8BS4

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

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.248 
• R-Value Work: 0.214 
• R-Value Observed: 0.216 

Starting Model: experimental

Literature

Crystal structure of YTHDF1 YTH domain dimer

Bedi, R.K., Caflisch, A.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content

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

Macromolecules

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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	D [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
ACT	C [auth A]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.248 
• R-Value Work: 0.214 
• R-Value Observed: 0.216 
• 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

Entry History & Funding Information

Deposition Data

• Released Date: 2023-12-13 
Deposition Author(s): Bedi, R.K., Caflisch, A.

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

Revision History  

• Version 1.0: 2023-12-13
  Type: Initial release