3H8K Ligase date Apr 29, 2009
title Crystal Structure Of Ube2g2 Complxed With The G2br Domain Of 1.8-A Resolution
authors R.C.Kalathur, R.Das, J.Li, R.A.Byrd, X.Ji
compound source
Molecule: Ubiquitin-Conjugating Enzyme E2 G2
Chain: A
Synonym: Ubiquitin-Protein Ligase G2, Ubiquitin Carrier Pro
Ec: 6.3.2.19
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Ube2g2
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet3a

Molecule: Autocrine Motility Factor Receptor, Isoform 2
Chain: B
Fragment: Residues 573-600
Synonym: Amf Receptor, Isoform 2, Gp78, Ring Finger Protein
Ec: 6.3.2.-
Engineered: Yes
Mutation: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Amfr, Rnf45
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet3a
symmetry Space Group: P 21 21 21
R_factor 0.193 R_Free 0.242
crystal
cell
length a length b length c angle alpha angle beta angle gamma
48.920 60.150 61.640 90.00 90.00 90.00
method X-Ray Diffractionresolution 1.80 Å
ligand
enzyme Ligase E.C.6.3.2.19 BRENDA
note 3H8K is a representative structure
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceAllosteric activation of E2-RING finger-mediated ubiquitylation by a structurally defined specific E2-binding region of gp78., Das R, Mariano J, Tsai YC, Kalathur RC, Kostova Z, Li J, Tarasov SG, McFeeters RL, Altieri AS, Ji X, Byrd RA, Weissman AM, Mol Cell. 2009 Jun 26;34(6):674-85. PMID:19560420
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (40 Kb) [Save to disk]
  • Biological Unit Coordinates (3h8k.pdb1.gz) 36 Kb
  • CSU: Contacts of Structural Units for 3H8K
  • Likely Quarternary Molecular Structure file(s) for 3H8K
  • Structure Factors (113 Kb)
  • Retrieve 3H8K in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3H8K from S2C, [Save to disk]
  • Re-refined 3h8k structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3H8K 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 3H8K
  • 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 3H8K, from MSDmotif at EBI
  • Fold representative 3h8k from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3h8k] [3h8k_B] [3h8k_A]
  • SWISS-PROT database: [Q9UKV5] [P60604]
  • Domain organization of [AMFR2_HUMAN] [UB2G2_HUMAN] by SWISSPFAM
  • Domain found in 3H8K: [UBCc ] by SMART
  • Other resources with information on 3H8K
  • Community annotation for 3H8K 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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