6HT5

Oct4/Sox2:UTF1 structure

• PDB DOI: https://doi.org/10.2210/pdb6HT5/pdb
• NAKB: 6HT5

• Classification: TRANSCRIPTION
• Organism(s): Mus musculus
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2018-10-03 Released: 2019-10-23 
• Deposition Author(s): Vahokoski, J., Meusch, D., Groves, M., Pogenberg, V., Wilmanns, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.45 Å
• R-Value Free: 0.248 
• R-Value Work: 0.201 
• R-Value Observed: 0.205 

Starting Model: experimental

Literature

Oct4/Sox2:UTF1 structure

Vahokoski, J., Pogenberg, V., Wilmanns, M.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 41.14 kDa 
• Atom Count: 2,287 
• Modelled Residue Count: 221 
• Deposited Residue Count: 280 
• Unique protein chains: 2
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Transcription factor SOX-2	C [auth D]	83	Mus musculus	Mutation(s): 0  Gene Names: Sox2, Sox-2
UniProt & NIH Common Fund Data Resources
Find proteins for P48432 (Mus musculus) Explore P48432  Go to UniProtKB:  P48432
IMPC:  MGI:98364

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
POU domain, class 5, transcription factor 1	D [auth E]	154	Mus musculus	Mutation(s): 5  Gene Names: Pou5f1, Oct-3, Oct-4, Otf-3, Otf3
UniProt
Find proteins for P20263 (Mus musculus) Explore P20263  Go to UniProtKB:  P20263

Entity ID: 1
Molecule	Chains	Length	Organism	Image
DNA (5'-D(P*CP*CP*TP*CP*AP*TP*TP*GP*TP*TP*AP*TP*GP*CP*TP*AP*GP*TP*GP*AP*AP*G)-3')	A	22	Mus musculus

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*TP*TP*CP*AP*CP*TP*AP*GP*CP*AP*TP*AP*AP*CP*AP*AP*TP*GP*AP*GP*G)-3')	B	21	Mus musculus

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.45 Å
• R-Value Free: 0.248 
• R-Value Work: 0.201 
• R-Value Observed: 0.205 
• Space Group: P 6₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 165.17	α = 90
b = 165.17	β = 90
c = 39.78	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2019-10-23 
Deposition Author(s): Vahokoski, J., Meusch, D., Groves, M., Pogenberg, V., Wilmanns, M.

Revision History  

• Version 1.0: 2019-10-23
  Type: Initial release
  
• Version 1.1: 2024-01-24
  Changes: Data collection, Database references, Refinement description