4JGH Ligase date Mar 01, 2013
title Structure Of The Socs2-Elongin Bc Complex Bound To An N-Term Fragment Of Cullin5
authors Y.K.Kim, M.J.Kwak, B.Ku, H.Y.Suh, K.Joo, J.Lee, J.U.Jung, B.H.Oh
compound source
Molecule: Suppressor Of Cytokine Signaling 2
Chain: A
Fragment: Unp Residues 32-198
Synonym: Socs-2, Cytokine-Inducible Sh2 Protein 2, Cis-2, S Induced Stat Inhibitor 2, Ssi-2;
Engineered: Yes
 Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Cis2, Homo Sapiens, Socs2, Ssi2, Stati2
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pproex Hta

Molecule: Transcription Elongation Factor B Polypeptide 2
Chain: B
Synonym: Elongin 18 Kda Subunit, Elongin-B, Elob, Rna Polym Transcription Factor Siii Subunit B, Siii P18;
Engineered: Yes
Organism_scientific: Mus Musculus
Organism_common: Mouse
Organism_taxid: 10090
Gene: Mus Musculus, Tceb2
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Prsfduet

Molecule: Transcription Elongation Factor B Polypeptide 1
Chain: C
Fragment: Unp Residues 17-112
Synonym: Elongin 15 Kda Subunit, Elongin-C, Eloc, Rna Polym Transcription Factor Siii Subunit C, Siii P15, Stromal Memb Associated Protein Smap1b Homolog;
Engineered: Yes
Organism_scientific: Mus Musculus
Organism_common: Mouse
Organism_taxid: 10090
Gene: Mus Musculus, Tceb1
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Prsfduet

Molecule: Cullin-5
Chain: D
Fragment: Unp Residues 10-386
Synonym: Cul-5, Vasopressin-Activated Calcium-Mobilizing Re Vacm-1;
Engineered: Yes
Mutation: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Cul5, Homo Sapiens, Vacm1
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21(De3)Ripl
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet22b-Cpd10h
symmetry Space Group: C 2 2 21
R_factor 0.225 R_Free 0.248
crystal
cell
length a length b length c angle alpha angle beta angle gamma
138.849 141.456 182.001 90.00 90.00 90.00
method X-Ray Diffractionresolution 3.00 Å
Gene
Ontology
ChainFunctionProcessComponent
A


B


C


D


Primary referenceStructural basis of intersubunit recognition in elongin BC-cullin 5-SOCS box ubiquitin-protein ligase complexes., Kim YK, Kwak MJ, Ku B, Suh HY, Joo K, Lee J, Jung JU, Oh BH, Acta Crystallogr D Biol Crystallogr. 2013 Aug;69(Pt 8):1587-97. doi:, 10.1107/S0907444913011220. Epub 2013 Jul 20. PMID:23897481
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (125 Kb) [Save to disk]
  • Biological Unit Coordinates (4jgh.pdb1.gz) 120 Kb
  • Biological Unit Coordinates (4jgh.pdb2.gz) 120 Kb
  • CSU: Contacts of Structural Units for 4JGH
  • Structure Factors (415 Kb)
  • Retrieve 4JGH in mmCIF format [Save to disk]
  • Re-refined 4jgh structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 4JGH 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 4JGH
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
    • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • 3D motif for 4JGH, from MSDmotif at EBI
  • Fold representative 4jgh from FSSP and Dali (Families of Structurally Similar Proteins)
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4jgh_C] [4jgh_D] [4jgh_B] [4jgh_A] [4jgh]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 4JGH: [SH2] [SOCS] [SOCS_box] [Skp1] [UBQ ] by SMART
    • Other resources with information on 4JGH
  • Community annotation for 4JGH at PDBWiki (http://pdbwiki.org)

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