Structure analysis

Cryo-EM structure of Spinacia oleracea cytochrome b6f complex with water molecules at 1.94 A resolution

Electron Microscopy
1.94Å resolution
Source organism: Spinacia oleracea
Assembly composition:
hetero octadecamer (preferred)
Entry contents: 9 distinct polypeptide molecules

Assemblies

Assembly 1 (preferred)
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Multimeric state: hetero octadecamer
Accessible surface area: 85767.82 Å2
Buried surface area: 80787.77 Å2
Dissociation area: 2,750.19 Å2
Dissociation energy (ΔGdiss): 17.43 kcal/mol
Dissociation entropy (TΔSdiss): 19.94 kcal/mol
Symmetry number: 2
PDBe Complex ID: PDB-CPX-275746

Macromolecules

Chains: A, I
Length: 215 amino acids
Theoretical weight: 24.19 KDa
Source organism: Spinacia oleracea
UniProt:
  • Canonical: P00165 (Residues: 1-215; Coverage: 100%)
Gene name: petB
Pfam: Cytochrome b/b6/petB
PDBe-KB: UniProt Coverage View: P00165  
121520406080100120140160180200
 
100200MSKVYDWFEERLEIQAIADDITSKYVPPHVNIFYCLGGITLTCFLVQVATGFAMTFYYRPTVTDAFASVQYIMTEVNFGWLIRSVHRWSASMMVLMMILHVFRVYLTGGFKKPRELTWVTGVVLGVLTASFGVTGYSLPWDQIGYWAVKIVTGVPDAIPVIGSPLVELLRGSASVGQSTLTRFYSLHTFVLPLLTAVFMLMHFLMIRKQGISGPL
UniProt
P00165
Chains
Secondary structure
Ligand binding sites
Interaction interfaces
Sequence conservation

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Chains: B, J
Length: 160 amino acids
Theoretical weight: 17.46 KDa
Source organism: Spinacia oleracea
UniProt:
  • Canonical: P00166 (Residues: 1-160; Coverage: 100%)
Gene name: petD
Pfam: Cytochrome b(C-terminal)/b6/petD
PDBe-KB: UniProt Coverage View: P00166  
116020406080100120140160
 
50100150MGVTKKPDLNDPVLRAKLAKGMGHNYYGEPAWPNDLLYIFPVVILGTIACNVGLAVLEPSMIGEPADPFATPLEILPEWYFFPVFQILRTVPNKLLGVLLMASVPAGLLTVPFLENVNKFQNPFRRPVATTVFLVGTVVALWLGIGATLPIDKSLTLGLF
UniProt
P00166
Chains
Secondary structure
Ligand binding sites
Interaction interfaces
Sequence conservation

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Chains: C, K
Length: 320 amino acids
Theoretical weight: 35.36 KDa
Source organism: Spinacia oleracea
UniProt:
  • Canonical: P16013 (Residues: 1-320; Coverage: 100%)
Gene name: petA
Pfam:
PDBe-KB: UniProt Coverage View: P16013  
132050100150200250300
 
100200300MQTINTFSWIKEQITRSISISLILYIITRSSIANAYPIFAQQGYENPREATGRIVCANCHLANKPVDIEVPQAVLPDTVFEAVVRIPYDMQLKQVLANGKKGGLNVGAVLILPEGFELAPPDRISPEMKEKMGNLSFQSYRPNKQNILVIGPVPGQKYSEITFPILAPDPATKKDVHFLKYPIYVGGNRGRGQIYPDGSKSNNTVYNSTATGIVKKIVRKEKGGYEINIADASDGREVVDIIPRGPELLVSEGESIKLDQPLTSNPNVGGFGQGDAEVVLQDPLRIQGLLFFFASVILAQIFLVLKKKQFEKVQLSEMNF
UniProt
P16013
Chains
Secondary structure
Ligand binding sites
Interaction interfaces
Sequence conservation

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Chains: D, L
Length: 230 amino acids
Theoretical weight: 24.35 KDa
Source organism: Spinacia oleracea
UniProt:
  • Canonical: P08980 (Residues: 1-230; Coverage: 100%)
Gene name: petC
Pfam: Rieske [2Fe-2S] domain
PDBe-KB: UniProt Coverage View: P08980  
123020406080100120140160180200220
 
