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

Validation slider image for 9URH

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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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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O95319
Sequence Annotations Expand
Reference Sequence

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Molecule	Chains	Length	Organism	Image
Entity ID: 2
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

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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

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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.