3U2B Transcription Dna date Oct 03, 2011
title Structure Of The Sox4 Hmg Domain Bound To Dna
authors R.Jauch, C.K.L.Ng, P.R.Kolatkar
compound source
Molecule: Dna (5'-D(Gptpcptpcptpaptptpgptpcpcp 3');
Chain: A
Engineered: Yes
Other_details: Sequence Derived From The Lama1 Gene
Synthetic: Yes
Other_details: Synthetic Dna

Molecule: Dna (5'-D(Cpcpapgpgpapcpapaptpapgpap 3');
Chain: B
Engineered: Yes
Other_details: Sequence Derived From The Lama1 Gene

Synthetic: Yes
Other_details: Synthetic Dna

Molecule: Transcription Factor Sox-4
Chain: C
Fragment: Unp Residues 57-135
Engineered: Yes

Organism_scientific: Mus Musculus
Organism_common: Mouse
Organism_taxid: 10090
Gene: Sox4, Sox-4
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_vector_type: Plasmid
symmetry Space Group: P 32 2 1
R_factor 0.235 R_Free 0.280
length a length b length c angle alpha angle beta angle gamma
69.941 69.941 63.205 90.00 90.00 120.00
method X-Ray Diffractionresolution 2.40 Å
note 3U2B is a representative structure
Primary referenceCrystal structure of the Sox4 HMG/DNA complex suggests a mechanism for the positional interdependence in DNA recognition., Jauch R, Ng CK, Narasimhan K, Kolatkar PR, Biochem J. 2011 Dec 19. PMID:22181698
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (62 Kb) [Save to disk]
  • Biological Unit Coordinates (3u2b.pdb1.gz) 56 Kb
  • CSU: Contacts of Structural Units for 3U2B
  • Structure Factors (83 Kb)
  • Retrieve 3U2B in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3U2B from S2C, [Save to disk]
  • Re-refined 3u2b structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3U2B 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 3U2B
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • 3D motif for 3U2B, from MSDmotif at EBI
  • Fold representative 3u2b from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3u2b_A] [3u2b_C] [3u2b_B] [3u2b]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 3U2B: [HMG ] by SMART
  • Other resources with information on 3U2B
  • Community annotation for 3U2B at PDBWiki (http://pdbwiki.org)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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