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
crystal cell	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 Diffraction	resolution	2.40 Å
ligand	M3L, MSE	enzyme	Ligase E.C.6.3.2 BRENDA
Primary reference	Recognition 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

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 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]

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)

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