5XNM Membrane Protein date May 23, 2017
title Structure Of Unstacked C2s2m2-Type Psii-Lhcii Supercomplex F Sativum
authors X.D.Su, J.Ma, X.P.Wei, P.Cao, D.J.Zhu, W.R.Chang, Z.F.Liu, X.Z.Zhan
compound source
Molecule: Chlorophyll A-B Binding Protein 8, Chloroplastic
Chain: 1, 2, G, N, Y, 5, 6, g, n, y
Fragment: Unp Residues 23-265
Synonym: Lhcii Type I Cab-8
 Organism_scientific: Pisum Sativum
Organism_common: Garden Pea
Organism_taxid: 3888

Molecule: Chlorophyll A-B Binding Protein, Chloroplastic
Chain: 3, 7
Fragment: Unp Residues 23-265
Organism_scientific: Pisum Sativum
Organism_common: Garden Pea
Organism_taxid: 3888

Molecule: Light Harvesting Chlorophyll Ab-Binding Protein Cp24;
Chain: 4, 8
Organism_scientific: Pisum Sativum
Organism_taxid: 3888

Molecule: Photosystem II Protein D1
Chain: A, a
Synonym: Psii D1 Protein,32 Kda Thylakoid Membrane Protein, Photosystem II Q(B) Protein;
Ec: 1.10.3.9
Organism_scientific: Pisum Sativum
Organism_common: Garden Pea
Organism_taxid: 3888

Molecule: Photosystem II Cp47 Reaction Center Protein
Chain: B, b
Synonym: Psii 47 Kda Protein,Protein Cp-47
Organism_scientific: Pisum Sativum
Organism_common: Garden Pea
Organism_taxid: 3888

Molecule: Photosystem II Cp43 Reaction Center Protein
Chain: C, c
Synonym: Psii 43 Kda Protein,Photosystem II 44 Kda Chloroph Apoprotein,Protein Cp-43;
Organism_scientific: Pisum Sativum
Organism_common: Garden Pea
Organism_taxid: 3888

Molecule: Photosystem II D2 Protein
Chain: D, d
Synonym: Psii D2 Protein,Photosystem Q(A) Protein
Ec: 1.10.3.9
Organism_scientific: Pisum Sativum
Organism_common: Garden Pea
Organism_taxid: 3888

Molecule: Cytochrome B559 Subunit Alpha
Chain: E, e
Synonym: Psii Reaction Center Subunit V
Organism_scientific: Pisum Sativum
Organism_common: Garden Pea
Organism_taxid: 3888

Molecule: Cytochrome B559 Subunit Beta, Psbf
Chain: F, f
Organism_scientific: Pisum Sativum
Organism_taxid: 3888

Molecule: Photosystem II Reaction Center Protein H
Chain: H, h
Synonym: Psii-H,Photosystem II 10 Kda Phosphoprotein,Photos Kda Phosphoprotein;
Organism_scientific: Pisum Sativum
Organism_common: Garden Pea
Organism_taxid: 3888

Molecule: Photosystem II Reaction Center Protein I, Psbi
Chain: I, I
Organism_scientific: Pisum Sativum
Organism_taxid: 3888

Molecule: Photosystem II Reaction Center Protein J
Chain: J, j
Synonym: Psii-J
Organism_scientific: Pisum Sativum
Organism_common: Garden Pea
Organism_taxid: 3888

Molecule: Photosystem II Reaction Center Protein K
Chain: K, k
Synonym: Psii-K
Organism_scientific: Pisum Sativum
Organism_common: Garden Pea
Organism_taxid: 3888

Molecule: Photosystem II Reaction Center Protein L
Chain: L, l
Synonym: Psii-L
Organism_scientific: Pisum Sativum
Organism_common: Garden Pea
Organism_taxid: 3888

Molecule: Photosystem II Reaction Center Protein M
Chain: M, m
Synonym: Psii-M
Organism_scientific: Pisum Sativum
Organism_common: Garden Pea
Organism_taxid: 3888

Molecule: Oxygen-Evolving Enhancer Protein 1, Chloroplastic
Chain: O, o
Fragment: Unp Residues 82-329
Synonym: Oee1,33 Kda Subunit Of Oxygen Evolving System Of P II,33 Kda Thylakoid Membrane Protein,Oec 33 Kda Subunit;
Organism_scientific: Pisum Sativum
Organism_common: Garden Pea
Organism_taxid: 3888

