1IZL

Crystal Structure of Photosystem II


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.7 Å
  • R-Value Work: 0.530 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Crystal structure of oxygen-evolving photosystem II from Thermosynechococcus vulcanus at 3.7-A resolution

Kamiya, N.Shen, J.-R.

(2003) Proc.Natl.Acad.Sci.USA 100: 98-103

  • DOI: 10.1073/pnas.0135651100

  • PubMed Abstract: 
  • Photosystem II (PSII) is a multisubunit membrane protein complex performing light-induced electron transfer and water-splitting reactions, leading to the formation of molecular oxygen. The first crystal structure of PSII from a thermophilic cyanobact ...

    Photosystem II (PSII) is a multisubunit membrane protein complex performing light-induced electron transfer and water-splitting reactions, leading to the formation of molecular oxygen. The first crystal structure of PSII from a thermophilic cyanobacterium Thermosynechococcus elongatus was reported recently [Zouni, A., Witt, H. T., Kern, J., Fromme, P., Krauss, N., Saenger, W. & Orth, P. (2001) Nature 409, 739-743)] at 3.8-A resolution. To analyze the PSII structure in more detail, we have obtained the crystal structure of PSII from another thermophilic cyanobacterium, Thermosynechococcus vulcanus, at 3.7-A resolution. The present structure was built on the basis of the sequences of PSII large subunits D1, D2, CP47, and CP43; extrinsic 33- and 12-kDa proteins and cytochrome c550; and several low molecular mass subunits, among which the structure of the 12-kDa protein was not reported previously. This yielded much information concerning the molecular interactions within this large protein complex. We also show the arrangement of chlorophylls and cofactors, including two beta-carotenes recently identified in a region close to the reaction center, which provided important clues to the secondary electron transfer pathways around the reaction center. Furthermore, possible ligands for the Mn-cluster were determined. In particular, the C terminus of D1 polypeptide was shown to be connected to the Mn cluster directly. The structural information obtained here provides important insights into the mechanism of PSII reactions.


    Organizational Affiliation

    RIKEN Harima InstituteSPring-8, Kouto 1-1-1, Mikazuki-cho, Sayou-gun, Hyogo 679-5148, Japan. nkamiya@sp8sun.spring8.or.jp




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Photosystem II: Subunit PsbA
A, J
360Thermosynechococcus vulcanusGene Names: psbA (psbA-1)
EC: 1.10.3.9
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Photosystems
Protein: 
Photosystem II
Find proteins for P51765 (Thermosynechococcus vulcanus)
Go to UniProtKB:  P51765
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Photosystem II: Subunit PsbB
B, L
472Thermosynechococcus elongatus (strain BP-1)Gene Names: psbB
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Photosystems
Protein: 
Photosystem II
Find proteins for Q8DIQ1 (Thermosynechococcus elongatus (strain BP-1))
Go to UniProtKB:  Q8DIQ1
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Photosystem II: Subunit PsbC
C, M
473Thermosynechococcus elongatus (strain BP-1)Gene Names: psbC
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Photosystems
Protein: 
Photosystem II
Find proteins for Q8DIF8 (Thermosynechococcus elongatus (strain BP-1))
Go to UniProtKB:  Q8DIF8
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Photosystem II: Subunit PsbD
D, N
352Thermosynechococcus elongatus (strain BP-1)Gene Names: psbD1, psbD2
EC: 1.10.3.9
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Photosystems
Protein: 
Photosystem II
Find proteins for Q8CM25 (Thermosynechococcus elongatus (strain BP-1))
Go to UniProtKB:  Q8CM25
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
Photosystem II: Subunit PsbE
E, P
83Thermosynechococcus elongatus (strain BP-1)Gene Names: psbE
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Photosystems
Protein: 
Photosystem II
Find proteins for Q8DIP0 (Thermosynechococcus elongatus (strain BP-1))
Go to UniProtKB:  Q8DIP0
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
Photosystem II: Subunit PsbF
F, Q
44Thermosynechococcus elongatus (strain BP-1)Gene Names: psbF
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Photosystems
Protein: 
Photosystem II
Find proteins for Q8DIN9 (Thermosynechococcus elongatus (strain BP-1))
Go to UniProtKB:  Q8DIN9
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
Photosystem II: Subunit PsbG
G, R
220N/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
Photosystem II: Subunit PsbH
H, S
33N/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
Photosystem II: Subunit PsbI
I, T
26N/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
Photosystem II: Subunit PsbK
K, W
37Thermosynechococcus elongatus (strain BP-1)Gene Names: psbK
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Photosystems
Protein: 
Photosystem II
Find proteins for Q9F1K9 (Thermosynechococcus elongatus (strain BP-1))
Go to UniProtKB:  Q9F1K9
Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
Photosystem II: Subunit PsbO
O, Y
205N/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
Photosystem II: Subunit PsbU
U, Z
97N/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
Photosystem II: Subunit PsbV
V, 0
137Thermosynechococcus vulcanusGene Names: psbV
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Photosystems
Protein: 
Photosystem II
Find proteins for P0A387 (Thermosynechococcus vulcanus)
Go to UniProtKB:  P0A387
Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
Photosystem II: Subunit PsbX
X, 1
25N/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 7 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MN
Query on MN

Download SDF File 
Download CCD File 
A, J
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
CLA
Query on CLA

Download SDF File 
Download CCD File 
A, B, C, D, G, J, L, M, N, R, W
CHLOROPHYLL A
C55 H72 Mg N4 O5
VIQFHHZSLDFWDU-AENOIHSZSA-M
 Ligand Interaction
PLA
Query on PLA

Download SDF File 
Download CCD File 
D, N
2-[(3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YLMETHYL)-AMINO]-2-METHYL-SUCCINIC ACID
N-PYRIDOXYL-2-METHYLASPARTIC ACID-5-MONOPHOSPHATE
C13 H19 N2 O9 P
ZFKRUCNEKPIDBK-ZDUSSCGKSA-N
 Ligand Interaction
HEM
Query on HEM

Download SDF File 
Download CCD File 
0, E, P, V
PROTOPORPHYRIN IX CONTAINING FE
HEME
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
FE
Query on FE

Download SDF File 
Download CCD File 
D, N
FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
 Ligand Interaction
BCR
Query on BCR

Download SDF File 
Download CCD File 
D, K
BETA-CAROTENE
C40 H56
OENHQHLEOONYIE-JLTXGRSLSA-N
 Ligand Interaction
PHO
Query on PHO

Download SDF File 
Download CCD File 
A, D, J, N
PHEOPHYTIN A
C55 H74 N4 O5
CQIKWXUXPNUNDV-RCBXBCQGSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
UNK
Query on UNK
1, B, C, G, H, I, L, M, O, R, S, T, U, X, Y, Z
L-PEPTIDE LINKINGC4 H9 N O2

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.7 Å
  • R-Value Work: 0.530 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 129.377α = 90.00
b = 225.192β = 90.00
c = 308.672γ = 90.00
Software Package:
Software NamePurpose
SHARPphasing
CCP4data scaling
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2003-01-14
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Source and taxonomy, Version format compliance
  • Version 1.3: 2012-11-28
    Type: Other