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
crystal cell	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 Diffraction	resolution	2.80 Å
related structures	by homologous chain: 1F9J, 1G6J
Gene Ontology	Chain Function Process Component H, G
Primary reference	Structural 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] (60 Kb) [Save to disk] Biological Unit Coordinates (1yd8.pdb1.gz) 29 Kb Biological Unit Coordinates (1yd8.pdb2.gz) 28 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

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 1YD8, from MSDmotif at EBI

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)

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