4UB6 Electron Transport, Photosynthesis date Aug 12, 2014
title Native Structure Of Photosystem II (Dataset-1) By A Femtosec Laser
authors M.Suga, F.Akita, K.Hirata, G.Ueno, H.Murakami, Y.Nakajima, T.Shimi K.Yamashita, M.Yamamoto, H.Ago, J.R.Shen
compound source
Molecule: Photosystem Q(B) Protein
Chain: A, a
Ec: 1.10.3.9
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

Organism_scientific: Thermosynechococcus Vulcanus
Organism_taxid: 32053

Molecule: Photosystem II D2 Protein
Chain: D, d
Synonym: Psii D2 Protein,Photosystem Q(A) Protein
Ec: 1.10.3.9

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

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

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-Tc

Organism_scientific: Thermosynechococcus Vulcanus
Organism_taxid: 32053

Molecule: Photosystem II 12 Kda Extrinsic Protein
Chain: U, 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

Molecule: Photosystem II Protein Y
Chain: R

Organism_scientific: Thermosynechococcus Vulcanus
Organism_taxid: 32053
symmetry Space Group: P 21 21 21
R_factor 0.198 R_Free 0.238
crystal
cell
length a length b length c angle alpha angle beta angle gamma
123.744 229.989 288.337 90.00 90.00 90.00
method X-Ray Diffractionresolution 1.95 Å
ligand BCR, BCT, CA, CL, CLA, DGD, FE2, FME, GOL, HEM, HTG, LHG, LMG, LMT, MG, OEX, PHO, PL9, SQD, UNL enzyme Oxidoreductase E.C.1.10.3.9 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A


B


C


D


E


F


H


I


J


K


L


M


O


R


T


U


V


X


Y


Z


a


c, b


d


e, f


j, y, k, t, z, x, h, i, m, l


o


u


v


Primary referenceNative structure of photosystem II at 1.95 A resolution viewed by femtosecond X-ray pulses., Suga M, Akita F, Hirata K, Ueno G, Murakami H, Nakajima Y, Shimizu T, Yamashita K, Yamamoto M, Ago H, Shen JR, Nature. 2015 Jan 1;517(7532):99-103. doi: 10.1038/nature13991. Epub 2014 Nov 26. PMID:25470056
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (2312 Kb) [Save to disk]
  • Biological Unit Coordinates (4ub6.pdb1.gz) 1139 Kb
  • Biological Unit Coordinates (4ub6.pdb2.gz) 1121 Kb
  • LPC: Ligand-Protein Contacts for 4UB6
  • CSU: Contacts of Structural Units for 4UB6
  • Structure Factors (7563 Kb)
  • Retrieve 4UB6 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4UB6 from S2C, [Save to disk]
  • Re-refined 4ub6 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4UB6 in 3D
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  • Visual 3D analysis of 4UB6
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  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • 3D motif for 4UB6, from MSDmotif at EBI
  • Fold representative 4ub6 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4ub6_K] [4ub6_H] [4ub6_t] [4ub6_J] [4ub6_L] [4ub6_o] [4ub6_e] [4ub6_I] [4ub6_f] [4ub6_R] [4ub6_k] [4ub6_h] [4ub6_U] [4ub6_j] [4ub6_A] [4ub6_y] [4ub6_E] [4ub6_x] [4ub6_d] [4ub6_b] [4ub6_Y] [4ub6_T] [4ub6_C] [4ub6_i] [4ub6_l] [4ub6] [4ub6_u] [4ub6_M] [4ub6_F] [4ub6_B] [4ub6_v] [4ub6_z] [4ub6_c] [4ub6_m] [4ub6_Z] [4ub6_a] [4ub6_O] [4ub6_X] [4ub6_D] [4ub6_V]
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  • Community annotation for 4UB6 at PDBWiki (http://pdbwiki.org)

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