3DQV Ligase date Jul 09, 2008
title Structural Insights Into Nedd8 Activation Of Cullin-Ring Ligases: Conformational Control Of Conjugation
authors D.M.Duda, L.A.Borg, D.C.Scott, H.W.Hunt, M.Hammel, B.A.Schulman
compound source
Molecule: Nedd8
Chain: A, B
Fragment: Nedd8 C-Terminus Covalently Linked To Cul5 Lys724;
Synonym: Ubiquitin-Like Protein Nedd8, Neddylin
Engineered: Yes
Mutation: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Nedd8
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Cullin-5
Chain: C, D
Fragment: Cullin-5 Residues 401-780
Synonym: Cul-5, Vasopressin-Activated Calcium-Mobilizing Receptor, Vacm-1;
Engineered: Yes
Mutation: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Cul5, Vacm1
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Rbx1
Chain: R, Y
Fragment: Rbx1 Residues 5-108
Synonym: Rbx1, Regulator Of Cullins 1, Ring Finger Protein 75, Protein Zyp;
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Rbx1, Rnf75, Roc1
Expression_system: Escherichia Coli
Expression_system_taxid: 562
symmetry Space Group: P 21 21 21
R_factor 0.249 R_Free 0.299
crystal
cell
length a length b length c angle alpha angle beta angle gamma
88.315 122.442 128.647 90.00 90.00 90.00
method X-Ray Diffractionresolution 3.00 Å
ligand MSE, ZN enzyme
Gene
Ontology
ChainFunctionProcessComponent
A, B


D, C


R, Y


Primary referenceStructural insights into NEDD8 activation of cullin-RING ligases: conformational control of conjugation., Duda DM, Borg LA, Scott DC, Hunt HW, Hammel M, Schulman BA, Cell. 2008 Sep 19;134(6):995-1006. PMID:18805092
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (189 Kb) [Save to disk]
  • Biological Unit Coordinates (3dqv.pdb1.gz) 93 Kb
  • Biological Unit Coordinates (3dqv.pdb2.gz) 91 Kb
  • Biological Unit Coordinates (3dqv.pdb3.gz) 179 Kb
  • LPC: Ligand-Protein Contacts for 3DQV
  • CSU: Contacts of Structural Units for 3DQV
  • Likely Quarternary Molecular Structure file(s) for 3DQV
  • Structure Factors (379 Kb)
  • Retrieve 3DQV in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3DQV from S2C, [Save to disk]
  • Re-refined 3dqv structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3DQV 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 3DQV
  • 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 3DQV, from MSDmotif at EBI
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3dqv] [3dqv_A] [3dqv_B] [3dqv_C] [3dqv_Y] [3dqv_D] [3dqv_R]
  • SWISS-PROT database: [Q93034] [Q15843] [P62877]
  • Domain organization of [CUL5_HUMAN] [NEDD8_HUMAN] [RBX1_HUMAN] by SWISSPFAM
  • Domains found in 3DQV: [CULLIN] [Cullin_Nedd8] [RING] [UBQ ] by SMART
  • Other resources with information on 3DQV
  • Community annotation for 3DQV 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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