1H9D Transcription Factor date Mar 07, 2001
title Aml1cbf-Betadna Complex
authors J.Bravo, A.J.Warren
compound source
Molecule: Core-Binding Factor Alpha Subunit1
Chain: A, C
Fragment: Runt Domain Residues 50-183
Synonym: Cbfa2pepbp2abrunx1, Aml-1
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Aml1
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008
Expression_system_variant: C41
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Prset

Molecule: Core-Binding Factor Cbf-Beta
Chain: B, D
Fragment: Heterodimerisation Domain Residues 2-135
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Cbfb
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008
Expression_system_variant: C41
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Prset

Molecule: Dna (5'-(Gptptpgpcpgpgptptpg)-3')
Chain: E, G
Engineered: Yes

Synthetic: Yes

Molecule: Dna (5'-(Cpapapcpcpgpcpapapc)-3')
Chain: F, H
Engineered: Yes

Synthetic: Yes
symmetry Space Group: P 43 21 2
R_factor 0.237 R_Free 0.271
crystal
cell
length a length b length c angle alpha angle beta angle gamma
115.033 115.033 133.925 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.60 Å
note 1H9D is a representative structure
related structures by homologous chain: 1E50, 1LJM
Gene
Ontology
ChainFunctionProcessComponent
A, C


D, B


Primary referenceThe leukemia-associated AML1 (Runx1)--CBF beta complex functions as a DNA-induced molecular clamp., Bravo J, Li Z, Speck NA, Warren AJ, Nat Struct Biol 2001 Apr;8(4):371-8. PMID:11276260
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (104 Kb) [Save to disk]
  • Biological Unit Coordinates (1h9d.pdb1.gz) 50 Kb
  • Biological Unit Coordinates (1h9d.pdb2.gz) 50 Kb
  • CSU: Contacts of Structural Units for 1H9D
  • Likely Quarternary Molecular Structure file(s) for 1H9D
  • Structure Factors (197 Kb)
  • Retrieve 1H9D in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1H9D from S2C, [Save to disk]
  • Re-refined 1h9d structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1H9D 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 1H9D
  • 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 1H9D, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1h9da_, region A [Jmol] [rasmolscript] [script source]
        - Domain d1h9db_, region B [Jmol] [rasmolscript] [script source]
        - Domain d1h9dc_, region C [Jmol] [rasmolscript] [script source]
        - Domain d1h9dd_, region D [Jmol] [rasmolscript] [script source]
  • Fold representative 1h9d 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: [1h9d_H] [1h9d_A] [1h9d_F] [1h9d_D] [1h9d] [1h9d_B] [1h9d_E] [1h9d_G] [1h9d_C]
  • SWISS-PROT database: [Q13951] [Q01196]
  • Domain organization of [PEBB_HUMAN] [RUNX1_HUMAN] by SWISSPFAM
  • Other resources with information on 1H9D
  • Community annotation for 1H9D 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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