3OMC Transcription Regulator date Aug 26, 2010
title Structure Of Human Snd1 Extended Tudor Domain In Complex Wit Symmetrically Dimethylated Arginine Piwil1 Peptide R4me2s
authors R.Lam, K.Liu, Y.H.Guo, C.B.Bian, C.Xu, F.Mackenzie, C.Bountra, J.We C.H.Arrowsmith, A.M.Edwards, A.Bochkarev, J.Min, Structural Gen Consortium (Sgc)
compound source
Molecule: Staphylococcal Nuclease Domain-Containing Protein
Chain: A, B
Fragment: Tudor Domain (Unp Residues 650-910)
Synonym: 100 Kda Coactivator,Ebna2 Coactivator P100,Tudor D Containing Protein 11,P100 Co-Activator;
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Snd1, Tdrd11
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21-(De3)-V2r-Prare2
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet28-Mhl

Molecule: Synthetic Peptide
Chain: C, D
Engineered: Yes

Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630
Other_details: Symmetrically Dimethylated Arginine Peptide Derived From Piwil1
symmetry Space Group: P 1 21 1
R_factor 0.179 R_Free 0.213
crystal
cell
length a length b length c angle alpha angle beta angle gamma
35.622 75.834 80.177 90.00 90.37 90.00
method X-Ray Diffractionresolution 1.77 Å
ligand 2MR, CL enzyme
Primary referenceStructural basis for recognition of arginine methylated Piwi proteins by the extended Tudor domain., Liu K, Chen C, Guo Y, Lam R, Bian C, Xu C, Zhao DY, Jin J, MacKenzie F, Pawson T, Min J, Proc Natl Acad Sci U S A. 2010 Oct 26;107(43):18398-403. Epub 2010 Oct 11. PMID:20937909
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (149 Kb) [Save to disk]
  • Biological Unit Coordinates (3omc.pdb1.gz) 74 Kb
  • Biological Unit Coordinates (3omc.pdb2.gz) 72 Kb
  • LPC: Ligand-Protein Contacts for 3OMC
  • CSU: Contacts of Structural Units for 3OMC
  • Structure Factors (936 Kb)
  • Retrieve 3OMC in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3OMC from S2C, [Save to disk]
  • Re-refined 3omc structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3OMC 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 3OMC
  • 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 3OMC, from MSDmotif at EBI
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3omc_D] [3omc_C] [3omc_A] [3omc] [3omc_B]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 3OMC: [TUDOR ] by SMART
  • Other resources with information on 3OMC
  • Community annotation for 3OMC 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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