8PN4

transcription factor BARHL2 bound to DNA sequences

PDB DOI: https://doi.org/10.2210/pdb8PN4/pdb
NAKB: 8PN4

Classification: TRANSCRIPTION
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2023-06-29 Released: 2024-07-10
Deposition Author(s): Morgunova, E., Yin, Y., Popov, A., Taipale, J.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.60 Å
R-Value Free: 0.274
R-Value Work: 0.243
R-Value Observed: 0.245

wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

transcription factor BARHL2 bound to DNA sequences

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

To be published.

Macromolecule Content

Total Structure Weight: 66.91 kDa
Atom Count: 4,562
Modelled Residue Count: 379
Deposited Residue Count: 406
Unique protein chains: 1
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
BarH-like 2 homeobox protein	A, D, G, J, M	62	Homo sapiens	Mutation(s): 0 Gene Names: BARHL2
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NY43 (Homo sapiens) Explore Q9NY43 Go to UniProtKB: Q9NY43
PHAROS: Q9NY43 GTEx: ENSG00000143032
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9NY43
Sequence Annotations Expand
Reference Sequence

Find similar nucleic acids by: Sequence | 3D Structure

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA	B, E, H, K	12	Homo sapiens
Sequence Annotations Expand
Reference Sequence

Find similar nucleic acids by: Sequence | 3D Structure

Entity ID: 3
Molecule	Chains	Length	Organism	Image
DNA	C, F, I, L	12	Homo sapiens
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ACT Query on ACT Download Ideal Coordinates CCD File SDF format, chain N [auth B] MOL2 format, chain N [auth B] mmCIF format, chain N [auth B]	N [auth B]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain N [auth B] Interactions & Density Focus chain N [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.60 Å
R-Value Free: 0.274
R-Value Work: 0.243
R-Value Observed: 0.245
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 39.426	α = 90
b = 134.56	β = 93.18
c = 64.491	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2024-07-10

Deposition Author(s):

Funding Organization	Location	Grant Number
Not funded		--

Revision History (Full details and data files)

Version 1.0: 2024-07-10
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.