9H35

Crystal structure of the YTHDC2 YTH domain

PDB DOI: https://doi.org/10.2210/pdb9H35/pdb

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

Deposited: 2024-10-15 Released: 2024-10-30
Deposition Author(s): Bedi, R.K., Caflisch, A.
Funding Organization(s): Swiss National Science Foundation

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.68 Å
R-Value Free: 0.284
R-Value Work: 0.227
R-Value Observed: 0.229

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

Crystal structure of the YTHDC2 YTH domain

Bedi, R.K., Caflisch, A.

To be published.

Macromolecule Content

Total Structure Weight: 65.08 kDa
Atom Count: 4,170
Modelled Residue Count: 538
Deposited Residue Count: 564
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3'-5' RNA helicase YTHDC2	A, B, C, D	141	Homo sapiens	Mutation(s): 0 Gene Names: YTHDC2 EC: 3.6.4.13
UniProt & NIH Common Fund Data Resources
Find proteins for Q9H6S0 (Homo sapiens) Explore Q9H6S0 Go to UniProtKB: Q9H6S0
PHAROS: Q9H6S0 GTEx: ENSG00000047188
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9H6S0
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.68 Å
R-Value Free: 0.284
R-Value Work: 0.227
R-Value Observed: 0.229
Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 115.972	α = 90
b = 115.972	β = 90
c = 205.847	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

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Entry History & Funding Information

Deposition Data

Released Date: 2024-10-30

Deposition Author(s):

Funding Organization	Location	Grant Number
Swiss National Science Foundation	Switzerland	310030B_189363

Revision History (Full details and data files)

Version 1.0: 2024-10-30
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.