3WU2 Electron Transport, Photosynthesis date Apr 21, 2014
title Crystal Structure Analysis Of Photosystem II Complex
authors Y.Umena, K.Kawakami, J.R.Shen, N.Kamiya
compound source
Molecule: Photosystem Q(B) Protein
Chain: A, a
Synonym: 32 Kda Thylakoid Membrane Protein, Photosystem II D1;
 Organism_scientific: Thermosynechococcus Vulcanus
Organism_taxid: 32053

Molecule: Photosystem II Cp47 Chlorophyll Apoprotein
Chain: B, b
Synonym: Protein Cp-47
Organism_scientific: Thermosynechococcus Vulcanus
Organism_taxid: 32053

Molecule: Photosystem II 44 Kda Reaction Center Protein
Chain: C, c
Synonym: Psii 43 Kda Protein, Protein Cp-43, Protein P6
Organism_scientific: Thermosynechococcus Vulcanus
Organism_taxid: 32053

Molecule: Photosystem II D2 Protein
Chain: D, d
Synonym: Psii D2 Protein, Photosystem Q(A) Protein
Organism_scientific: Thermosynechococcus Vulcanus
Organism_taxid: 32053

Molecule: Cytochrome B559 Subunit Alpha
Chain: E, e
Synonym: Psii Reaction Center Subunit V
Organism_scientific: Thermosynechococcus Vulcanus
Organism_taxid: 32053

Molecule: Cytochrome B559 Subunit Beta
Chain: F, f
Synonym: Psii Reaction Center Subunit Vi
Organism_scientific: Thermosynechococcus Vulcanus
Organism_taxid: 32053

Molecule: Photosystem II Reaction Center Protein H
Chain: H, h
Synonym: Psii-H
Organism_scientific: Thermosynechococcus Vulcanus
Organism_taxid: 32053

Molecule: Photosystem II Reaction Center Protein I
Chain: I, I
Synonym: Psii-I, Psii 4.4 Kda Protein
Organism_scientific: Thermosynechococcus Vulcanus
Organism_taxid: 32053

Molecule: Photosystem II Reaction Center Protein J
Chain: J, j
Synonym: Psii-J
Organism_scientific: Thermosynechococcus Vulcanus
Organism_taxid: 32053

Molecule: Photosystem II Reaction Center Protein K
Chain: K, k
Synonym: Psii-K
Organism_scientific: Thermosynechococcus Vulcanus
Organism_taxid: 32053

Molecule: Photosystem II Reaction Center Protein L
Chain: L, l
Synonym: Psii-L, Psii 5 Kda Protein
Organism_scientific: Thermosynechococcus Vulcanus
Organism_taxid: 32053

Molecule: Photosystem II Reaction Center Protein M
Chain: M, m
Synonym: Psii-M
Organism_scientific: Thermosynechococcus Vulcanus
Organism_taxid: 32053

Molecule: Photosystem II Manganese-Stabilizing Polypeptide
Chain: O, o
Synonym: Msp
Organism_scientific: Thermosynechococcus Vulcanus
Organism_taxid: 32053

Molecule: Photosystem II Reaction Center Protein T
Chain: T, t
Synonym: Psii-T, Psii-Tc
Organism_scientific: Thermosynechococcus Vulcanus
Organism_taxid: 32053

Molecule: Photosystem II 12 Kda Extrinsic Protein
Chain: U, u
Synonym: Ps II Complex 12 Kda Extrinsic Protein, Psii-U
Organism_scientific: Thermosynechococcus Vulcanus
Organism_taxid: 32053

Molecule: Cytochrome C-550
Chain: V, v
Synonym: Cytochrome C550, Low-Potential Cytochrome C
Organism_scientific: Thermosynechococcus Vulcanus
Organism_taxid: 32053

Molecule: Photosystem II Reaction Center Protein Ycf12
Chain: Y, y
Organism_scientific: Thermosynechococcus Vulcanus
Organism_taxid: 32053

Molecule: Photosystem II Reaction Center Protein X
Chain: X, x
Organism_scientific: Thermosynechococcus Vulcanus
Organism_taxid: 32053

Molecule: Photosystem II Reaction Center Protein Z
Chain: Z, z
Synonym: Psii-Z
Organism_scientific: Thermosynechococcus Vulcanus
Organism_taxid: 32053
symmetry Space Group: P 21 21 21
R_factor 0.156 R_Free 0.194
crystal
cell
length a length b length c angle alpha angle beta angle gamma
122.190 228.510 286.400 90.00 90.00 90.00
method X-Ray Diffractionresolution 1.90 Å
ligand BCR, BCT, CA, CL, CLA, DGD, FE2, FME, GOL, HEM, HSK, HTG, LHG, LMG, LMT, MG, OEX, PHO, PL9, RRX, SO4, SQD, UNL enzyme
note 3WU2 supersedes 3ARC
Gene
Ontology
ChainFunctionProcessComponent
B, b


E, e


F, f


H, h


I, i


K, k


L, l


M, m


O, o
  • oxygen evolving activity


    • T, t


    Y, y


    Z, z


    a, A


    c, C


    d, D


    j, J


    u, U


    v, V


    x, X


    Primary referenceCrystal structure of oxygen-evolving photosystem II at a resolution of 1.9 A., Umena Y, Kawakami K, Shen JR, Kamiya N, Nature. 2011 May 5;473(7345):55-60. Epub 2011 Apr 17. PMID:21499260
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (1135 Kb) [Save to disk]
  • Biological Unit Coordinates (3wu2.pdb1.gz) 1062 Kb
  • LPC: Ligand-Protein Contacts for 3WU2
  • CSU: Contacts of Structural Units for 3WU2
  • Structure Factors (9312 Kb)
  • Retrieve 3WU2 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3WU2 from S2C, [Save to disk]
  • Re-refined 3wu2 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 3WU2 in 3D
  • Proteopedia, because life has more than 2D.
  • On Jmol, a nice Rasmol like molecule viewer. This is good for easiest viewing of basic structure.
  • On FirstGlance, an excellent tool for a guided tour on the structure components, by E. Martz.
    • Visual 3D analysis of 3WU2
  • Ramachandran plot from PDBSum
    • Structure-derived information
  • Electron Density related parameters from EDS Electron Density Server, at Upsala
  • Dipole moment, from Dipole Server at Weizmann Institute
  • 3D motif for 3WU2, from MSDmotif at EBI
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3wu2_E] [3wu2_l] [3wu2_B] [3wu2_u] [3wu2_Y] [3wu2_i] [3wu2_K] [3wu2_Z] [3wu2_v] [3wu2_D] [3wu2_a] [3wu2_e] [3wu2_M] [3wu2_z] [3wu2_A] [3wu2_c] [3wu2_h] [3wu2_C] [3wu2_o] [3wu2_F] [3wu2_m] [3wu2] [3wu2_U] [3wu2_x] [3wu2_V] [3wu2_L] [3wu2_k] [3wu2_I] [3wu2_O] [3wu2_f] [3wu2_j] [3wu2_d] [3wu2_T] [3wu2_t] [3wu2_X] [3wu2_J] [3wu2_H] [3wu2_y] [3wu2_b]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
    • Other resources with information on 3WU2
  • Community annotation for 3WU2 at PDBWiki (http://pdbwiki.org)

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