8K2E

Crystal structure of YTHDC1 and Y3 complex

• PDB DOI: https://doi.org/10.2210/pdb8K2E/pdb

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


• Deposited: 2023-07-12 Released: 2024-07-17 
• Deposition Author(s): Zhang, H.L., Yang, S.Y.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 0.224 
• R-Value Work: 0.185 
• R-Value Observed: 0.188 

Starting Model: experimental

Literature

PocketFlow is a data-and-knowledge-driven structure-based molecular generative model

Jiang, Y., Zhang, G., You, J., Zhang, H., Yao, R., Xie, H., Zhang, L., Xia, Z., Dai, M., Wu, Y., Li, L., Yang, S.

(2024) Nat Mach Intell 6: 326-337

• DOI: https://doi.org/10.1038/s42256-024-00808-8

Biological Assembly 1  

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

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

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 37.96 kDa 
• Atom Count: 2,896 
• Modelled Residue Count: 328 
• Deposited Residue Count: 330 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
YTH domain-containing protein 1	A [auth B], B [auth A]	165	Homo sapiens	Mutation(s): 0  Gene Names: YTHDC1, KIAA1966, YT521
UniProt & NIH Common Fund Data Resources
Find proteins for Q96MU7 (Homo sapiens) Explore Q96MU7  Go to UniProtKB:  Q96MU7
PHAROS:  Q96MU7 GTEx:  ENSG00000083896

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
VIM (Subject of Investigation/LOI)	C [auth B], E [auth A]	2-chloranyl-6-(4-fluoranylphenoxy)benzoic acid C13 H8 Cl F O3 XDDFAQWRNVXRFE-UHFFFAOYSA-N
SO4	D [auth B], F [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 0.224 
• R-Value Work: 0.185 
• R-Value Observed: 0.188 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 39.644	α = 90
b = 103.515	β = 102.425
c = 41.815	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-07-17 
Deposition Author(s): Zhang, H.L., Yang, S.Y.

---

Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	--

Revision History  

• Version 1.0: 2024-07-17
  Type: Initial release