1CQT

CRYSTAL STRUCTURE OF A TERNARY COMPLEX CONTAINING AN OCA-B PEPTIDE, THE OCT-1 POU DOMAIN, AND AN OCTAMER ELEMENT


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 0.326 
  • R-Value Work: 0.264 
  • R-Value Observed: 0.264 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Crystal structure of an OCA-B peptide bound to an Oct-1 POU domain/octamer DNA complex: specific recognition of a protein-DNA interface.

Chasman, D.Cepek, K.Sharp, P.A.Pabo, C.O.

(1999) Genes Dev 13: 2650-2657

  • DOI: 10.1101/gad.13.20.2650
  • Primary Citation of Related Structures:  
    1CQT

  • PubMed Abstract: 
  • We have determined the crystal structure, at 3.2 A, of a ternary complex containing an OCA-B peptide, the Oct-1 POU domain, and an octamer DNA site. The OCA-B peptide binds in the major groove near the center of the octamer site, and its polypeptide ...

    We have determined the crystal structure, at 3.2 A, of a ternary complex containing an OCA-B peptide, the Oct-1 POU domain, and an octamer DNA site. The OCA-B peptide binds in the major groove near the center of the octamer site, and its polypeptide backbone forms a pair of hydrogen bonds with the adenine base at position 5 of the octamer DNA. Numerous protein-protein contacts between the OCA-B peptide and the POU domain are also involved in the ternary complex. In particular, the hydrophobic surface from a short alpha-helix of OCA-B helps to stabilize the complex by binding to a hydrophobic pocket on the POU-specific domain. The structure of this ternary complex is consistent with previous biochemical studies and shows how peptide-DNA and peptide-protein contacts from OCA-B provide structural and functional specificity in the regulation of immunoglobulin transcription.


    Related Citations: 
    • Crystal Structure of the Oct-1 POU Domain Bound to an Octamer Site: DNA Recognition with Tethered DNA-Binding Modules
      Klemm, J.D., Rould, M.A., Aurora, R., Herr, W., Pabo, C.O.
      (1994) Cell 77: 21

    Organizational Affiliation

    Center for Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
POU DOMAIN, CLASS 2, TRANSCRIPTION FACTOR 1AB163Homo sapiensMutation(s): 0 
Gene Names: POU2F1OCT1OTF1
Find proteins for P14859 (Homo sapiens)
Explore P14859 
Go to UniProtKB:  P14859
NIH Common Fund Data Resources
PHAROS  P14859
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
POU DOMAIN, CLASS 2, ASSOCIATING FACTOR 1IJ44Homo sapiensMutation(s): 0 
Gene Names: POU2AF1BOB1OBF1
Find proteins for Q16633 (Homo sapiens)
Explore Q16633 
Go to UniProtKB:  Q16633
NIH Common Fund Data Resources
PHAROS  Q16633
Protein Feature View
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  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 1
    MoleculeChainsLengthOrganismImage
    DNA (5'-D(*TP*GP*TP*AP*TP*GP*CP*AP*AP*AP*TP*AP*AP*GP*G)-3')M, O15N/A
    • Find similar nucleic acids by:  Sequence   |   Structure
    • Entity ID: 2
      MoleculeChainsLengthOrganismImage
      DNA (5'-D(*AP*CP*CP*TP*TP*AP*TP*TP*TP*GP*CP*AP*TP*AP*C)-3')N, P15N/A
      Experimental Data & Validation

      Experimental Data

      • Method: X-RAY DIFFRACTION
      • Resolution: 3.20 Å
      • R-Value Free: 0.326 
      • R-Value Work: 0.264 
      • R-Value Observed: 0.264 
      • Space Group: P 41 21 2
      Unit Cell:
      Length ( Å )Angle ( ˚ )
      a = 93.722α = 90
      b = 93.722β = 90
      c = 152.651γ = 90
      Software Package:
      Software NamePurpose
      AMoREphasing
      SHARPphasing
      Omodel building
      X-PLORrefinement
      DENZOdata reduction
      SCALEPACKdata scaling

      Structure Validation

      View Full Validation Report



      Entry History 

      Deposition Data

      Revision History 

      • Version 1.0: 1999-11-15
        Type: Initial release
      • Version 1.1: 2008-04-27
        Changes: Version format compliance
      • Version 1.2: 2011-07-13
        Changes: Version format compliance