4R3I

The crystal structure of an RNA complex

• PDB DOI: https://doi.org/10.2210/pdb4R3I/pdb
• NAKB: 4R3I

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


• Deposited: 2014-08-15 Released: 2014-09-17 
• Deposition Author(s): Tempel, W., Xu, C., Liu, K., Li, Y., Bountra, C., Arrowsmith, C.H., Edwards, A.M., Min, J., Structural Genomics Consortium (SGC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.264 
• R-Value Work: 0.203 
• R-Value Observed: 0.206 

Starting Model: experimental

Literature

Structural basis for selective binding of m(6)A RNA by the YTHDC1 YTH domain.

Xu, C., Wang, X., Liu, K., Roundtree, I.A., Tempel, W., Li, Y., Lu, Z., He, C., Min, J.

(2014) Nat Chem Biol 10: 927-929

• PubMed: 25242552 
• DOI: https://doi.org/10.1038/nchembio.1654
• Primary Citation of Related Structures:  
  4R3H, 4R3I


• PubMed Abstract: 
  

  N(6)-methyladenosine (m(6)A) is the most abundant internal modification of nearly all eukaryotic mRNAs and has recently been reported to be recognized by the YTH domain family proteins. Here we present the crystal structures of the YTH domain of YTHDC1, a member of the YTH domain family, and its complex with an m(6)A-containing RNA. Our structural studies, together with transcriptome-wide identification of YTHDC1-binding sites and biochemical experiments, not only reveal the specific mode of m(6)A-YTH binding but also explain the preferential recognition of the GG(m(6)A)C sequences by YTHDC1.

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Organizational Affiliation: 

1] Structural Genomics Consortium, University of Toronto, Toronto, Ontario, Canada. [2]. [e-mail].

Biological Assembly 1  

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

Biological assembly 1 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 20.42 kDa 
• Atom Count: 1,484 
• Modelled Residue Count: 169 
• Deposited Residue Count: 171 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
YTH domain-containing protein 1	A	166	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

Entity ID: 2
Molecule	Chains	Length	Organism	Image
RNA (5'-R(*GP*GP*(6MZ)P*CP*U)-3')	B	5	synthetic construct

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
UNX	C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A]	UNKNOWN ATOM OR ION X

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.264 
• R-Value Work: 0.203 
• R-Value Observed: 0.206 
• Space Group: P 1 2₁ 1
• Diffraction Data: https://doi.org/10.18430/m34r3i

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 35.728	α = 90
b = 39.748	β = 103.56
c = 56.238	γ = 90

Software Package:

Software Name	Purpose
Aimless	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-09-17 
Deposition Author(s): Tempel, W., Xu, C., Liu, K., Li, Y., Bountra, C., Arrowsmith, C.H., Edwards, A.M., Min, J., Structural Genomics Consortium (SGC)

Revision History  

• Version 1.0: 2014-09-17
  Type: Initial release
  
• Version 1.1: 2014-10-01
  Changes: Database references
• Version 1.2: 2014-11-19
  Changes: Database references
• Version 2.0: 2024-02-28
  Changes: Data collection, Database references, Derived calculations, Polymer sequence
• Version 2.1: 2024-04-03
  Changes: Refinement description