3JW0 Ligase Signaling Protein date Sep 17, 2009
title E2~Ubiquitin-Hect
authors H.B.Kamadurai, B.A.Schulman
compound source
Molecule: Ubiquitin-Conjugating Enzyme E2 D2
Chain: A, B
Synonym: Ubiquitin-Protein Ligase D2, Ubiquitin Carrier Pro Ubiquitin-Conjugating Enzyme E2-17 Kda 2, E2(17)Kb 2;
Ec: 6.3.2.19
Engineered: Yes
Mutation: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Ube2d2, Ubc4, Ubch5b
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_vector_type: Plasmid

Molecule: E3 Ubiquitin-Protein Ligase Nedd4-Like
Chain: C, D
Fragment: Nedd4l Hect Domain (Unp 576-955)
Synonym: Nedd4-2, Nedd4.2
Ec: 6.3.2.-
Engineered: Yes
Mutation: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Nedd4l, Kiaa0439, Nedl3
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_vector_type: Plasmid

Molecule: Ubiquitin
Chain: X, Y
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Rps27a, Uba80, Ubcep1, Uba52, Ubcep2, Ubb, Ubc
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_vector_type: Plasmid
symmetry Space Group: C 2 2 21
R_factor 0.252 R_Free 0.287
crystal
cell
length a length b length c angle alpha angle beta angle gamma
174.167 200.571 109.820 90.00 90.00 90.00
method X-Ray Diffractionresolution 3.10 Å
ligand
enzyme Ligase E.C.6.3.2.19 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A, B


D, C


Primary referenceInsights into ubiquitin transfer cascades from a structure of a UbcH5B approximately ubiquitin-HECT(NEDD4L) complex., Kamadurai HB, Souphron J, Scott DC, Duda DM, Miller DJ, Stringer D, Piper RC, Schulman BA, Mol Cell. 2009 Dec 25;36(6):1095-102. PMID:20064473
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (198 Kb) [Save to disk]
  • Biological Unit Coordinates (3jw0.pdb1.gz) 98 Kb
  • Biological Unit Coordinates (3jw0.pdb2.gz) 99 Kb
  • CSU: Contacts of Structural Units for 3JW0
  • Structure Factors (275 Kb)
  • Retrieve 3JW0 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3JW0 from S2C, [Save to disk]
  • Re-refined 3jw0 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3JW0 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 3JW0
  • 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 3JW0, from MSDmotif at EBI
  • Fold representative 3jw0 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3jw0_X] [3jw0_A] [3jw0_C] [3jw0_B] [3jw0] [3jw0_Y] [3jw0_D]
  • SWISS-PROT database: [Q96PU5] [P62988]
  • Domain organization of [NED4L_HUMAN] [UBIQ_HUMAN] by SWISSPFAM
  • Domains found in 3JW0: [HECTc] [UBCc] [UBQ ] by SMART
  • Other resources with information on 3JW0
  • Community annotation for 3JW0 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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