3SFV Protein Transport Protein Binding date Jun 14, 2011
title Crystal Structure Of The Gdp-Bound Rab1a S25n Mutant In Comp The Coiled-Coil Domain Of Lida From Legionella Pneumophila
authors K.Yin, D.Lu, D.Zhu, H.Zhang, B.Li, S.Xu, L.Gu
compound source
Molecule: Ras-Related Protein Rab-1a
Chain: A
Fragment: Residues 1-176
Synonym: Ypt1-Related Protein
Engineered: Yes
Mutation: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Rab1a
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet15b

Molecule: Lida Protein, Substrate Of The Doticm System
Chain: B
Fragment: Coiled-Coil Domain
Engineered: Yes

Organism_scientific: Legionella Pneumophila
Organism_taxid: 400673
Strain: Corby
Gene: Lida
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet29b
symmetry Space Group: P 21 21 21
R_factor 0.192 R_Free 0.228
crystal
cell
length a length b length c angle alpha angle beta angle gamma
154.314 54.673 61.699 90.00 90.00 90.00
method X-Ray Diffractionresolution 1.73 Å
ligand GDP enzyme
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceStructural Insights into a Unique Legionella pneumophila Effector LidA Recognizing Both GDP and GTP Bound Rab1 in Their Active State., Cheng W, Yin K, Lu D, Li B, Zhu D, Chen Y, Zhang H, Xu S, Chai J, Gu L, PLoS Pathog. 2012 Mar;8(3):e1002528. Epub 2012 Mar 1. PMID:22416225
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (99 Kb) [Save to disk]
  • Biological Unit Coordinates (3sfv.pdb1.gz) 94 Kb
  • LPC: Ligand-Protein Contacts for 3SFV
  • CSU: Contacts of Structural Units for 3SFV
  • Structure Factors (657 Kb)
  • Retrieve 3SFV in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3SFV from S2C, [Save to disk]
  • Re-refined 3sfv structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3SFV 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 3SFV
  • 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 3SFV, from MSDmotif at EBI
  • Fold representative 3sfv from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3sfv_A] [3sfv] [3sfv_B]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 3SFV: [RAB ] by SMART
  • Other resources with information on 3SFV
  • Community annotation for 3SFV at PDBWiki (http://pdbwiki.org)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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