7Q3O

Structure of CDX1 bound to hydroxymethylated DNA

• PDB DOI: https://doi.org/10.2210/pdb7Q3O/pdb
• NAKB: 7Q3O

• Classification: TRANSCRIPTION
• Organism(s): synthetic construct, Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2021-10-28 Released: 2022-11-16 
• Deposition Author(s): Morgunova, E., Yin, Y., Popov, A., Taipale, J.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.78 Å
• R-Value Free: 0.286 
• R-Value Work: 0.217 
• R-Value Observed: 0.220 

Literature

Structure of CDX1 bound to hydroxymethylated DNA

Morgunova, E., Yin, Y., Popov, A., Taipale, J.

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)

Biological Assembly Evidence: isothermal titration calorimetry

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

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

Biological assembly 3 assigned by authors and generated by PISA (software)

Biological Assembly 4  

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

Biological assembly 4 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 76.82 kDa 
• Atom Count: 5,202 
• Modelled Residue Count: 389 
• Deposited Residue Count: 404 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Homeobox protein CDX-1	I [auth K], J [auth C], K [auth E], L [auth G]	65	Homo sapiens	Mutation(s): 0  Gene Names: CDX1
UniProt & NIH Common Fund Data Resources
Find proteins for P47902 (Homo sapiens) Explore P47902  Go to UniProtKB:  P47902
PHAROS:  P47902 GTEx:  ENSG00000113722

Entity ID: 1
Molecule	Chains	Length	Organism	Image
hydroxymethylated DNA (18-MER)	A, C [auth B], E [auth D], G [auth F]	18	synthetic construct

Entity ID: 2
Molecule	Chains	Length	Organism	Image
hydroxymethylated DNA (18-MER)	B [auth H], D [auth I], F [auth J], H [auth L]	18	synthetic construct

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.78 Å
• R-Value Free: 0.286 
• R-Value Work: 0.217 
• R-Value Observed: 0.220 
• Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 45.373	α = 112.37
b = 64.669	β = 108.11
c = 67.028	γ = 93.93

Software Package:

Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2022-11-16 
Deposition Author(s): Morgunova, E., Yin, Y., Popov, A., Taipale, J.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2022-11-16
  Type: Initial release
  
• Version 1.1: 2024-01-31
  Changes: Data collection, Refinement description