3X3B Membrane Protein date Jan 18, 2015
title Crystal Structure Of The Light-Driven Sodium Pump Kr2 In Aci
authors H.E.Kato, K.Inoue, R.Abe-Yoshizumi, Y.Kato, H.Ono, M.Konno, T.Ishi M.R.Hoque, S.Hososhima, H.Kunitomo, J.Ito, S.Yoshizawa, K.Yamash M.Takemoto, T.Nishizawa, R.Taniguchi, K.Kogure, A.D.Maturana, Y. H.Yawo, R.Ishitani, H.Kandori, O.Nureki
compound source
Molecule: Sodium Pumping Rhodopsin
Chain: A
Engineered: Yes
 Organism_scientific: Dokdonia Eikasta
Organism_taxid: 308116
Gene: Nar
Expression_system: Escherichia Coli
Expression_system_taxid: 562
symmetry Space Group: I 2 2 2
R_factor 0.207 R_Free 0.249
crystal
cell
length a length b length c angle alpha angle beta angle gamma
40.582 81.544 233.775 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.30 Å
ligand OLA, PEG, RET enzyme
Gene
Ontology
ChainFunctionProcessComponent
A
  • ion channel activity


    • Primary referenceStructural basis for Na(+) transport mechanism by a light-driven Na(+) pump., Kato HE, Inoue K, Abe-Yoshizumi R, Kato Y, Ono H, Konno M, Hososhima S, Ishizuka T, Hoque MR, Kunitomo H, Ito J, Yoshizawa S, Yamashita K, Takemoto M, Nishizawa T, Taniguchi R, Kogure K, Maturana AD, Iino Y, Yawo H, Ishitani R, Kandori H, Nureki O, Nature. 2015 May 7;521(7550):48-53. doi: 10.1038/nature14322. Epub 2015 Apr 6. PMID:25849775
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (51 Kb) [Save to disk]
  • Biological Unit Coordinates (3x3b.pdb1.gz) 46 Kb
  • Biological Unit Coordinates (3x3b.pdb2.gz) 90 Kb
  • LPC: Ligand-Protein Contacts for 3X3B
  • CSU: Contacts of Structural Units for 3X3B
  • Structure Factors (346 Kb)
  • Retrieve 3X3B in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3X3B from S2C, [Save to disk]
  • Re-refined 3x3b structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 3X3B 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 3X3B
  • 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
  • 3D motif for 3X3B, from MSDmotif at EBI
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3x3b_A] [3x3b]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 3X3B: [Bac_rhodopsin ] by SMART
    • Other resources with information on 3X3B
  • Community annotation for 3X3B at PDBWiki (http://pdbwiki.org)

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