1HF0

Crystal structure of the DNA-binding domain of Oct-1 bound to DNA as a dimer

• PDB DOI: https://doi.org/10.2210/pdb1HF0/pdb
• NAKB: 1HF0

• Classification: TRANSCRIPTION
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2000-11-27 Released: 2001-11-10 
• Deposition Author(s): Remenyi, A., Tomilin, A., Pohl, E., Scholer, H.R., Wilmanns, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 0.294 
• R-Value Work: 0.239 
• R-Value Observed: 0.239 

Literature

Differential Dimer Activities of the Transcription Factor Oct-1 by DNA-Induced Interface Swapping

Remenyi, A., Tomilin, A., Pohl, E., Lins, K., Philippsen, A., Reinbold, R., Scholer, H.R., Wilmanns, M.

(2001) Mol Cell 8: 569

• PubMed: 11583619 
• DOI: https://doi.org/10.1016/s1097-2765(01)00336-7
• Primary Citation of Related Structures:  
  1E3O, 1HF0


• PubMed Abstract: 
  

  Two crystal structures of Oct-1 POU domain bound to DNA provide a rationale for differential, conformation-dependent recruitment of transcription cofactors. The POU-homeo and POU-specific subdomains of Oct-1 contain two different nonoverlapping pairs of surface patches that are capable of forming unrelated protein-protein interfaces. Members of the POU factor family contain one or two conserved sequence motifs in the interface that are known to be phosphorylated, as noted for Oct-1 and Pit-1. Modeling of Oct-4 reveals the unique case where the same conserved sequence is located in both interfaces. Our studies provide the basis for two distinct dimeric POU factor arrangements that are dictated by the architecture of each DNA response element. We suggest interface swapping in dimers could be a general mechanism of modulating the activity of transcription factors.

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Organizational Affiliation: 

European Molecular Biology Laboratory, Hamburg Outstation, c/o DESY, Notkestrasse 85, D-22603 Hamburg, Germany.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 50.16 kDa 
• Atom Count: 3,079 
• Modelled Residue Count: 300 
• Deposited Residue Count: 362 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
OCTAMER-BINDING TRANSCRIPTION FACTOR 1	A, B	159	Homo sapiens	Mutation(s): 2
UniProt & NIH Common Fund Data Resources
Find proteins for P14859 (Homo sapiens) Explore P14859  Go to UniProtKB:  P14859
PHAROS:  P14859 GTEx:  ENSG00000143190

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA 5'-D(*CP*AP*CP*AP*TP*TP*TP*GP*AP*AP*AP*GP*GP* CP*AP*AP*AP*TP*GP*GP*AP*G)-3'	C [auth M]	22	N/A

Entity ID: 3
Molecule	Chains	Length	Organism	Image
DNA 5'-D(*CP*TP*CP*CP*AP*TP*TP*TP*GP*CP*CP*TP*TP* TP*CP*AP*AP*AP*TP*GP*TP*G)-3'	D [auth N]	22	N/A

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 0.294 
• R-Value Work: 0.239 
• R-Value Observed: 0.239 
• Space Group: P 6₂ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 131.25	α = 90
b = 131.25	β = 90
c = 116.5	γ = 120

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
SHELX	phasing
SHARP	phasing
CNS	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2001-11-10 
Deposition Author(s): Remenyi, A., Tomilin, A., Pohl, E., Scholer, H.R., Wilmanns, M.

Revision History  

• Version 1.0: 2001-11-10
  Type: Initial release
  
• Version 1.1: 2012-11-14
  Changes: Data collection, Database references, Derived calculations, Non-polymer description, Other, Refinement description, Structure summary, Version format compliance
• Version 1.2: 2019-07-24
  Changes: Data collection
• Version 1.3: 2024-05-08
  Changes: Data collection, Database references