4H75 Gene Regulation date Sep 20, 2012
title Crystal Structure Of Human Spindlin1 In Complex With A Histo H3k4(Me3) Peptide
authors N.Yang, W.Wang, Y.Wang, M.Wang, Q.Zhao, Z.Rao, B.Zhu, R.M.Xu
compound source
Molecule: Spindlin-1
Chain: A
Fragment: Unp Residues 27-262
Synonym: Ovarian Cancer-Related Protein
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Spin1, Ocr, Spin
Expression_system: Escherichia Coli
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pgex-2t

Molecule: Histone H3
Chain: B
Fragment: H3k4(Me3) Peptide (Unp Residues 2-9)
Engineered: Yes

Synthetic: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
symmetry Space Group: P 21 21 2
R_factor 0.181 R_Free 0.218
length a length b length c angle alpha angle beta angle gamma
122.429 42.685 50.307 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.10 Å
ligand GOL, M3L, NHE, SO4 enzyme

Primary referenceDistinct mode of methylated lysine-4 of histone H3 recognition by tandem tudor-like domains of Spindlin1., Yang N, Wang W, Wang Y, Wang M, Zhao Q, Rao Z, Zhu B, Xu RM, Proc Natl Acad Sci U S A. 2012 Oct 17. PMID:23077255
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (83 Kb) [Save to disk]
  • Biological Unit Coordinates (4h75.pdb1.gz) 78 Kb
  • LPC: Ligand-Protein Contacts for 4H75
  • CSU: Contacts of Structural Units for 4H75
  • Structure Factors (243 Kb)
  • Retrieve 4H75 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4H75 from S2C, [Save to disk]
  • Re-refined 4h75 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4H75 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 4H75
  • 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 4H75, from MSDmotif at EBI
  • Fold representative 4h75 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4h75_B] [4h75] [4h75_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 4H75
  • Community annotation for 4H75 at PDBWiki (http://pdbwiki.org)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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