD [auth 3] FC [auth Q] ID [auth 5] JB [auth A] BC [auth O], DD [auth 3], FC [auth Q], ID [auth 5], JB [auth A], JC [auth S], LD [auth 7], MB [auth D], NC [auth U], OA [auth C], PB [auth F], PD [auth 9], RC [auth W], TB [auth I], WC [auth Y], XB [auth K], ZC [auth 1]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain BC [auth O] Focus chain DD [auth 3] Focus chain FC [auth Q] Focus chain ID [auth 5] Focus chain JB [auth A] Focus chain JC [auth S] Focus chain LD [auth 7] Focus chain MB [auth D] Focus chain NC [auth U] Focus chain OA [auth C] Focus chain PB [auth F] Focus chain PD [auth 9] Focus chain RC [auth W] Focus chain TB [auth I] Focus chain WC [auth Y] Focus chain XB [auth K] Focus chain ZC [auth 1] Interactions & Density Focus chain BC [auth O] Focus chain DD [auth 3] Focus chain FC [auth Q] Focus chain ID [auth 5] Focus chain JB [auth A] Focus chain JC [auth S] Focus chain LD [auth 7] Focus chain MB [auth D] Focus chain NC [auth U] Focus chain OA [auth C] Focus chain PB [auth F] Focus chain PD [auth 9] Focus chain RC [auth W] Focus chain TB [auth I] Focus chain WC [auth Y] Focus chain XB [auth K] Focus chain ZC [auth 1]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.01 Å
R-Value Free: 0.337
R-Value Work: 0.314
R-Value Observed: 0.315
Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 227.341	α = 90
b = 148.238	β = 117.59
c = 161.792	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
SOLVE	phasing
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

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Entry History

Deposition Data

Released Date: 2014-04-09

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2014-04-09
Type: Initial release
Version 1.1: 2014-04-16
Changes: Database references
Version 1.2: 2017-06-07
Changes: Other
Version 1.3: 2024-03-20
Changes: Data collection, Database references, Derived calculations, Structure summary

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3WMM

Crystal structure of the LH1-RC complex from Thermochromatium tepidum in C2 form

Structure of the LH1-RC complex from Thermochromatium tepidum at 3.0 angstrom

Entity ID: 1

UniProt

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Entity ID: 2

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Entity ID: 3

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Entity ID: 4

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Entity ID: 5

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Entity ID: 6

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Structure Validation

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Deposition Data

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