5YQ7 Photosynthesis date Nov 05, 2017
title Cryo-Em Structure Of The Rc-Lh Core Complex From Roseiflexus Castenholzii
authors Y.Shi, Y.Y.Xin, T.X.Niu, Q.Q.Wang, W.Q.Niu, X.J.Huang, W.Ding, R.E.Blankenship, X.L.Xu, F.Sun
compound source
Molecule: Beta Subunit Of Light-Harvesting 1
Chain: E, B, 0, 8, 6, 4, 2, K, I, G, W, U, S, Q, O
 Organism_scientific: Roseiflexus Castenholzii
Organism_taxid: 120962

Molecule: Precursor For L Subunits Of Photosynthetic Reacti
Chain: L
Organism_scientific: Roseiflexus Castenholzii
Organism_taxid: 120962

Molecule: Cytochrome Subunit Of Photosynthetic Reaction Cen
Chain: C
Organism_scientific: Roseiflexus Castenholzii
Organism_taxid: 120962

Molecule: Alpha Subunit Of Light-Harvesting 1
Chain: T, V, R, P, N, J, H, F, D, A, 9, 7, 5, 3, 1
Organism_scientific: Roseiflexus Castenholzii
Organism_taxid: 120962

Molecule: Peptide From Precursor For L And M Subunits Of Photosynthetic Reaction Center;
Chain: Y
Other_details: The Peptide Could Be Either An Unidentified Product Or A Proteolytic Fragment Of The Puflm Gene Product Cleaved Twice During Processing.;
Organism_scientific: Roseiflexus Castenholzii
Organism_taxid: 120962

Molecule: Subunit X
Chain: X
Other_details: Subunit X With Its Flexible Transmembrane He Flanking The Gap Of Light Harvesting Complex.;
Organism_scientific: Roseiflexus Castenholzii
Organism_taxid: 120962

Molecule: Precursor For M Subunits Of Photosynthetic Reacti
Chain: M
Organism_scientific: Roseiflexus Castenholzii
Organism_taxid: 120962
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 4.10 Å
ligand BCL, BPH, FE, HEM, KGD, MQE enzyme
Gene
Ontology
ChainFunctionProcessComponent
C
  • electron transfer activity


    • F, T, N, 7, V, 1, A, J, 3, P, 9, H, D, R, 5
  • electron transporter, transf...


    • L


    M


    S, K, E, 2, Q, 0, 6, O, W, B, 8, 4, I, G, U
  • electron transporter, transf...


    • Primary referenceCryo-EM structure of the RC-LH core complex from an early branching photosynthetic prokaryote., Xin Y, Shi Y, Niu T, Wang Q, Niu W, Huang X, Ding W, Yang L, Blankenship RE, Xu X, Sun F, Nat Commun. 2018 Apr 19;9(1):1568. doi: 10.1038/s41467-018-03881-x. PMID:29674684
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (403 Kb) [Save to disk]
  • Biological Unit Coordinates (5yq7.pdb1.gz) 362 Kb
  • LPC: Ligand-Protein Contacts for 5YQ7
  • CSU: Contacts of Structural Units for 5YQ7
  • Retrieve 5YQ7 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5YQ7 from S2C, [Save to disk]
    • View 5YQ7 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 5YQ7
  • 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: [5yq7_W] [5yq7_3] [5yq7_L] [5yq7_E] [5yq7_1] [5yq7_P] [5yq7_R] [5yq7_O] [5yq7_B] [5yq7_5] [5yq7_K] [5yq7_M] [5yq7_N] [5yq7_6] [5yq7_G] [5yq7_0] [5yq7_H] [5yq7_A] [5yq7_T] [5yq7_9] [5yq7_J] [5yq7_F] [5yq7_4] [5yq7_D] [5yq7_Y] [5yq7_S] [5yq7_8] [5yq7_C] [5yq7_U] [5yq7_V] [5yq7_Q] [5yq7_2] [5yq7_7] [5yq7_X] [5yq7_I]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
    • Other resources with information on 5YQ7
  • Community annotation for 5YQ7 at PDBWiki (http://pdbwiki.org)

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