1H88 Transcription Dna date Jan 29, 2001
title Crystal Structure Of Ternary Protein-Dna Complex1
authors T.H.Tahirov, K.Ogata
compound source
Molecule: Ccaatenhancer Binding Protein Beta
Chain: A, B
Fragment: Residues 259-336
Synonym: Cebp Beta, Nfil-6
Engineered: Yes
Other_details: Bzip Domain
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Escherichia Coli
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Par2156

Molecule: Myb Proto-Oncogene Protein
Chain: C
Fragment: Residues 35-193
Synonym: C-Myb
Engineered: Yes
Mutation: Yes
Other_details: Dna Binding Domain

Organism_scientific: Mus Musculus
Organism_common: House Mouse
Organism_taxid: 10090
Expression_system: Escherichia Coli
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Par2156

Molecule: Dna(5'-(Gpaptpgptpgpgpcpgpcpap Aptpcpcptptpapapcpgpgpapcptpg)-3');
Chain: D
Fragment: Fragment From Tom-1a Promoter
Engineered: Yes

Synthetic: Yes
Organism_scientific: Homo Sapiens
Organism_taxid: 9606

Molecule: Dna(5'-(Cpcpapgptpcpcpgptptpap Apgpgpaptptpgpcpgpcpcpapcpapt)-3');
Chain: E
Fragment: Fragment From Tom-1a Promoter
Engineered: Yes

Synthetic: Yes
Organism_scientific: Homo Sapiens
Organism_taxid: 9606
symmetry Space Group: P 1 21 1
R_factor 0.222 R_Free 0.277
crystal
cell
length a length b length c angle alpha angle beta angle gamma
41.735 156.966 55.868 90.00 100.16 90.00
method X-Ray Diffractionresolution 2.80 Å
ligand NH4 enzyme
related structures by homologous chain: 1H89, 1HJB, 1IDY, 1MBF, 1NWQ
Gene
Ontology
ChainFunctionProcessComponent
A, B


C


Primary referenceMechanism of c-Myb-C/EBP beta cooperation from separated sites on a promoter., Tahirov TH, Sato K, Ichikawa-Iwata E, Sasaki M, Inoue-Bungo T, Shiina M, Kimura K, Takata S, Fujikawa A, Morii H, Kumasaka T, Yamamoto M, Ishii S, Ogata K, Cell 2002 Jan 11;108(1):57-70. PMID:11792321
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (79 Kb) [Save to disk]
  • Biological Unit Coordinates (1h88.pdb1.gz) 74 Kb
  • LPC: Ligand-Protein Contacts for 1H88
  • CSU: Contacts of Structural Units for 1H88
  • Likely Quarternary Molecular Structure file(s) for 1H88
  • Structure Factors (194 Kb)
  • Retrieve 1H88 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1H88 from S2C, [Save to disk]
  • Re-refined 1h88 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1H88 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 1H88
  • 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 1H88, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1h88a_, region A [Jmol] [rasmolscript] [script source]
        - Domain d1h88b_, region B [Jmol] [rasmolscript] [script source]
        - Domain d1h88c3, region C:144-190 [Jmol] [rasmolscript] [script source]
        - Domain d1h88c1, region C:39-88 [Jmol] [rasmolscript] [script source]
        - Domain d1h88c2, region C:89-143 [Jmol] [rasmolscript] [script source]
  • Fold representative 1h88 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Class (fold), Architecture (subfold), Topology, Homologous superfamily from CATH
  • Summaries and structural analyses of PDB data files from PDBSum
  • Identification of Protein Pockets & Cavities at CASTp
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [1h88_D] [1h88_B] [1h88_C] [1h88_A] [1h88] [1h88_E]
  • SWISS-PROT database: [P17676] [P06876]
  • Domain organization of [CEBPB_HUMAN] [MYB_MOUSE] by SWISSPFAM
  • Domains found in 1H88: [BRLZ] [SANT ] by SMART
  • Other resources with information on 1H88
  • Community annotation for 1H88 at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

  • You may enter another PDB ID code
    Go [Back], to the [PDB Lite page], to the [OCA Search page] or to the [PDB Home page]
    OCA© by Jaime Prilusky, 1996-2014
    Bioinformatics Unit
    Weizmann Institute of Science