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Cryo-EM Structure of PSII at 2.08 angstrom resolution

Electron Microscopy
2.08Å resolution
PDB entry 7d1u coloured by chain, front view.
PDB entry 7d1u coloured by chain, side view.
PDB entry 7d1u coloured by chain, top view.
Source organism: Thermostichus vulcanus
Assembly composition:
hetero 40-mer (preferred)
Entry contents: 20 distinct polypeptide molecules

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Assemblies

Assembly 1 (preferred)
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Assembly Name: Photosystem II
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Multimeric state: hetero 40-mer
PDBe Complex ID: PDB-CPX-112071

Macromolecules

Photosystem II protein D1
Chains: A, a
Length: 334 amino acids
Theoretical weight: 37.03 KDa
Source organism: Thermostichus vulcanus
UniProt:
  • Canonical: P51765 (Residues: 11-344; Coverage: 93%)
Gene names: psbA, psbA-1
Pfam: Photosynthetic reaction centre protein
InterPro:
Photosystem II protein D1 in PDB entry 7d1u, assembly 1, front view.
Photosystem II protein D1 in PDB entry 7d1u, assembly 1, side view.
Photosystem II protein D1 in PDB entry 7d1u, assembly 1, top view.
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Photosystem II CP47 reaction center protein
Chains: B, b
Length: 505 amino acids
Theoretical weight: 56.07 KDa
Source organism: Thermostichus vulcanus
UniProt:
  • Canonical: D0VWR1 (Residues: 1-505; Coverage: 100%)
Gene name: psbB
Pfam: Photosystem II protein
InterPro:
Photosystem II CP47 reaction center protein in PDB entry 7d1u, assembly 1, front view.
Photosystem II CP47 reaction center protein in PDB entry 7d1u, assembly 1, side view.
Photosystem II CP47 reaction center protein in PDB entry 7d1u, assembly 1, top view.
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Photosystem II CP43 reaction center protein
Chains: C, c
Length: 451 amino acids
Theoretical weight: 49.21 KDa
Source organism: Thermostichus vulcanus
UniProt:
  • Canonical: D0VWR7 (Residues: 1-451; Coverage: 100%)
Gene name: psbC
Pfam: Photosystem II protein
InterPro:
Photosystem II CP43 reaction center protein in PDB entry 7d1u, assembly 1, front view.
Photosystem II CP43 reaction center protein in PDB entry 7d1u, assembly 1, side view.
Photosystem II CP43 reaction center protein in PDB entry 7d1u, assembly 1, top view.
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Photosystem II D2 protein
Chains: D, d
Length: 342 amino acids
Theoretical weight: 38.42 KDa
Source organism: Thermostichus vulcanus
UniProt:
  • Canonical: D0VWR8 (Residues: 1-342; Coverage: 100%)
Gene name: psbD
Pfam: Photosynthetic reaction centre protein
InterPro:
Photosystem II D2 protein in PDB entry 7d1u, assembly 1, front view.
Photosystem II D2 protein in PDB entry 7d1u, assembly 1, side view.
Photosystem II D2 protein in PDB entry 7d1u, assembly 1, top view.
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Cytochrome b559 subunit alpha
Chains: E, e
Length: 81 amino acids
Theoretical weight: 9.32 KDa
Source organism: Thermostichus vulcanus
UniProt:
  • Canonical: P12238 (Residues: 4-84; Coverage: 96%)
Gene name: psbE
Pfam:
InterPro:
Cytochrome b559 subunit alpha in PDB entry 7d1u, assembly 1, front view.
Cytochrome b559 subunit alpha in PDB entry 7d1u, assembly 1, side view.
Cytochrome b559 subunit alpha in PDB entry 7d1u, assembly 1, top view.
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Cytochrome b559 subunit beta
Chains: F, f
Length: 34 amino acids
Theoretical weight: 3.87 KDa
Source organism: Thermostichus vulcanus
UniProt:
  • Canonical: P12239 (Residues: 12-45; Coverage: 76%)
Gene name: psbF
Pfam: Cytochrome b559, alpha (gene psbE) and beta (gene psbF)subunits
InterPro:
Cytochrome b559 subunit beta in PDB entry 7d1u, assembly 1, front view.
Cytochrome b559 subunit beta in PDB entry 7d1u, assembly 1, side view.
Cytochrome b559 subunit beta in PDB entry 7d1u, assembly 1, top view.
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Photosystem II reaction center protein H
