1TU3 Protein Transport date Jun 24, 2004
title Crystal Structure Of Rab5 Complex With Rabaptin5 C-Terminal
authors G.Zhu, P.Zhai, J.Liu, S.Terzyan, G.Li, X.C.Zhang
compound source
Molecule: Ras-Related Protein Rab-5a
Chain: A, B, C, D, E
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Rab5a, Rab5
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet11a

Molecule: Rab Gtpase Binding Effector Protein 1
Chain: F, G, H, I, J
Synonym: Rabaptin-5, Rabaptin-5alpha, Rabaptin-4
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Rabep1, Rabpt5, Rabpt5a
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pgex6p-1
symmetry Space Group: C 1 2 1
R_factor 0.222 R_Free 0.277
crystal
cell
length a length b length c angle alpha angle beta angle gamma
112.400 83.500 144.900 90.00 102.20 90.00
method X-Ray Diffractionresolution 2.31 Å
ligand GNP, MG enzyme
related structures by homologous chain: 1TU4
Gene
Ontology
ChainFunctionProcessComponent
A, E, B, C, D


F, J, H, I, G


Primary referenceStructural basis of Rab5-Rabaptin5 interaction in endocytosis., Zhu G, Zhai P, Liu J, Terzyan S, Li G, Zhang XC, Nat Struct Mol Biol 2004 Oct;11(10):975-83. Epub 2004 Sep 19. PMID:15378032
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (184 Kb) [Save to disk]
  • Biological Unit Coordinates (1tu3.pdb1.gz) 74 Kb
  • Biological Unit Coordinates (1tu3.pdb2.gz) 68 Kb
  • Biological Unit Coordinates (1tu3.pdb3.gz) 77 Kb
  • LPC: Ligand-Protein Contacts for 1TU3
  • CSU: Contacts of Structural Units for 1TU3
  • Likely Quarternary Molecular Structure file(s) for 1TU3
  • Structure Factors (783 Kb)
  • Retrieve 1TU3 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1TU3 from S2C, [Save to disk]
  • Re-refined 1tu3 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1TU3 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 1TU3
  • 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 1TU3, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1tu3a_, region A [Jmol] [rasmolscript] [script source]
        - Domain d1tu3b_, region B [Jmol] [rasmolscript] [script source]
        - Domain d1tu3c_, region C [Jmol] [rasmolscript] [script source]
        - Domain d1tu3d_, region D [Jmol] [rasmolscript] [script source]
        - Domain d1tu3e_, region E [Jmol] [rasmolscript] [script source]
        - Domain d1tu3f_, region F [Jmol] [rasmolscript] [script source]
        - Domain d1tu3g_, region G [Jmol] [rasmolscript] [script source]
        - Domain d1tu3h_, region H [Jmol] [rasmolscript] [script source]
        - Domain d1tu3i_, region I [Jmol] [rasmolscript] [script source]
        - Domain d1tu3j_, region J [Jmol] [rasmolscript] [script source]
  • Class (fold), Architecture (subfold), Topology, Homologous superfamily from CATH
  • Summaries and structural analyses of PDB data files from PDBSum
  • Identification of Protein Pockets & Cavities at CASTp
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [1tu3_G] [1tu3_C] [1tu3_J] [1tu3_A] [1tu3_H] [1tu3_I] [1tu3_E] [1tu3_B] [1tu3_F] [1tu3_D] [1tu3]
  • SWISS-PROT database: [P20339] [Q15276]
  • Domain organization of [RAB5A_HUMAN] [RABE1_HUMAN] by SWISSPFAM
  • Domain found in 1TU3: [RAB ] by SMART
  • Other resources with information on 1TU3
  • Community annotation for 1TU3 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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