1IO4 Transcription Dna date Jan 10, 2001
title Crystal Structure Of Runx-1aml1cbfalpha Runt Domain- Cbfbeta Core Domain Heterodimer And Cebpbeta Bzip Homodimer Bound To A Dna Fragment From The Csf-1r Promoter
authors T.H.Tahirov, K.Ogata
compound source
Molecule: Csf-1r Promoter
Chain: E
Engineered: Yes
Synthetic: Yes

Molecule: Csf-1r Promoter
Chain: F
Engineered: Yes

Synthetic: Yes

Molecule: Caatenhancer Binding Protein Beta
Chain: A, B
Fragment: Bzip Domain
Synonym: Cebp Beta
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_vector: Plasmid
Expression_system_plasmid: Par2156

Molecule: Runt-Related Transcription Factor 1
Chain: C
Fragment: Runt Domain
Synonym: Core-Binding Factor, Alpha B Subunit, Pepb2-Alpha B;
Engineered: Yes

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

Molecule: Core-Binding Factor, Beta Subunit
Chain: D
Fragment: Core Domain
Synonym: Pebp2-Beta, Cbf-Beta
Engineered: Yes

Organism_scientific: Mus Musculus
Organism_common: House Mouse
Organism_taxid: 10090
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_vector: Plasmid
Expression_system_plasmid: Par2156
symmetry Space Group: C 2 2 21
R_factor 0.247 R_Free 0.299
crystal
cell
length a length b length c angle alpha angle beta angle gamma
121.108 163.600 109.326 90.00 90.00 90.00
method X-Ray Diffractionresolution 3.00 Å
ligand AU enzyme
related structures by homologous chain: 1CO1, 1E50, 1HJB, 1ILF
Gene
Ontology
ChainFunctionProcessComponent
A, B


C


D


Primary referenceStructural analyses of DNA recognition by the AML1/Runx-1 Runt domain and its allosteric control by CBFbeta., Tahirov TH, Inoue-Bungo T, Morii H, Fujikawa A, Sasaki M, Kimura K, Shiina M, Sato K, Kumasaka T, Yamamoto M, Ishii S, Ogata K, Cell 2001 Mar 9;104(5):755-67. PMID:11257229
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (92 Kb) [Save to disk]
  • Biological Unit Coordinates (1io4.pdb1.gz) 87 Kb
  • LPC: Ligand-Protein Contacts for 1IO4
  • CSU: Contacts of Structural Units for 1IO4
  • Likely Quarternary Molecular Structure file(s) for 1IO4
  • Structure Factors (218 Kb)
  • Retrieve 1IO4 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1IO4 from S2C, [Save to disk]
  • Re-refined 1io4 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1IO4 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 1IO4
  • 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 1IO4, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1io4a_, region A [Jmol] [rasmolscript] [script source]
        - Domain d1io4b_, region B [Jmol] [rasmolscript] [script source]
        - Domain d1io4c_, region C [Jmol] [rasmolscript] [script source]
        - Domain d1io4d_, region D [Jmol] [rasmolscript] [script source]
  • Fold representative 1io4 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: [1io4_B] [1io4_E] [1io4] [1io4_D] [1io4_C] [1io4_F] [1io4_A]
  • SWISS-PROT database: [P17676] [Q08024] [Q03347]
  • Domain organization of [CEBPB_HUMAN] [PEBB_MOUSE] [RUNX1_MOUSE] by SWISSPFAM
  • Domain found in 1IO4: [BRLZ ] by SMART
  • Other resources with information on 1IO4
  • Community annotation for 1IO4 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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