9URH | pdb_00009urh

Structural insight into DNA recognition by RRM1+2 domain of human ETR-3 protein

PDB DOI: https://doi.org/10.2210/pdb9URH/pdb
NAKB: 9URH

Classification: RNA BINDING PROTEIN
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2025-04-29 Released: 2025-05-28
Deposition Author(s): Patra, A., Bhavesh, N.S.
Funding Organization(s): Other government

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.82 Å
R-Value Free:
0.221 (Depositor), 0.220 (DCC)
R-Value Work:
0.197 (Depositor), 0.197 (DCC)
R-Value Observed:
0.198 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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

Literature

Structural insight into DNA recognition by RRM1+2 domain of human ETR-3 protein

Patra, A., Bhavesh, N.S.

To be published.

Macromolecule Content

Total Structure Weight: 22.04 kDa
Atom Count: 1,600
Modeled Residue Count: 182
Deposited Residue Count: 186
Unique protein chains: 1
Unique nucleic acid chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CUGBP Elav-like family member 2	A	180	Homo sapiens	Mutation(s): 0 Gene Names: CELF2, BRUNOL3, CUGBP2, ETR3, NAPOR
UniProt & NIH Common Fund Data Resources
Find proteins for O95319 (Homo sapiens) Explore O95319 Go to UniProtKB: O95319
PHAROS: O95319 GTEx: ENSG00000048740
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O95319
Sequence Annotations Expand
Reference Sequence

Find similar nucleic acids by: Sequence | 3D Structure

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(PTPGPGPTP*C)-3')	B	6	Homo sapiens
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain C [auth B] MOL2 format, chain C [auth B] mmCIF format, chain C [auth B]	C [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain C [auth B] Interactions & Density Focus chain C [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.82 Å
R-Value Free: 0.221 (Depositor), 0.220 (DCC)
R-Value Work: 0.197 (Depositor), 0.197 (DCC)
R-Value Observed: 0.198 (Depositor)

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 45.116	α = 90
b = 70.77	β = 90
c = 134.009	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
autoPROC	data reduction
autoPROC	data scaling
PHENIX	phasing

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2025-05-28

Deposition Author(s):

Funding Organization	Location	Grant Number
Other government	India	ICGEB New Delhi Core funds

Revision History (Full details and data files)

Version 1.0: 2025-05-28
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.