4XK8 Photosynthesis date Jan 10, 2015
title Crystal Structure Of Plant Photosystem I-Lhci Super-Complex Angstrom Resolution
authors M.Suga, X.Qin, T.Kuang, J.R.Shen
compound source
Molecule: Photosystem I P700 Chlorophyll A Apoprotein A1
Chain: A, a
Synonym: Psi-A,Psaa
Organism_scientific: Pisum Sativum
Organism_common: Garden Pea
Organism_taxid: 3888

Molecule: Photosystem I P700 Chlorophyll A Apoprotein A2
Chain: B, b
Synonym: Psi-B,Psab

Organism_scientific: Pisum Sativum
Organism_common: Garden Pea
Organism_taxid: 3888

Molecule: Photosystem I Iron-Sulfur Center
Chain: C, c
Fragment: Unp Residues 2-81
Synonym: 9 Kda Polypeptide,Psi-C,Photosystem I Subunit Vii,
Ec: 1.97.1.12

Organism_scientific: Pisum Sativum
Organism_common: Garden Pea
Organism_taxid: 3888

Molecule: Uncharacterized Protein
Chain: D, d
Fragment: Unp Residues 63-203

Organism_scientific: Glycine Max
Organism_common: Soybean
Organism_taxid: 3847

Molecule: Putative Uncharacterized Protein
Chain: E, e

Organism_scientific: Pisum Sativum
Organism_common: Garden Pea
Organism_taxid: 3888

Molecule: Photosystem I Reaction Center Subunit III, Chloro
Chain: F, f
Synonym: Light-Harvesting Complex I 17 Kda Protein,Psi-F

Organism_scientific: Spinacia Oleracea
Organism_common: Spinach
Organism_taxid: 3562

Molecule: Photosystem I Reaction Center Subunit V, Chloropl
Chain: G, g
Synonym: Psi-G,Photosystem I 9 Kda Protein

Organism_scientific: Spinacia Oleracea
Organism_common: Spinach
Organism_taxid: 3562

Molecule: Putative Uncharacterized Protein
Chain: H, h

Organism_scientific: Glycine Max
Organism_common: Soybean
Organism_taxid: 3847

Molecule: Photosystem I Reaction Center Subunit Viii
Chain: I, I
Fragment: Unp Residues 2-31
Synonym: Psi-I

Organism_scientific: Pisum Sativum
Organism_common: Garden Pea
Organism_taxid: 3888

Molecule: Photosystem I Reaction Center Subunit Ix
Chain: J, j
Fragment: Unp Residues 1-39
Synonym: Psi-J

Organism_scientific: Phaseolus Vulgaris
Organism_common: Kidney Bean
Organism_taxid: 3885

Molecule: Photosystem I Reaction Center Subunit X Psak
Chain: K, k

Organism_scientific: Pisum Sativum
Organism_common: Garden Pea
Organism_taxid: 3888

Molecule: Putative Uncharacterized Protein
Chain: L, l
Fragment: Unp Residues 4-156

Organism_scientific: Pisum Sativum
Organism_common: Garden Pea
Organism_taxid: 3888

Molecule: Chlorophyll A-B Binding Protein 6, Chloroplastic
Chain: 1, 6
Synonym: Lhci-730,Lhcii Type III Cab-6,Light-Harvesting Com Protein Lhca1;

Organism_scientific: Arabidopsis Thaliana
Organism_common: Mouse-Ear Cress
Organism_taxid: 3702

Molecule: Type II Chlorophyll Ab Binding Protein From Phot
Chain: 2, 7
Fragment: Unp Residues 62-267

Organism_scientific: Pisum Sativum
Organism_common: Garden Pea
Organism_taxid: 3888

Molecule: Chlorophyll A-B Binding Protein 3, Chloroplastic
Chain: 3, 8
Fragment: Unp Residues 55-272
Synonym: Lhcii Type III Cab-3

Organism_scientific: Pisum Sativum
Organism_common: Garden Pea
Organism_taxid: 3888

Molecule: Chlorophyll A-B Binding Protein P4, Chloroplastic
Chain: 4, 9
Synonym: Lhci Type III Cab-P4

Organism_scientific: Pisum Sativum
Organism_common: Garden Pea
Organism_taxid: 3888
symmetry Space Group: P 1 21 1
R_factor 0.211 R_Free 0.248
crystal
cell
length a length b length c angle alpha angle beta angle gamma
165.624 192.220 175.089 90.00 91.41 90.00
method X-Ray Diffractionresolution 2.80 Å
ligand BCR, CHL, CLA, DGD, HTG, LHG, LMG, LMT, LUT, PQN, SF4, XAT enzyme Oxidoreductase E.C.1.97.1.12 BRENDA
subcellular loc. Membrane localization by OPM: Thylakoid membrane
thylakoid space side
stroma side
Gene
Ontology
ChainFunctionProcessComponent
7, 2, 1, 6, 3, 9, 8, 4


A


B


C


D


E


F


G


H


I


J


K


L


a, b


c


l


Primary referencePhotosynthesis. Structural basis for energy transfer pathways in the plant PSI-LHCI supercomplex., Qin X, Suga M, Kuang T, Shen JR, Science. 2015 May 29;348(6238):989-95. doi: 10.1126/science.aab0214. PMID:26023133
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (3146 Kb) [Save to disk]
  • Biological Unit Coordinates (4xk8.pdb1.gz) 1504 Kb
  • Biological Unit Coordinates (4xk8.pdb2.gz) 1500 Kb
  • LPC: Ligand-Protein Contacts for 4XK8
  • CSU: Contacts of Structural Units for 4XK8
  • Structure Factors (2765 Kb)
  • Retrieve 4XK8 in mmCIF format [Save to disk]
  • Re-refined 4xk8 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4XK8 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 4XK8
  • Cartoon representation from PDB Cartoon
  • 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
  • Crystal Contacts, from CryCo at Weizmann Institute
  • 3D motif for 4XK8, from MSDmotif at EBI
  • Fold representative 4xk8 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4xk8_D] [4xk8_3] [4xk8_G] [4xk8_I] [4xk8_J] [4xk8_e] [4xk8_8] [4xk8_b] [4xk8_9] [4xk8_d] [4xk8_c] [4xk8_F] [4xk8_1] [4xk8_4] [4xk8_a] [4xk8_7] [4xk8_K] [4xk8_h] [4xk8_f] [4xk8_g] [4xk8] [4xk8_H] [4xk8_E] [4xk8_6] [4xk8_A] [4xk8_C] [4xk8_k] [4xk8_l] [4xk8_B] [4xk8_2] [4xk8_i] [4xk8_j] [4xk8_L]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 4XK8
  • Community annotation for 4XK8 at PDBWiki (http://pdbwiki.org)

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