6K6U | pdb_00006k6u

Crystal structure of the human YTHDC2 YTH domain

• PDB DOI: https://doi.org/10.2210/pdb6K6U/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli K-12
• Mutation(s): No 


• Deposited: 2019-06-04 Released: 2019-12-25 
• Deposition Author(s): Ma, C., Liao, S., Xu, C.
• Funding Organization(s): National Natural Science Foundation of China

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.27 Å
• R-Value Free: 
  0.246 (Depositor), 0.248 (DCC) 
• R-Value Work: 
  0.195 (Depositor), 0.199 (DCC) 
• R-Value Observed: 
  0.198 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of human YTHDC2 YTH domain.

Ma, C., Liao, S., Zhu, Z.

(2019) Biochem Biophys Res Commun 518: 678-684

• PubMed: 31472957 
• DOI: https://doi.org/10.1016/j.bbrc.2019.08.107
• Primary Citation Related Structures: 
  6K6U


• PubMed Abstract: 
  

  N ⁶ -methyladenosine (m ⁶ A) "readers" play an important role in mRNA functions and metabolism. YTHDC2, as one of the m ⁶ A readers, controls fertileness through decreasing associated mRNA abundance and enhancing the translation efficiency of related mRNA via binding the targeted m ⁶ A RNA. However, how YTH domain of YTHDC2 recognize m ⁶ A RNA is still unknown. In this study, we determined the crystal structure of human YTHDC2 YTH domain, which adopts similar architecture to other solved YTH domain structures. YTHDC2 contains a conserved m ⁶ A binding pocket, and similar RNA binding surface shared by YTHDC1.

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Organizational Affiliation: 
• Hefei National Laboratory for Physical Sciences at the Microscale and School of Life Sciences, University of Science and Technology of China, 230027, Hefei, China.
Hefei National Laboratory for Physical Sciences at the Microscale and School of Life Sciences, University of Science and Technology of China, 230027, Hefei, China. Electronic address: [e-mail].

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 33.11 kDa 
• Atom Count: 2,180 
• Modeled Residue Count: 257 
• Deposited Residue Count: 286 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3'-5' RNA helicase YTHDC2	A, B	143	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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.27 Å
• R-Value Free:  0.246 (Depositor), 0.248 (DCC) 
• R-Value Work:  0.195 (Depositor), 0.199 (DCC) 
• R-Value Observed: 0.198 (Depositor) 

Space Group: P 4₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 49.52	α = 90
b = 49.52	β = 90
c = 119.05	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
xia2	data reduction
xia2	data scaling
PHENIX	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2019-12-25 
Deposition Author(s): Ma, C., Liao, S., Xu, C.

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

Revision History  

• Version 1.0: 2019-12-25
  Type: Initial release
  
• Version 1.1: 2023-11-22
  Changes: Data collection, Database references, Refinement description