1YD8 Protein Transport, Chromosomal Protein date Dec 23, 2004
title Complex Of Human Gga3 Gat Domain And Ubiquitin
authors G.Prag, S.Lee, R.Mattera, C.N.Arighi, B.M.Beach, J.S.Bonifacino, J
compound source
Molecule: Ubiquin
Chain: U, V
Organism_scientific: Bos Taurus
Organism_common: Cattle
Organism_taxid: 9913
Tissue: Red Blood Cells

Molecule: Adp-Ribosylation Factor Binding Protein Gga3
Chain: G, H
Synonym: Golgi-Localized, Gamma Ear-Containing, Arf-Binding 3;
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Gga3, Kiaa0154
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21(De3) Rosetta
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet-Parallel.3_his6_gat
symmetry Space Group: C 1 2 1
R_factor 0.221 R_Free 0.297
length a length b length c angle alpha angle beta angle gamma
47.886 97.293 66.459 90.00 90.03 90.00
method X-Ray Diffractionresolution 2.80 Å
related structures by homologous chain: 1F9J, 1G6J
H, G

Primary referenceStructural mechanism for ubiquitinated-cargo recognition by the Golgi-localized, {gamma}-ear-containing, ADP-ribosylation-factor-binding proteins., Prag G, Lee S, Mattera R, Arighi CN, Beach BM, Bonifacino JS, Hurley JH, Proc Natl Acad Sci U S A 2005 Feb 15;102(7):2334-2339. Epub 2005 Feb 8. PMID:15701688
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (61 Kb) [Save to disk]
  • Biological Unit Coordinates (1yd8.pdb1.gz) 29 Kb
  • Biological Unit Coordinates (1yd8.pdb2.gz) 29 Kb
  • CSU: Contacts of Structural Units for 1YD8
  • Likely Quarternary Molecular Structure file(s) for 1YD8
  • Structure Factors (57 Kb)
  • Retrieve 1YD8 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1YD8 from S2C, [Save to disk]
  • Re-refined 1yd8 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1YD8 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 1YD8
  • 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 1YD8, from MSDmotif at EBI
  • Fold representative 1yd8 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [1yd8] [1yd8_H] [1yd8_U] [1yd8_G] [1yd8_V]
  • SWISS-PROT database: [Q9NZ52] [P62990]
  • Domain organization of [GGA3_HUMAN] [UBIQ_BOVIN] by SWISSPFAM
  • Domain found in 1YD8: [UBQ ] by SMART
  • Other resources with information on 1YD8
  • Community annotation for 1YD8 at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

  • You may enter another PDB ID code
    Go [Back], to the [PDB Lite page], to the [OCA Search page] or to the [PDB Home page]
    OCA© by Jaime Prilusky, 1996-2014
    Bioinformatics Unit
    Weizmann Institute of Science