4KVG Signaling Protein date May 22, 2013
title Crystal Structure Of Riam Ra-Ph Domains In Complex With Gtp
authors H.Zhang, Y.E.Chang, M.L.Brennan, J.Wu
compound source
Molecule: Ras-Related Protein Rap-1a
Chain: A, C
Fragment: Unp Residues 1-167
Synonym: C21kg, G-22k, Gtp-Binding Protein Smg P21a, Ras-Re Protein Krev-1;
Engineered: Yes
Mutation: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Krev1, Rap1a
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet281

Molecule: Amyloid Beta A4 Precursor Protein-Binding Family 1-Interacting Protein;
Chain: B, D
Fragment: Ra-Ph Domains (Unp Residues 179-437)
Synonym: Apbb1-Interacting Protein 1, Proline-Rich Evh1 Lig Prel-1, Proline-Rich Protein 48;
Engineered: Yes

Organism_scientific: Mus Musculus
Organism_common: Mouse
Organism_taxid: 10090
Gene: Apbb1ip, Prel1
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet281
symmetry Space Group: P 21 21 21
R_factor 0.197 R_Free 0.219
crystal
cell
length a length b length c angle alpha angle beta angle gamma
82.467 85.848 160.852 90.00 90.00 90.00
method X-Ray Diffractionresolution 1.65 Å
ligand EDO, GTP, MG enzyme
Gene
Ontology
ChainFunctionProcessComponent
A, C


D, B


Primary referenceThe structure of Rap1 in complex with RIAM reveals specificity determinants and recruitment mechanism., Zhang H, Chang YC, Brennan ML, Wu J, J Mol Cell Biol. 2014 Apr;6(2):128-39. doi: 10.1093/jmcb/mjt044. Epub 2013 Nov, 28. PMID:24287201
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (306 Kb) [Save to disk]
  • Biological Unit Coordinates (4kvg.pdb1.gz) 154 Kb
  • Biological Unit Coordinates (4kvg.pdb2.gz) 150 Kb
  • LPC: Ligand-Protein Contacts for 4KVG
  • CSU: Contacts of Structural Units for 4KVG
  • Structure Factors (2956 Kb)
  • Retrieve 4KVG in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4KVG from S2C, [Save to disk]
  • Re-refined 4kvg structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4KVG 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 4KVG
  • 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 4KVG, from MSDmotif at EBI
  • Fold representative 4kvg from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4kvg_D] [4kvg_A] [4kvg_C] [4kvg_B] [4kvg]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 4KVG: [PH] [RA] [RAS ] by SMART
  • Other resources with information on 4KVG
  • Community annotation for 4KVG at PDBWiki (http://pdbwiki.org)

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