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 

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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: https://doi.org/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 backbone forms a pair of hydrogen bonds with the adenine base at position 5 of the octamer DNA ...

    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

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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
POU DOMAIN, CLASS 2, TRANSCRIPTION FACTOR 1E [auth A],
F [auth B]		163Homo sapiensMutation(s): 0 
Gene Names: POU2F1, OCT1, OTF1
UniProt & NIH Common Fund Data Resources
Find proteins for P14859 (Homo sapiens)
Explore P14859 
Go to UniProtKB:  P14859
PHAROS:  P14859
Entity Groups  
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UniProt GroupP14859
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
POU DOMAIN, CLASS 2, ASSOCIATING FACTOR 1G [auth I],
H [auth J]		44Homo sapiensMutation(s): 0 
Gene Names: POU2AF1, BOB1, OBF1
UniProt & NIH Common Fund Data Resources
Find proteins for Q16633 (Homo sapiens)
Explore Q16633 
Go to UniProtKB:  Q16633
PHAROS:  Q16633
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UniProt GroupQ16633
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  • Reference Sequence

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Entity ID: 1
MoleculeChainsLengthOrganismImage
DNA (5'-D(*TP*GP*TP*AP*TP*GP*CP*AP*AP*AP*TP*AP*AP*GP*G)-3')A [auth M],
C [auth O]		15N/A
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  • Reference Sequence

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Entity ID: 2
MoleculeChainsLengthOrganismImage
DNA (5'-D(*AP*CP*CP*TP*TP*AP*TP*TP*TP*GP*CP*AP*TP*AP*C)-3')B [auth N],
D [auth P]		15N/A
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  • Reference Sequence
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

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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