Molecule: Light Harvesting Chlorophyll Ab-Binding Protein Cp29;
Chain: R, r
Organism_scientific: Pisum Sativum
Organism_taxid: 3888

Molecule: Light Harvesting Chlorophyll Ab-Binding Protein Cp26;
Chain: S, s
Organism_scientific: Pisum Sativum
Organism_taxid: 3888

Molecule: Photosystem II Reaction Center Protein T
Chain: T, t
Synonym: Psii-T
Organism_scientific: Pisum Sativum
Organism_common: Garden Pea
Organism_taxid: 3888

Molecule: Photosystem II Luminal Extrinsic Protein Tn, Psbt
Chain: U, u
Organism_scientific: Pisum Sativum
Organism_taxid: 3888

Molecule: Photosystem II Reaction Center Protein W, Psbw
Chain: W, w
Organism_scientific: Pisum Sativum
Organism_taxid: 3888

Molecule: Photosystem II Reaction Center Protein X
Chain: X, x
Organism_scientific: Pisum Sativum
Organism_common: Garden Pea
Organism_taxid: 3888

Molecule: Photosystem II Reaction Center Protein Z
Chain: Z, z
Synonym: Psii-Z
Organism_scientific: Pisum Sativum
Organism_common: Garden Pea
Organism_taxid: 3888
symmetry Space Group: P 1
R_factor
R_Free
crystal
cell
length a length b length c angle alpha angle beta angle gamma
1.000 1.000 1.000 90.00 90.00 90.00
method Electron Microscopyresolution 3.20 Å
ligand BCR, BCT, CHL, CLA, DGD, FE2, HEM, LHG, LMG, LUT, NEX, OEX, PHO, PL9, SQD, XAT enzyme Oxidoreductase E.C.1.10.3.9 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
8, 4


B, b


E, e


F, f


H, h


I, i


K, k


L, l


M, m


N, Y, 2, y, 1, g, G, 6, n, 5


O, o


S, 7, s, r, 3, R


T, t


W, w


Z, z


a, A


c, C


d, D


j, J


x, X


Primary referenceStructure and assembly mechanism of plant C2S2M2-type PSII-LHCII supercomplex., Su X, Ma J, Wei X, Cao P, Zhu D, Chang W, Liu Z, Zhang X, Li M, Science. 2017 Aug 25;357(6353):815-820. doi: 10.1126/science.aan0327. PMID:28839073
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (2052 Kb) [Save to disk]
  • Biological Unit Coordinates (5xnm.pdb1.gz) 1845 Kb
  • LPC: Ligand-Protein Contacts for 5XNM
  • CSU: Contacts of Structural Units for 5XNM
  • Retrieve 5XNM in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5XNM from S2C, [Save to disk]
    • View 5XNM 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 5XNM
  • Ramachandran plot from PDBSum
    • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5xnm_2] [5xnm_U] [5xnm_J] [5xnm_b] [5xnm_s] [5xnm_k] [5xnm_N] [5xnm_5] [5xnm_h] [5xnm_r] [5xnm_Z] [5xnm_w] [5xnm_7] [5xnm_S] [5xnm_E] [5xnm_f] [5xnm_n] [5xnm_F] [5xnm_R] [5xnm_D] [5xnm_X] [5xnm_O] [5xnm_H] [5xnm_K] [5xnm_C] [5xnm_x] [5xnm_l] [5xnm_3] [5xnm_g] [5xnm_o] [5xnm_i] [5xnm_u] [5xnm_1] [5xnm_c] [5xnm_M] [5xnm_t] [5xnm_A] [5xnm_d] [5xnm_j] [5xnm_Y] [5xnm_y] [5xnm_a] [5xnm_B] [5xnm_W] [5xnm_4] [5xnm_T] [5xnm_L] [5xnm_6] [5xnm_z] [5xnm_e] [5xnm_8] [5xnm_m] [5xnm_G] [5xnm_I]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
    • Other resources with information on 5XNM
  • Community annotation for 5XNM at PDBWiki (http://pdbwiki.org)

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