6ZOT | pdb_00006zot

Crystal structure of YTHDF3 YTH domain in complex with m6A RNA

• PDB DOI: https://doi.org/10.2210/pdb6ZOT/pdb
• NAKB: 6ZOT

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


• Deposited: 2020-07-07 Released: 2020-10-28 
• 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: 2.70 Å
• R-Value Free: 
  0.276 (Depositor), 0.274 (DCC) 
• R-Value Work: 
  0.215 (Depositor), 0.216 (DCC) 
• R-Value Observed: 
  0.218 (Depositor) 

Starting Model: experimental

Literature

Structural and Dynamic Insights into Redundant Function of YTHDF Proteins.

Li, Y., Bedi, R.K., Moroz-Omori, E.V., Caflisch, A.

(2020) J Chem Inf Model 60: 5932-5935

• PubMed: 33073985 
• DOI: https://doi.org/10.1021/acs.jcim.0c01029
• Primary Citation Related Structures: 
  6ZOT


• PubMed Abstract: 
  

  Three YTH-domain family proteins (YTHDF1, YTHDF2, and YTHDF3) recognize the N ⁶ -methyladenosine (m ⁶ A) modification of mRNA in cells. However, the redundancy of their cellular functions has been disputed. We investigate their interactions with m ⁶ A-containing RNA using X-ray crystallography and molecular dynamics (MD). The new X-ray structures and MD simulations show that the three proteins share identical interactions with the m ⁶ A-containing RNA and have similar intrinsic plasticity, thus evidencing the redundant roles of the three proteins in cellular functions.

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Organizational Affiliation: 
• Department of Biochemistry, University of Zurich, CH-8057 Zurich, Switzerland.
Department of Chemistry, Umeå University, SE-90187 Umeå, Sweden.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content 

• Total Structure Weight: 48.17 kDa 
• Atom Count: 2,825 
• Modeled Residue Count: 334 
• Deposited Residue Count: 403 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
YTH domain-containing family protein 3	A [auth B], B [auth A]	199	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

Entity ID: 2
Molecule	Chains	Length	Organism	Image
RNA	C	5	Homo sapiens

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free:  0.276 (Depositor), 0.274 (DCC) 
• R-Value Work:  0.215 (Depositor), 0.216 (DCC) 
• R-Value Observed: 0.218 (Depositor) 

Space Group: P 4 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 100.75	α = 90
b = 100.75	β = 90
c = 72.88	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: 2020-10-28 
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: 2020-10-28
  Type: Initial release
  
• Version 1.1: 2020-11-04
  Changes: Database references
• Version 1.2: 2021-01-13
  Changes: Database references
• Version 1.3: 2024-01-31
  Changes: Data collection, Database references, Refinement description