8BX2 | pdb_00008bx2

Oct4/Sox2 protein:DNA complex

PDB DOI: https://doi.org/10.2210/pdb8BX2/pdb
NAKB: 8BX2

Classification: TRANSCRIPTION
Organism(s): Mus musculus
Expression System: Escherichia coli O111:NM str. 01-3076, Escherichia coli
Mutation(s): No

Deposited: 2022-12-07 Released: 2023-12-20
Deposition Author(s): Chojnowski, G., Wilmanns, M., Round, E.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.14 Å
R-Value Free:
0.252 (Depositor), 0.252 (DCC)
R-Value Work:
0.199 (Depositor), 0.197 (DCC)
R-Value Observed:
0.201 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 8BX2

This is version 1.1 of the entry. See complete history.

Literature

Crystal structure of Oct4-Soc2-UTF1 complex

Chojnowski, G., Wilmanns, M., Round, E.

To be published.

Macromolecule Content

Total Structure Weight: 41.56 kDa
Atom Count: 2,298
Modeled Residue Count: 220
Deposited Residue Count: 282
Unique protein chains: 2
Unique nucleic acid chains: 2

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Transcription factor SOX-2	A [auth E]	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 Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P48432
Sequence Annotations Expand
Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
POU domain, class 5, transcription factor 1	B [auth A]	155	Mus musculus	Mutation(s): 0 Gene Names: Pou5f1, Oct-3, Oct-4, Otf-3, Otf3
UniProt
Find proteins for P20263 (Mus musculus) Explore P20263 Go to UniProtKB: P20263
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P20263
Sequence Annotations Expand
Reference Sequence

Find similar nucleic acids by: Sequence

Molecule	Chains	Length	Organism	Image
Entity ID: 3
UTF1_r	C	22	Mus musculus
Sequence Annotations Expand
Reference Sequence

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Molecule	Chains	Length	Organism	Image
Entity ID: 4
UTF1_f	D	22	Mus musculus
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.14 Å
R-Value Free: 0.252 (Depositor), 0.252 (DCC)
R-Value Work: 0.199 (Depositor), 0.197 (DCC)
R-Value Observed: 0.201 (Depositor)

Space Group: P 6₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 163.169	α = 90
b = 163.169	β = 90
c = 39.792	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
STARANISO	data scaling
MOLREP	phasing

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2023-12-20

Deposition Author(s):

Funding Organization	Location	Grant Number
Not funded		--

Revision History (Full details and data files)

Version 1.0: 2023-12-20
Type: Initial release
Version 1.1: 2026-03-04
Changes: Refinement description, Structure summary

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.