3DB3 Ligase date May 30, 2008
title Crystal Structure Of The Tandem Tudor Domains Of The E3 Ubiq Protein Ligase Uhrf1 In Complex With Trimethylated Histone Peptide
authors J.R.Walker, G.V.Avvakumov, S.Xue, A.Dong, Y.Li, C.Bountra, J.Weige C.H.Arrowsmith, A.M.Edwards, A.Bochkarev, S.Dhe-Paganon, Struct Genomics Consortium (Sgc)
compound source
Molecule: E3 Ubiquitin-Protein Ligase Uhrf1
Chain: A
Fragment: Tandem Tudor Domains (Unp Residues 126-285)
Synonym: Ubiquitin-Like Phd And Ring Finger Domain-Containi 1, Ubiquitin-Like-Containing Phd And Ring Finger Domains Pr Inverted Ccaat Box-Binding Protein Of 90 Kda, Transcription Icbp90, Nuclear Zinc Finger Protein Np95, Nuclear Protein 9 Ring Finger Protein 106;
Ec: 6.3.2.-
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Uhrf1, Icbp90, Np95, Rnf106
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21 (De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet28-Mhl

Molecule: Trimethylated Histone H3-K9 Peptide
Chain: B
Engineered: Yes

Synthetic: Yes
Other_details: Trimethylated Histone Peptide H3-K9 Was Chem Synthesized. The Sequence Naturally Occurs In Homo Sapiens
symmetry Space Group: P 62
R_factor 0.212 R_Free 0.282
length a length b length c angle alpha angle beta angle gamma
99.622 99.622 41.232 90.00 90.00 120.00
method X-Ray Diffractionresolution 2.40 Å
ligand M3L, MSE enzyme Ligase E.C.6.3.2 BRENDA
Primary referenceRecognition of multivalent histone states associated with heterochromatin by UHRF1., Nady N, Lemak A, Walker JR, Avvakumov GV, Kareta MS, Achour M, Xue S, Duan S, Allali-Hassani A, Zuo X, Wang YX, Bronner C, Chedin F, Arrowsmith CH, Dhe-Paganon S, J Biol Chem. 2011 Apr 13. PMID:21489993
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (58 Kb) [Save to disk]
  • Biological Unit Coordinates (3db3.pdb1.gz) 51 Kb
  • LPC: Ligand-Protein Contacts for 3DB3
  • CSU: Contacts of Structural Units for 3DB3
  • Likely Quarternary Molecular Structure file(s) for 3DB3
  • Structure Factors (145 Kb)
  • Retrieve 3DB3 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3DB3 from S2C, [Save to disk]
  • Re-refined 3db3 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3DB3 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 3DB3
  • 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 3DB3, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1p3db3, region B:107-321 [Jmol] [rasmolscript] [script source]
  • Fold representative 3db3 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3db3_A] [3db3] [3db3_B]
  • SWISS-PROT database: [Q71DI3] [Q96T88]
  • Domain organization of [H32_HUMAN] [UHRF1_HUMAN] by SWISSPFAM
  • Other resources with information on 3DB3
  • Community annotation for 3DB3 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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