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), 0.250 (DCC)
R-Value Work:
0.199 (Depositor), 0.200 (DCC)
R-Value Observed:
0.201 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.0 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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(by identity cutoff) | 3D Structure

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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P48432
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P20263
Sequence Annotations Expand
Reference Sequence

Find similar nucleic acids by: Sequence | 3D Structure

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

Find similar nucleic acids by: Sequence | 3D Structure

Entity ID: 4
Molecule	Chains	Length	Organism	Image
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), 0.250 (DCC)
R-Value Work: 0.199 (Depositor), 0.200 (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

View Full Validation Report

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

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.