8BS5

Crystal structure of YTHDF3 YTH domain open conformation

• PDB DOI: https://doi.org/10.2210/pdb8BS5/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: 2.49 Å
• R-Value Free: 0.306 
• R-Value Work: 0.275 
• R-Value Observed: 0.277 

Literature

Crystal structure of YTHDF3 YTH domain open conformation

Bedi, R.K., Caflisch, A.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 23.36 kDa 
• Atom Count: 1,366 
• Modelled Residue Count: 163 
• Deposited Residue Count: 198 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
YTH domain-containing family protein 3	A	198	Homo sapiens	Mutation(s): 0  Gene Names: YTHDF3
UniProt & NIH Common Fund Data Resources
Find proteins for Q7Z739 (Homo sapiens) Explore Q7Z739  Go to UniProtKB:  Q7Z739
PHAROS:  Q7Z739 GTEx:  ENSG00000185728

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
TLA	B [auth A]	L(+)-TARTARIC ACID C4 H6 O6 FEWJPZIEWOKRBE-JCYAYHJZSA-N
PEG	C [auth A]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.49 Å
• R-Value Free: 0.306 
• R-Value Work: 0.275 
• R-Value Observed: 0.277 
• Space Group: P 4 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 80.86	α = 90
b = 80.86	β = 90
c = 122.34	γ = 90

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