1PUF Transcription Dna date Jun 24, 2003
title Crystal Structure Of Hoxa9 And Pbx1 Homeodomains Bound To Dna
authors N.A.Laronde-Leblanc, C.Wolberger
compound source
Molecule: 5'- D(Apcptpcptpaptpgpaptptptpapcpgpapcpgpcp T)-3';
Chain: D
Engineered: Yes
Synthetic: Yes

Molecule: 5'- D(Tpapgpcpgptpcpgptpapapaptpcpaptpapgpap G)-3';
Chain: E
Engineered: Yes

Synthetic: Yes

Molecule: Homeobox Protein Hox-A9
Chain: A
Fragment: Residues 193-269
Synonym: Hox-1.7
Engineered: Yes
Other_details: Homeodomain

Organism_scientific: Mus Musculus
Organism_common: House Mouse
Organism_taxid: 10090
Gene: Hoxa9
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21(De3) Codon + -Ril
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet28a+

Molecule: Pre-B-Cell Leukemia Transcription Factor-1
Chain: B
Fragment: Residues 233-305
Synonym: Homeobox Protein Pbx1, Homeobox Protein Prl
Engineered: Yes
Other_details: Homeodomain

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Pbx1
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet11d
symmetry Space Group: C 2 2 21
R_factor 0.233 R_Free 0.268
length a length b length c angle alpha angle beta angle gamma
60.769 114.853 108.170 90.00 90.00 90.00
method X-Ray Diffractionresolution 1.90 Å


Primary referenceStructure of HoxA9 and Pbx1 bound to DNA: Hox hexapeptide and DNA recognition anterior to posterior., LaRonde-LeBlanc NA, Wolberger C, Genes Dev 2003 Aug 15;17(16):2060-72. PMID:12923056
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (52 Kb) [Save to disk]
  • Biological Unit Coordinates (1puf.pdb1.gz) 47 Kb
  • CSU: Contacts of Structural Units for 1PUF
  • Likely Quarternary Molecular Structure file(s) for 1PUF
  • Structure Factors (330 Kb)
  • Retrieve 1PUF in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1PUF from S2C, [Save to disk]
  • Re-refined 1puf structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1PUF 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 1PUF
  • 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 1PUF, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1pufa_, region A [Jmol] [rasmolscript] [script source]
        - Domain d1pufb_, region B [Jmol] [rasmolscript] [script source]
  • Fold representative 1puf 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: [1puf] [1puf_E] [1puf_B] [1puf_A] [1puf_D]
  • SWISS-PROT database: [P09631] [P40424]
  • Domain organization of [HXA9_MOUSE] [PBX1_HUMAN] by SWISSPFAM
  • Domain found in 1PUF: [HOX ] by SMART
  • Other resources with information on 1PUF
  • Community annotation for 1PUF 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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