8T0F

Crystal structure of the PEG10 promoter-bound ONECUT2 DNA-binding domain

• PDB DOI: https://doi.org/10.2210/pdb8T0F/pdb
• NAKB: 8T0F

• Classification: TRANSCRIPTION/DNA
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2023-05-31 Released: 2024-08-28 
• Deposition Author(s): Chatterjee, A., Katiki, M., Murali, R.
• Funding Organization(s): Department of Defense (DOD, United States)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.61 Å
• R-Value Free: 0.282 
• R-Value Work: 0.228 
• R-Value Observed: 0.231 

Starting Model: experimental

Literature

Crystal structure of the PEG10 promoter-bound ONECUT2 DNA-binding domain

Chatterjee, A., Katiki, M., Murali, R.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 26.02 kDa 
• Atom Count: 1,668 
• Modelled Residue Count: 159 
• Deposited Residue Count: 180 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
One cut domain family member 2	A	156	Homo sapiens	Mutation(s): 0  Gene Names: ONECUT2, HNF6B
UniProt & NIH Common Fund Data Resources
Find proteins for O95948 (Homo sapiens) Explore O95948  Go to UniProtKB:  O95948
PHAROS:  O95948 GTEx:  ENSG00000119547

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(P*AP*GP*AP*TP*CP*GP*AP*TP*TP*TP*GP*C)-3')	B	12	Homo sapiens

Entity ID: 3
Molecule	Chains	Length	Organism	Image
DNA (5'-D(P*GP*CP*AP*AP*AP*TP*CP*GP*AP*TP*CP*T)-3')	C	12	Homo sapiens

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.61 Å
• R-Value Free: 0.282 
• R-Value Work: 0.228 
• R-Value Observed: 0.231 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 96.229	α = 90
b = 78.303	β = 110.99
c = 39.447	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data scaling
HKL-2000	data reduction
MOLREP	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-08-28 
Deposition Author(s): Chatterjee, A., Katiki, M., Murali, R.

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Funding Organization	Location	Grant Number
Department of Defense (DOD, United States)	United States	PC210486

Revision History  

• Version 1.0: 2024-08-28
  Type: Initial release