2OT3 Protein Transport date Feb 07, 2007
title Crystal Structure Of Rabex-5 Vps9 Domain In Complex With Nuc Free Rab21
authors A.Delprato, D.Lambright
compound source
Molecule: Rab5 Gdpgtp Exchange Factor
Chain: A
Fragment: Residues 132-297
Synonym: Rabex-5, Rabaptin-5-Associated Exchange Factor For Rap1;
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Rabgef1, Rabex5
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet15b

Molecule: Ras-Related Protein Rab-21
Chain: B
Fragment: Residues 16-183
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Rab21, Kiaa0118
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pgex4t1
symmetry Space Group: P 21 21 2
R_factor 0.188 R_Free 0.243
crystal
cell
length a length b length c angle alpha angle beta angle gamma
71.897 113.400 60.533 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.10 Å
Gene
Ontology
ChainFunctionProcessComponent
B


Primary referenceStructural basis for Rab GTPase activation by VPS9 domain exchange factors., Delprato A, Lambright DG, Nat Struct Mol Biol. 2007 May;14(5):406-12. Epub 2007 Apr 22. PMID:17450153
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (79 Kb) [Save to disk]
  • Biological Unit Coordinates (2ot3.pdb1.gz) 74 Kb
  • CSU: Contacts of Structural Units for 2OT3
  • Likely Quarternary Molecular Structure file(s) for 2OT3
  • Structure Factors (238 Kb)
  • Retrieve 2OT3 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2OT3 from S2C, [Save to disk]
  • Re-refined 2ot3 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 2OT3 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 2OT3
  • 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 2OT3, from MSDmotif at EBI
  • Fold representative 2ot3 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2ot3_B] [2ot3] [2ot3_A]
  • SWISS-PROT database: [Q9UL25] [Q9UJ41]
  • Belongs to the synaptosomal vesicle fusion pore (svf-pore) family according to TCDB.
  • Domain organization of [RAB21_HUMAN] [RABX5_HUMAN] by SWISSPFAM
  • Domains found in 2OT3: [RAB] [VPS9 ] by SMART
  • Other resources with information on 2OT3
  • Community annotation for 2OT3 at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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