3AM6 Transport Protein date Aug 16, 2010
title Crystal Structure Of The Proton Pumping Rhodopsin Ar2 From M Acetabularia Acetabulum
authors T.Wada, S.Yokoyama
compound source
Molecule: Rhodopsin-2
Chain: A, B, C, D
Synonym: Ar2
Engineered: Yes
 Organism_scientific: Acetabularia Acetabulum
Organism_common: Mermaid'S Wine Glass
Organism_taxid: 35845
Expression_system: Cell-Free Synthesis
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pcr2.1-Topo
symmetry Space Group: P 21 21 21
R_factor 0.290 R_Free 0.324
crystal
cell
length a length b length c angle alpha angle beta angle gamma
84.120 110.487 129.116 90.00 90.00 90.00
method X-Ray Diffractionresolution 3.20 Å
ligand CLR, RET enzyme
Gene
Ontology
ChainFunctionProcessComponent
A, D, C, B
  • ion channel activity


    • Primary referenceCrystal structure of the eukaryotic light-driven proton-pumping rhodopsin, Acetabularia rhodopsin II, from marine alga., Wada T, Shimono K, Kikukawa T, Hato M, Shinya N, Kim SY, Kimura-Someya T, Shirouzu M, Tamogami J, Miyauchi S, Jung KH, Kamo N, Yokoyama S, J Mol Biol. 2011 Sep 2;411(5):986-98. Epub 2011 Jun 25. PMID:21726566
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (152 Kb) [Save to disk]
  • Biological Unit Coordinates (3am6.pdb1.gz) 38 Kb
  • Biological Unit Coordinates (3am6.pdb2.gz) 38 Kb
  • Biological Unit Coordinates (3am6.pdb3.gz) 38 Kb
  • Biological Unit Coordinates (3am6.pdb4.gz) 38 Kb
  • Biological Unit Coordinates (3am6.pdb5.gz) 146 Kb
  • LPC: Ligand-Protein Contacts for 3AM6
  • CSU: Contacts of Structural Units for 3AM6
  • Structure Factors (293 Kb)
  • Retrieve 3AM6 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3AM6 from S2C, [Save to disk]
  • Re-refined 3am6 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 3AM6 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 3AM6
  • 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 3AM6, from MSDmotif at EBI
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3am6_B] [3am6_D] [3am6] [3am6_A] [3am6_C]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 3AM6: [Bac_rhodopsin ] by SMART
    • Other resources with information on 3AM6
  • Community annotation for 3AM6 at PDBWiki (http://pdbwiki.org)
    • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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