4FMB Protein Binding date Jun 16, 2012
title Vira-Rab1 Complex Structure
authors F.Shao, Y.Zhu
compound source
Molecule: Cysteine Protease-Like Vira
Chain: A, C, E
Synonym: Effector Protein Vira
Ec: 3.4.22.-
Engineered: Yes
Organism_scientific: Shigella Flexneri
Organism_taxid: 623
Strain: 301
Gene: Cp0181, Pwr501_0191, Vira
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pgex-6p-2

Molecule: Ras-Related Protein Rab-1a
Chain: B, D, F
Synonym: Ypt1-Related Protein
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Rab1, Rab1a
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet28a
symmetry Space Group: C 1 2 1
R_factor 0.228 R_Free 0.247
crystal
cell
length a length b length c angle alpha angle beta angle gamma
186.118 127.311 107.325 90.00 94.45 90.00
method X-Ray Diffractionresolution 3.20 Å
ligand AF3, GDP, MG enzyme Hydrolase E.C.3.4.22 BRENDA
Gene PWR501
Gene
Ontology
ChainFunctionProcessComponent
A, C, E


F, D, B


Primary referenceStructurally Distinct Bacterial TBC-like GAPs Link Arf GTPase to Rab1 Inactivation to Counteract Host Defenses., Dong N, Zhu Y, Lu Q, Hu L, Zheng Y, Shao F, Cell. 2012 Aug 31;150(5):1029-41. PMID:22939626
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (257 Kb) [Save to disk]
  • Biological Unit Coordinates (4fmb.pdb1.gz) 87 Kb
  • Biological Unit Coordinates (4fmb.pdb2.gz) 86 Kb
  • Biological Unit Coordinates (4fmb.pdb3.gz) 86 Kb
  • Biological Unit Coordinates (4fmb.pdb4.gz) 495 Kb
  • LPC: Ligand-Protein Contacts for 4FMB
  • CSU: Contacts of Structural Units for 4FMB
  • Structure Factors (449 Kb)
  • Retrieve 4FMB in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4FMB from S2C, [Save to disk]
  • Re-refined 4fmb structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4FMB 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 4FMB
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • 3D motif for 4FMB, from MSDmotif at EBI
  • Fold representative 4fmb from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4fmb_C] [4fmb_B] [4fmb] [4fmb_A] [4fmb_F] [4fmb_D] [4fmb_E]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 4FMB: [RAB ] by SMART
  • Other resources with information on 4FMB
  • Community annotation for 4FMB at PDBWiki (http://pdbwiki.org)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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