5Y5S Photosynthesis date Aug 09, 2017
title Structure Of Photosynthetic Lh1-Rc Super-Complex At 1.9 Angs Resolution
authors L.J.Yu, M.Suga, Z.Y.Wang-Otomo, J.R.Shen
compound source
Molecule: Photosynthetic Reaction Center Cytochrome C Subun
Chain: C
 Organism_scientific: Thermochromatium Tepidum
Organism_taxid: 1050

Molecule: Photosynthetic Reaction Center L Subunit
Chain: L
Organism_scientific: Thermochromatium Tepidum
Organism_taxid: 1050

Molecule: Photosynthetic Reaction Center M Subunit
Chain: M
Organism_scientific: Thermochromatium Tepidum
Organism_taxid: 1050

Molecule: Photosynthetic Reaction Center H Subunit
Chain: H
Organism_scientific: Thermochromatium Tepidum
Organism_taxid: 1050

Molecule: Lh1 Alpha Polypeptide
Chain: A, D, F, I, K, O, Q, S, U, W, Y, 1, 3, 5, 7, 9
Organism_scientific: Thermochromatium Tepidum
Organism_taxid: 1050

Molecule: Lh1 Beta Polypeptide
Chain: B, E, G, J, N, P, R, T, V, X, Z, 2, 4, 6, 8, 0
Organism_scientific: Thermochromatium Tepidum
Organism_taxid: 1050
symmetry Space Group: C 1 2 1
R_factor 0.181 R_Free 0.215
crystal
cell
length a length b length c angle alpha angle beta angle gamma
145.280 143.810 210.280 90.00 90.74 90.00
method X-Ray Diffractionresolution 1.90 Å
ligand BCL, BPH, CA, CDL, CRT, FE, GOL, HEC, LDA, LHG, LMT, MG, MQ8, PEF, PGV, SO4, UNL, UQ8 enzyme
Gene
Ontology
ChainFunctionProcessComponent
C


H
  • electron transporter, transf...


    • L


    M


    S, K, 7, Y, 1, W, D, I, U, F, Q, A, O, 3, 9, 5
  • electron transporter, transf...


    • T, N, E, 2, Z, J, B, G, V, 0, 6, X, P, 8, 4, R
  • electron transporter, transf...


    • Primary referenceStructure of photosynthetic LH1-RC supercomplex at 1.9 A resolution., Yu LJ, Suga M, Wang-Otomo ZY, Shen JR, Nature. 2018 Apr;556(7700):209-213. doi: 10.1038/s41586-018-0002-9. Epub 2018 Apr, 4. PMID:29618814
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (1197 Kb) [Save to disk]
  • Biological Unit Coordinates (5y5s.pdb1.gz) 1154 Kb
  • LPC: Ligand-Protein Contacts for 5Y5S
  • CSU: Contacts of Structural Units for 5Y5S
  • Structure Factors (7107 Kb)
  • Retrieve 5Y5S in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5Y5S from S2C, [Save to disk]
    • View 5Y5S 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 5Y5S
  • 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: [5y5s_W] [5y5s_8] [5y5s_A] [5y5s_K] [5y5s_O] [5y5s_H] [5y5s_0] [5y5s_Q] [5y5s_6] [5y5s_Y] [5y5s_X] [5y5s_E] [5y5s_Z] [5y5s_V] [5y5s_M] [5y5s_S] [5y5s_T] [5y5s_3] [5y5s_F] [5y5s_R] [5y5s_U] [5y5s_B] [5y5s_7] [5y5s_2] [5y5s_P] [5y5s_C] [5y5s_I] [5y5s_9] [5y5s_4] [5y5s_G] [5y5s_L] [5y5s_J] [5y5s_1] [5y5s_D] [5y5s_5] [5y5s_N]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
    • Other resources with information on 5Y5S
  • Community annotation for 5Y5S at PDBWiki (http://pdbwiki.org)

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