› 7o0v

Electron Microscopy
2.5Å resolution

Cryo-EM structure (model_2a) of the RC-dLH complex from Gemmatimonas phototrophica at 2.5 A

Released:
DOI: 10.2210/pdb7o0v/pdb
PDB entry 7o0v coloured by chain, front view.
PDB entry 7o0v coloured by chain, side view.
PDB entry 7o0v coloured by chain, top view.
Source organism: Gemmatimonas phototrophica
Primary publication:
2.4-Å structure of the double-ring Gemmatimonas phototrophica photosystem.
Qian P, Gardiner AT, Šímová I, Naydenova K, Croll TI, Jackson PJ, Kloz M, Čubáková P, Kuzma M, Zeng Y, Castro-Hartmann P, van Knippenberg B, Goldie KN, Kaftan D, Hrouzek P, Hájek J, Agirre J, Siebert CA, Bína D, Sader K, Stahlberg H, Sobotka R, Russo CJ, Polívka T, Hunter CN, Koblížek M
OpenAccess logo Sci Adv 8 eabk3139 (2022)
PMID: 35171663
Related structures: EMD-12680

Function and Biology Details

Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero 86-mer (preferred)
PDBe Complex ID:
PDB-CPX-495177 (preferred)
Entry contents:
12 distinct polypeptide molecules
Macromolecules (13 distinct):
LHh-alpha Chains: AA, AB, AE, AF, AG, AH, AI, AJ, AK, AL, AM, AN, AO, AP, AQ, AR, AS, AT, AU, AV, AW, AX
Molecule details ›
Chains: AA, AB, AE, AF, AG, AH, AI, AJ, AK, AL, AM, AN, AO, AP, AQ, AR, AS, AT, AU, AV, AW, AX
Length: 54 amino acids
Theoretical weight: 6.06 KDa
Source organism: Gemmatimonas phototrophica
LHh-alpha Chains: AC, AD
Molecule details ›
Chains: AC, AD
Length: 54 amino acids
Theoretical weight: 6.06 KDa
Source organism: Gemmatimonas phototrophica
Antenna complex alpha/beta subunit domain-containing protein Chains: BA, BC, BF, BG, BH, BJ, BK, BL, BM, BN, BO, BP, BU, BX, ba, bb, bc, bd, be, bf, bg, bh, bi, bj, bk, bl, bm, bo, bp
Molecule details ›
Chains: BA, BC, BF, BG, BH, BJ, BK, BL, BM, BN, BO, BP, BU, BX, ba, bb, bc, bd, be, bf, bg, bh, bi, bj, bk, bl, bm, bo, bp
Length: 44 amino acids
Theoretical weight: 5.08 KDa
Source organism: Gemmatimonas phototrophica
UniProt:
  • Canonical: A0A143BHS8 (Residues: 1-44; Coverage: 100%)
Gene name: GEMMAAP_06500
Sequence domains: Antenna complex alpha/beta subunit
Antenna complex alpha/beta subunit domain-containing protein Chains: BB, BD, BE, BI, BQ, BR, BS, BT, BV, BW, bn
Molecule details ›
Chains: BB, BD, BE, BI, BQ, BR, BS, BT, BV, BW, bn
Length: 43 amino acids
Theoretical weight: 4.96 KDa
Source organism: Gemmatimonas phototrophica
Expression system: Gemmatimonas phototrophica
UniProt:
  • Canonical: A0A143BHS8 (Residues: 1-44; Coverage: 98%)
Gene name: GEMMAAP_06500
Sequence domains: Antenna complex alpha/beta subunit
MULTIHEME_CYTC domain-containing protein Chain: C
Molecule details ›
Chain: C
Length: 354 amino acids
Theoretical weight: 38.46 KDa
Source organism: Gemmatimonas phototrophica
UniProt:
  • Canonical: A0A143BHR6 (Residues: 1-354; Coverage: 100%)
Gene name: GEMMAAP_06480
Sequence domains: Photosynthetic reaction centre cytochrome C subunit
RC-S Chain: C1
Molecule details ›
Chain: C1
Length: 202 amino acids
Theoretical weight: 21.08 KDa
Source organism: Gemmatimonas phototrophica
Photosynthetic reaction centre H subunit N-terminal domain-containing protein Chain: H1
Molecule details ›
Chain: H1
Length: 67 amino acids
Theoretical weight: 7.85 KDa
Source organism: Gemmatimonas phototrophica
UniProt:
  • Canonical: A0A143BJ28 (Residues: 1-67; Coverage: 100%)
Gene name: GEMMAAP_06435
Sequence domains: Photosynthetic reaction centre, H-chain N-terminal region
RC-Hc Chain: H2
Molecule details ›
Chain: H2
Length: 181 amino acids
Theoretical weight: 20.02 KDa
Source organism: Gemmatimonas phototrophica
Reaction center protein L chain Chain: L
Molecule details ›
Chain: L
Length: 274 amino acids
Theoretical weight: 30.58 KDa
Source organism: Gemmatimonas phototrophica
UniProt:
  • Canonical: A0A143BHR2 (Residues: 1-274; Coverage: 100%)
Gene name: GEMMAAP_06490
Sequence domains: Photosynthetic reaction centre protein
RC-M Chain: M
Molecule details ›
Chain: M
Length: 367 amino acids
Theoretical weight: 41.15 KDa
Source organism: Gemmatimonas phototrophica
Antenna complex alpha/beta subunit domain-containing protein Chain: aa
Molecule details ›
Chain: aa
Length: 71 amino acids
Theoretical weight: 7.7 KDa
Source organism: Gemmatimonas phototrophica
UniProt:
  • Canonical: A0A143BHS7 (Residues: 1-71; Coverage: 100%)
Gene name: GEMMAAP_06495
Sequence domains: Antenna complex alpha/beta subunit
Antenna complex alpha/beta subunit domain-containing protein Chains: ab, ac, ad, ae, af, ag, ah, ai, aj, ak, al, am, an, ao, ap
Molecule details ›
Chains: ab, ac, ad, ae, af, ag, ah, ai, aj, ak, al, am, an, ao, ap
Length: 71 amino acids
Theoretical weight: 7.72 KDa
Source organism: Gemmatimonas phototrophica
UniProt:
  • Canonical: A0A143BHS7 (Residues: 1-71; Coverage: 100%)
Gene name: GEMMAAP_06495
Sequence domains: Antenna complex alpha/beta subunit

Ligands and Environments

Carbohydrate polymer : NEW Components: MAN, RAM
Carbohydrate polymer
15 bound ligands:
Ligand BCL 108 x BCL
Ligand LMT 120 x LMT
Ligand V7N 40 x V7N
Ligand HEC 4 x HEC
Ligand V75 2 x V75
Ligand NDG 2 x NDG
Ligand 0V9 20 x 0V9
Ligand CD4 6 x CD4
Ligand PGW 1 x PGW
Ligand MQ8 3 x MQ8
Ligand V7B 2 x V7B
Ligand BPH 2 x BPH
Ligand FE 1 x FE
Ligand CRT 1 x CRT
Ligand UYH 1 x UYH
1 modified residue:
Ligand FME 40 x FME

Experiments and Validation Details

Entry percentile scores
Resolution: 2.5Å
Relevant EMDB volumes: EMD-12680
Expression system: Gemmatimonas phototrophica

Quick links

Citations

9 citation in other articles

The structure and assembly of reaction centre-light-harvesting 1 complexes in photosynthetic bacteria.
Swainsbury et al. (2023)
8 more