8BS4 | pdb_00008bs4

Crystal structure of YTHDF1 YTH domain dimer

PDB DOI: https://doi.org/10.2210/pdb8BS4/pdb

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

Deposited: 2022-11-24 Released: 2023-12-13
Deposition Author(s): Bedi, R.K., Caflisch, A.
Funding Organization(s): Swiss National Science Foundation

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free:
0.248 (Depositor), 0.250 (DCC)
R-Value Work:
0.214 (Depositor), 0.210 (DCC)
R-Value Observed:
0.216 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

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

Literature

Crystal structure of YTHDF1 YTH domain dimer

Bedi, R.K., Caflisch, A.

To be published.

Macromolecule Content

Total Structure Weight: 50.17 kDa
Atom Count: 3,232
Modeled Residue Count: 388
Deposited Residue Count: 426
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
YTH domain-containing family protein 1	A, B	213	Homo sapiens	Mutation(s): 0 Gene Names: YTHDF1, C20orf21
UniProt & NIH Common Fund Data Resources
Find proteins for Q9BYJ9 (Homo sapiens) Explore Q9BYJ9 Go to UniProtKB: Q9BYJ9
PHAROS: Q9BYJ9 GTEx: ENSG00000149658
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9BYJ9
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain D [auth B] MOL2 format, chain D [auth B] mmCIF format, chain D [auth B]	D [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain D [auth B] Interactions & Density Focus chain D [auth B]
ACT Query on ACT Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.248 (Depositor), 0.250 (DCC)
R-Value Work: 0.214 (Depositor), 0.210 (DCC)
R-Value Observed: 0.216 (Depositor)

Space Group: P 6₅ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 91.85	α = 90
b = 91.85	β = 90
c = 206.89	γ = 120

Software Package:

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

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2023-12-13

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: 2023-12-13
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.