2HYE Protein Binding date Aug 05, 2006
title Crystal Structure Of The Ddb1-Cul4a-Rbx1-Sv5v Complex
authors S.Angers, T.Li, X.Yi, M.J.Maccoss, R.T.Moon, N.Zheng
compound source
Molecule: Dna Damage-Binding Protein 1
Chain: A
Synonym: Damage-Specific Dna-Binding Protein 1, Uv-Damaged Binding Factor, Ddb P127 Subunit, Ddba, Uv-Damaged Dna-Bind Protein 1, Uv-Ddb 1, Xeroderma Pigmentosum Group E- Complem Protein, Xpce, Xpe-Binding Factor, Xpe-Bf, X- Associated Pr Xap-1;
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Ddb1
Expression_system: Spodoptera Frugiperda
Expression_system_common: Fall Armyworm
Expression_system_taxid: 7108

Molecule: Nonstructural Protein V
Chain: B
Engineered: Yes

Organism_scientific: Simian Virus 5
Organism_taxid: 11207
Gene: Pv
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Cullin-4a
Chain: C
Synonym: Cul-4a
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Cul4a
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Ring-Box Protein 1
Chain: D
Synonym: Rbx1, Regulator Of Cullins 1, Ring Finger Protein Protein;
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Rbx1
Expression_system: Escherichia Coli
Expression_system_taxid: 562
symmetry Space Group: C 2 2 21
R_factor 0.250 R_Free 0.316
crystal
cell
length a length b length c angle alpha angle beta angle gamma
83.452 203.165 424.875 90.00 90.00 90.00
method X-Ray Diffractionresolution 3.10 Å
ligand ZN enzyme
Gene
Ontology
ChainFunctionProcessComponent
A


B


C


D


Primary referenceMolecular architecture and assembly of the DDB1-CUL4A ubiquitin ligase machinery., Angers S, Li T, Yi X, Maccoss MJ, Moon RT, Zheng N, Nature. 2006 Sep 10;. PMID:16964240
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (325 Kb) [Save to disk]
  • Biological Unit Coordinates (2hye.pdb1.gz) 318 Kb
  • LPC: Ligand-Protein Contacts for 2HYE
  • CSU: Contacts of Structural Units for 2HYE
  • Likely Quarternary Molecular Structure file(s) for 2HYE
  • Structure Factors (716 Kb)
  • Retrieve 2HYE in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2HYE from S2C, [Save to disk]
  • Re-refined 2hye structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 2HYE 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 2HYE
  • 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 2HYE, from MSDmotif at EBI
  • Fold representative 2hye from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2hye_C] [2hye_A] [2hye_D] [2hye_B] [2hye]
  • SWISS-PROT database: [Q13619] [Q16531] [P62877] [P11207]
  • Domain organization of [CUL4A_HUMAN] [DDB1_HUMAN] [RBX1_HUMAN] [V_SV5] by SWISSPFAM
  • Domains found in 2HYE: [CULLIN] [Cullin_Nedd8] [RING ] by SMART
  • Other resources with information on 2HYE
  • Community annotation for 2HYE 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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