4HCA Transcription Dna date Sep 28, 2012
title Dna Binding By Gata Transcription Factor-Complex 1
authors Y.Chen, D.L.Bates, R.Dey, L.Chen
compound source
Molecule: Trans-Acting T-Cell-Specific Transcription Factor
Chain: A
Fragment: Unp Residues 260 -368
Synonym: Gata-Binding Factor 3
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Gata3
Expression_system: Escherichia Coli
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)

Molecule: Dna (5'- D(Apaptpgptpcpcpaptpcptpgpaptpapapgpapcp
Chain: X
Engineered: Yes

Synthetic: Yes
Other_details: This Sequence Occurs Naturally In Humans

Molecule: Dna (5'- D(Tptpcpgptpcptptpaptpcpapgpaptpgpgpapcp
Chain: Y
Engineered: Yes

Synthetic: Yes
Other_details: This Sequence Occurs Naturally In Humans
symmetry Space Group: P 1 21 1
R_factor 0.245 R_Free 0.296
crystal
cell
length a length b length c angle alpha angle beta angle gamma
54.486 36.550 66.118 90.00 103.70 90.00
method X-Ray Diffractionresolution 2.80 Å
ligand ZN enzyme
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceDNA Binding by GATA Transcription Factor Suggests Mechanisms of DNA Looping and Long-Range Gene Regulation., Chen Y, Bates DL, Dey R, Chen PH, Machado AC, Laird-Offringa IA, Rohs R, Chen L, Cell Rep. 2012 Nov 29;2(5):1197-206. doi: 10.1016/j.celrep.2012.10.012. Epub 2012, Nov 8. PMID:23142663
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (73 Kb) [Save to disk]
  • Biological Unit Coordinates (4hca.pdb1.gz) 68 Kb
  • LPC: Ligand-Protein Contacts for 4HCA
  • CSU: Contacts of Structural Units for 4HCA
  • Structure Factors (40 Kb)
  • Retrieve 4HCA in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4HCA from S2C, [Save to disk]
  • Re-refined 4hca structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4HCA 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 4HCA
  • 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 4HCA, from MSDmotif at EBI
  • Fold representative 4hca from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4hca_X] [4hca_A] [4hca] [4hca_Y]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Alignments of the sequence of 4HCA with the sequences similar proteins can be viewed for 4HCA's classification at ProtoMap. Click on "Neighbors List", then on the "See Alignments" button below the list.
  • A sequence distance tree ("phylogenetic tree") can be viewed for 1ACL's classification at ProtoMap. Click on the Cluster number.
  • Other resources with information on 4HCA
  • Community annotation for 4HCA at PDBWiki (http://pdbwiki.org)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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