2FIF	Protein Turnover Endocytosis	date	Dec 29, 2005
title	Crystal Structure Of A Bovine Rabex-5 Fragment Complexed Wit Ubiquitin
authors	S.Lee, J.H.Hurley
compound		source
Molecule: Ubiquitin Chain: A, C, E		Organism_scientific: Bos Taurus Organism_common: Cattle Organism_taxid: 9913
Molecule: Rab5 Gdpgtp Exchange Factor Chain: B, D, F Fragment: A20 Zinc Finger And Inverted Ubiquitin Interactin Domains; Synonym: Rabex-5 Engineered: Yes		Organism_scientific: Bos Taurus Organism_common: Cattle Organism_taxid: 9913 Gene: Rabgef1, Rabex5 Expression_system: Escherichia Coli Bl21(De3) Expression_system_taxid: 469008 Expression_system_strain: Bl21(De3) Expression_system_vector_type: Plasmid Expression_system_plasmid: Parallel Gst2
symmetry	Space Group: C 1 2 1	R_factor 0.228 R_Free 0.263
crystal cell	length a length b length c angle alpha angle beta angle gamma 192.200 44.420 69.170 90.00 108.98 90.00
method	X-Ray Diffraction	resolution	2.49 Å
ligand	SO4, ZN	enzyme
Gene Ontology	Chain Function Process Component F, D, B
Primary reference	Structural basis for ubiquitin recognition and autoubiquitination by Rabex-5., Lee S, Tsai YC, Mattera R, Smith WJ, Kostelansky MS, Weissman AM, Bonifacino JS, Hurley JH, Nat Struct Mol Biol. 2006 Mar;13(3):264-71. Epub 2006 Feb 5. PMID:16462746

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (70 Kb) [Save to disk] Biological Unit Coordinates (2fif.pdb1.gz) 22 Kb Biological Unit Coordinates (2fif.pdb2.gz) 22 Kb Biological Unit Coordinates (2fif.pdb3.gz) 22 Kb LPC: Ligand-Protein Contacts for 2FIF CSU: Contacts of Structural Units for 2FIF Likely Quarternary Molecular Structure file(s) for 2FIF Structure Factors (141 Kb) Retrieve 2FIF in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 2FIF from S2C, [Save to disk] Re-refined 2fif structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 2FIF 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 2FIF

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 2FIF, from MSDmotif at EBI

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [2fif_F] [2fif] [2fif_D] [2fif_C] [2fif_B] [2fif_E] [2fif_A] SWISS-PROT database: [O18973] [P62990] Domain organization of [RABX5_BOVIN] [UBIQ_BOVIN] by SWISSPFAM Domains found in 2FIF: [UBQ] [ZnF_A20 ] by SMART

Other resources with information on 2FIF

Community annotation for 2FIF at PDBWiki (http://pdbwiki.org) MMDB (Entrez's Structure Database)

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Images from IMB Jena Image Library of Biological Macromolecules.

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