Chains: H, h
Length: 63 amino acids
Theoretical weight: 7.06 KDa
Source organism: Thermostichus vulcanus
UniProt:
  • Canonical: P19052 (Residues: 1-63; Coverage: 97%)
Gene name: psbH
Pfam: Photosystem II 10 kDa phosphoprotein
InterPro:
Photosystem II reaction center protein H in PDB entry 7d1u, assembly 1, front view.
Photosystem II reaction center protein H in PDB entry 7d1u, assembly 1, side view.
Photosystem II reaction center protein H in PDB entry 7d1u, assembly 1, top view.
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Photosystem II reaction center protein I
Chains: I, i
Length: 36 amino acids
Theoretical weight: 4.2 KDa
Source organism: Thermostichus vulcanus
UniProt:
  • Canonical: P12240 (Residues: 1-36; Coverage: 95%)
Gene name: psbI
Pfam: Photosystem II reaction centre I protein (PSII 4.8 kDa protein)
InterPro:
Photosystem II reaction center protein I in PDB entry 7d1u, assembly 1, front view.
Photosystem II reaction center protein I in PDB entry 7d1u, assembly 1, side view.
Photosystem II reaction center protein I in PDB entry 7d1u, assembly 1, top view.
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Photosystem II reaction center protein J
Chains: J, j
Length: 37 amino acids
Theoretical weight: 3.76 KDa
Source organism: Thermostichus vulcanus
UniProt:
  • Canonical: Q7DGD4 (Residues: 4-40; Coverage: 93%)
Gene name: psbJ
Pfam: PsbJ
InterPro:
Photosystem II reaction center protein J in PDB entry 7d1u, assembly 1, front view.
Photosystem II reaction center protein J in PDB entry 7d1u, assembly 1, side view.
Photosystem II reaction center protein J in PDB entry 7d1u, assembly 1, top view.
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Photosystem II reaction center protein K
Chains: K, k
Length: 37 amino acids
Theoretical weight: 4.1 KDa
Source organism: Thermostichus vulcanus
UniProt:
  • Canonical: P19054 (Residues: 1-37; Coverage: 100%)
Gene name: psbK
Pfam: Photosystem II 4 kDa reaction centre component
InterPro:
Photosystem II reaction center protein K in PDB entry 7d1u, assembly 1, front view.
Photosystem II reaction center protein K in PDB entry 7d1u, assembly 1, side view.
Photosystem II reaction center protein K in PDB entry 7d1u, assembly 1, top view.
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Photosystem II reaction center protein L
Chains: L, l
Length: 37 amino acids
Theoretical weight: 4.3 KDa
Source organism: Thermostichus vulcanus
UniProt:
  • Canonical: P12241 (Residues: 1-37; Coverage: 100%)
Gene name: psbL
Pfam: PsbL protein
InterPro:
Photosystem II reaction center protein L in PDB entry 7d1u, assembly 1, front view.
Photosystem II reaction center protein L in PDB entry 7d1u, assembly 1, side view.
Photosystem II reaction center protein L in PDB entry 7d1u, assembly 1, top view.
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Photosystem II reaction center protein M
Chains: M, m
Length: 34 amino acids
Theoretical weight: 3.84 KDa
Source organism: Thermostichus vulcanus
UniProt:
  • Canonical: P12312 (Residues: 1-34; Coverage: 94%)
Gene name: psbM
Pfam: Photosystem II reaction centre M protein (PsbM)
InterPro:
Photosystem II reaction center protein M in PDB entry 7d1u, assembly 1, front view.
Photosystem II reaction center protein M in PDB entry 7d1u, assembly 1, side view.
Photosystem II reaction center protein M in PDB entry 7d1u, assembly 1, top view.
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Photosystem II extrinsic protein O
Chains: O, o
Length: 244 amino acids
Theoretical weight: 26.65 KDa
Source organism: Thermostichus vulcanus
UniProt:
  • Canonical: D0VWR2 (Residues: 1-244; Coverage: 100%)
Gene name: psbO
Pfam: Manganese-stabilising protein / photosystem II polypeptide
InterPro:
Photosystem II manganese-stabilizing polypeptide in PDB entry 7d1u, assembly 1, front view.
Photosystem II manganese-stabilizing polypeptide in PDB entry 7d1u, assembly 1, side view.
Photosystem II manganese-stabilizing polypeptide in PDB entry 7d1u, assembly 1, top view.
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Photosystem II reaction center protein T
