› 7r0w

Electron Microscopy
2.8Å resolution

2.8 Angstrom cryo-EM structure of the dimeric cytochrome b6f-PetP complex from Synechocystis sp. PCC 6803 with natively bound lipids and plastoquinone molecules

Released:
DOI: 10.2210/pdb7r0w/pdb
PDB entry 7r0w coloured by chain, front view.
PDB entry 7r0w coloured by chain, side view.
PDB entry 7r0w coloured by chain, top view.
Source organisms:
Primary publication:
Cryo-EM structures of the Synechocystis sp. PCC 6803 cytochrome b6f complex with and without the regulatory PetP subunit.
Proctor MS, Malone LA, Farmer DA, Swainsbury DJ, Hawkings FR, Pastorelli F, Emrich-Mills TZ, Siebert CA, Hunter CN, Johnson MP, Hitchcock A
Biochem J (2022)
PMID: 35726684
Related structures: EMD-14224

Function and Biology Details

Reaction catalysed: 
Plastoquinol + 2 oxidized plastocyanin + 2 H(+)(Side 1) = plastoquinone + 2 reduced plastocyanin + 4 H(+)(Side 2)
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero octadecamer (preferred)
PDBe Complex ID:
PDB-CPX-105801 (preferred)
Entry contents:
9 distinct polypeptide molecules
Macromolecules (9 distinct):
Cytochrome b6-f complex subunit PetP Chains: V, X
Molecule details ›
Chains: V, X
Length: 65 amino acids
Theoretical weight: 7.23 KDa
Source organism: Synechocystis
Expression system: Escherichia coli BL21
UniProt:
  • Canonical: P72798 (Residues: 1-65; Coverage: 100%)
Gene name: ssr2998
Sequence domains: Cytochrome b6f, subunit Tsr0524-like
Cytochrome b6 Chains: A, I
Molecule details ›
Chains: A, I
Length: 222 amino acids
Theoretical weight: 25.08 KDa
Source organism: Synechocystis sp. PCC 6803
UniProt:
  • Canonical: Q57038 (Residues: 1-222; Coverage: 100%)
Gene names: petB, slr0342
Sequence domains: Cytochrome b/b6/petB
Cytochrome b6-f complex subunit 4 Chains: B, J
Molecule details ›
Chains: B, J
Length: 160 amino acids
Theoretical weight: 17.46 KDa
Source organism: Synechocystis sp. PCC 6803
UniProt:
  • Canonical: P27589 (Residues: 1-160; Coverage: 100%)
Gene names: petD, slr0343
Sequence domains: Cytochrome b(C-terminal)/b6/petD
Cytochrome f Chains: C, K
Molecule details ›
Chains: C, K
Length: 328 amino acids
Theoretical weight: 35.26 KDa
Source organism: Synechocystis sp. PCC 6803
UniProt:
  • Canonical: P26287 (Residues: 1-328; Coverage: 100%)
Gene names: petA, sll1317
Sequence domains:
Cytochrome B6 Chains: E, M
Molecule details ›
Chains: E, M
Length: 32 amino acids
Theoretical weight: 3.38 KDa
Source organism: Synechocystis sp. PCC 6803
UniProt:
  • Canonical: A0A6P1VG96 (Residues: 1-32; Coverage: 100%)
Gene name: BWK47_07435
Cytochrome b6-f complex subunit 7 Chains: F, N
Molecule details ›
Chains: F, N
Length: 36 amino acids
Theoretical weight: 3.83 KDa
Source organism: Synechocystis sp. PCC 6803
UniProt:
  • Canonical: P74810 (Residues: 1-36; Coverage: 100%)
Gene names: petM, smr0003
Sequence domains: PetM family of cytochrome b6f complex subunit 7
Cytochrome b6-f complex subunit 5 Chains: G, O
Molecule details ›
Chains: G, O
Length: 38 amino acids
Theoretical weight: 4.18 KDa
Source organism: Synechocystis sp. PCC 6803
UniProt:
  • Canonical: P74149 (Residues: 1-38; Coverage: 100%)
Gene names: petG, smr0010
Sequence domains: Cytochrome B6-F complex subunit 5
Cytochrome b6-f complex subunit 8 Chains: H, P
Molecule details ›
Chains: H, P
Length: 29 amino acids
Theoretical weight: 3.33 KDa
Source organism: Synechocystis sp. PCC 6803
UniProt:
  • Canonical: P72717 (Residues: 1-29; Coverage: 100%)
Gene names: petN, sml0004
Sequence domains: PetN
Cytochrome b6-f complex iron-sulfur subunit 2 Chains: D, L
Molecule details ›
Chains: D, L
Length: 192 amino acids
Theoretical weight: 20.56 KDa
Source organism: Synechocystis sp. PCC 6803
UniProt:
  • Canonical: P26290 (Residues: 1-180; Coverage: 100%)
Gene names: petC2, sll1316
Sequence domains: Rieske [2Fe-2S] domain

Ligands and Environments

12 bound ligands:
Ligand HEM 6 x HEM
Ligand PGV 4 x PGV
Ligand ECH 2 x ECH
Ligand PL9 2 x PL9
Ligand CLA 2 x CLA
Ligand HEC 2 x HEC
Ligand LMG 1 x LMG
Ligand 6PL 2 x 6PL
Ligand 2WA 1 x 2WA
Ligand FES 2 x FES
Ligand SQD 2 x SQD
Ligand LFA 1 x LFA
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 2.8Å
Relevant EMDB volumes: EMD-14224
Expression system: Escherichia coli BL21

Quick links

Citations

3 citation in other articles

Zeta-Carotene Isomerase (Z-ISO) Is Required for Light-Independent Carotenoid Biosynthesis in the Cyanobacterium Synechocystis sp. PCC 6803.
Proctor et al. (2022)
2 more

1 mention without citation

Cryo-EM structure of the four-subunit Rhodobacter sphaeroides cytochrome bc1 complex in styrene maleic acid nanodiscs.
Swainsbury et al. (2023)