100200MASFTLSSATPSQLCSSKNGMFAPSLALAKAGRVNVLISKERIRGMKLTCQATSIPADNVPDMQKRETLNLLLLGALSLPTGYMLLPYASFFVPPGGGAGTGGTIAKDALGNDVIAAEWLKTHAPGDRTLTQGLKGDPTYLVVESDKTLATFGINAVCTHLGCVVPFNAAENKFICPCHGSQYNNQGRVVRGPAPLSLALAHCDVDDGKVVFVPWTETDFRTGEAPWWSA
UniProt
P08980
Chains
Secondary structure
Ligand binding sites
Interaction interfaces
Sequence conservation

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Chains: E, M
Length: 31 amino acids
Theoretical weight: 3.45 KDa
Source organism: Spinacia oleracea
UniProt:
  • Canonical: Q9M3L0 (Residues: 1-31; Coverage: 100%)
Gene name: petL
Pfam: Cytochrome B6-F complex subunit VI (PetL)
PDBe-KB: UniProt Coverage View: Q9M3L0  
13124681012141618202224262830
 
102030MFTLTSYFGFLLAALTITSALFIGLNKIRLI
UniProt
Q9M3L0
Chains
Secondary structure
Ligand binding sites
Interaction interfaces
Sequence conservation

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Chains: F, N
Length: 131 amino acids
Theoretical weight: 12.95 KDa
Source organism: Spinacia oleracea
UniProt:
  • Canonical: A0A9R0IV89 (Residues: 1-131; Coverage: 100%)
Gene name: LOC110795548
Pfam: PetM family of cytochrome b6f complex subunit 7
PDBe-KB: UniProt Coverage View: A0A9R0IV89  
1131102030405060708090100110120130
 
50100MATAAASTTLSSAAVPAISGSRGQRKMNKVVYMSGVNSYGGLKANNAVLGLGQAVCTEQCFANVVSSLRSTATKKGRSGGGGGAGGGALTSTCNAAAEIFRIAAVMNGLTLVGVAIGFVLLRIEATVEEAE
UniProt
A0A9R0IV89
Chains
Secondary structure
Ligand binding sites
Interaction interfaces
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Chains: G, O
Length: 37 amino acids
Theoretical weight: 4.17 KDa
Source organism: Spinacia oleracea
UniProt:
  • Canonical: P69461 (Residues: 1-37; Coverage: 100%)
Gene names: petE, petG
Pfam: Cytochrome B6-F complex subunit 5
PDBe-KB: UniProt Coverage View: P69461  
1375101520253035
 
102030MIEVFLFGIVLGLIPITLAGLFVTAYLQYRRGDQLDL
UniProt
P69461
Chains
Secondary structure
Ligand binding sites
Interaction interfaces
Sequence conservation

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Chains: H, P
Length: 29 amino acids
Theoretical weight: 3.17 KDa
Source organism: Spinacia oleracea
UniProt:
  • Canonical: P61045 (Residues: 1-29; Coverage: 100%)
Gene names: petN, ycf6
Pfam: PetN
PDBe-KB: UniProt Coverage View: P61045  
129246810121416182022242628
 
102030MDIVSLAWAALMVVFTFSLSLVVWGRSGL
UniProt
P61045
Chains
Secondary structure
Ligand binding sites
Interaction interfaces
Sequence conservation

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Chains: Q, R
Length: 103 amino acids
Theoretical weight: 10.61 KDa
Source organism: Spinacia oleracea
UniProt:
  • Canonical: Q8GT36 (Residues: 1-103; Coverage: 100%)
Gene name: tsp9
Pfam: Thylakoid soluble phosphoprotein TSP9
PDBe-KB: UniProt Coverage View: Q8GT36  
1103102030405060708090100
 
50100MSSLPFVFGAAASSRVVTAAAAKGTAETKQEKSFVDWLLGKITKEDQFYETDPILRGGDVKSSGSTSGKKGGTTSGKKGTVSIPSKKKNGNGGVFGGLFAKKD
UniProt
Q8GT36
Chains
Secondary structure
Flexibility predictions
Ligand binding sites
Interaction interfaces
Sequence conservation

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