Chains: T, t
Length: 31 amino acids
Theoretical weight: 3.78 KDa
Source organism: Thermostichus vulcanus
UniProt:
  • Canonical: P12313 (Residues: 1-31; Coverage: 97%)
Gene name: psbT
Pfam: Photosystem II reaction centre T protein
InterPro:
Photosystem II reaction center protein T in PDB entry 7d1u, assembly 1, front view.
Photosystem II reaction center protein T in PDB entry 7d1u, assembly 1, side view.
Photosystem II reaction center protein T in PDB entry 7d1u, assembly 1, top view.
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Photosystem II extrinsic protein U
Chains: U, u
Length: 97 amino acids
Theoretical weight: 10.97 KDa
Source organism: Thermostichus vulcanus
UniProt:
  • Canonical: P56152 (Residues: 8-104; Coverage: 93%)
Gene name: psbU
Pfam: Photosystem II 12 kDa extrinsic protein (PsbU)
InterPro: Photosystem II PsbU, oxygen evolving complex
Photosystem II 12 kDa extrinsic protein in PDB entry 7d1u, assembly 1, front view.
Photosystem II 12 kDa extrinsic protein in PDB entry 7d1u, assembly 1, side view.
Photosystem II 12 kDa extrinsic protein in PDB entry 7d1u, assembly 1, top view.
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Photosystem II extrinsic protein V
Chains: V, v
Length: 137 amino acids
Theoretical weight: 15.15 KDa
Source organism: Thermostichus vulcanus
UniProt:
  • Canonical: P0A387 (Residues: 27-163; Coverage: 100%)
Gene name: psbV
Pfam: Cytochrome c-550 domain
InterPro:
Cytochrome c-550 in PDB entry 7d1u, assembly 1, front view.
Cytochrome c-550 in PDB entry 7d1u, assembly 1, side view.
Cytochrome c-550 in PDB entry 7d1u, assembly 1, top view.
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Photosystem II reaction center protein Psb30
Chains: Y, y
Length: 30 amino acids
Theoretical weight: 3.23 KDa
Source organism: Thermostichus vulcanus
UniProt:
  • Canonical: D0VWR3 (Residues: 1-30; Coverage: 100%)
Gene names: psb30, psbY, ycf12
Pfam: Photosystem II complex subunit Ycf12
InterPro: Photosystem II reaction center protein Ycf12
Photosystem II reaction center protein Ycf12 in PDB entry 7d1u, assembly 1, front view.
Photosystem II reaction center protein Ycf12 in PDB entry 7d1u, assembly 1, side view.
Photosystem II reaction center protein Ycf12 in PDB entry 7d1u, assembly 1, top view.
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Photosystem II reaction center protein X
Chains: X, x
Length: 40 amino acids
Theoretical weight: 4.19 KDa
Source organism: Thermostichus vulcanus
UniProt:
  • Canonical: D0VWR4 (Residues: 1-40; Coverage: 100%)
Gene name: psbX
Pfam: Photosystem II reaction centre X protein (PsbX)
InterPro:
Photosystem II reaction center protein X in PDB entry 7d1u, assembly 1, front view.
Photosystem II reaction center protein X in PDB entry 7d1u, assembly 1, side view.
Photosystem II reaction center protein X in PDB entry 7d1u, assembly 1, top view.
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Photosystem II reaction center protein Z
Chains: Z, z
Length: 62 amino acids
Theoretical weight: 6.77 KDa
Source organism: Thermostichus vulcanus
UniProt:
  • Canonical: D0VWR5 (Residues: 1-62; Coverage: 100%)
Gene name: psbZ
Pfam: YCF9
InterPro:
Photosystem II reaction center protein Z in PDB entry 7d1u, assembly 1, front view.
Photosystem II reaction center protein Z in PDB entry 7d1u, assembly 1, side view.
Photosystem II reaction center protein Z in PDB entry 7d1u, assembly 1, top view.
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Photosystem II reaction center protein Y
Chains: R, r
Length: 34 amino acids
Theoretical weight: 3.86 KDa
Source organism: Thermostichus vulcanus
UniProt:
  • Canonical: P0DM37 (Residues: 1-34; Coverage: 100%)
Gene name: psbY
Pfam: Photosystem II protein Y (PsbY)
InterPro: Photosystem II PsbY
Photosystem II protein Y in PDB entry 7d1u, assembly 1, front view.
Photosystem II protein Y in PDB entry 7d1u, assembly 1, side view.
Photosystem II protein Y in PDB entry 7d1u, assembly 1, top view.
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