4RDN

Structure of YTH-YTHDF2 in complex with m6A

PDB DOI: https://doi.org/10.2210/pdb4RDN/pdb

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

Deposited: 2014-09-19 Released: 2014-12-24
Deposition Author(s): Li, F.D., Zhao, D.B., Wu, J.H., Shi, Y.Y.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.270
R-Value Work: 0.217
R-Value Observed: 0.220

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Structure of the YTH domain of human YTHDF2 in complex with an m(6)A mononucleotide reveals an aromatic cage for m(6)A recognition.

Li, F., Zhao, D., Wu, J., Shi, Y.

(2014) Cell Res 24: 1490-1492

PubMed: 25412658 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1038/cr.2014.153
Primary Citation of Related Structures:
4RDN, 4RDO

Organizational Affiliation

Hefei National Laboratory for Physical Sciences at Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230026, China.

Macromolecule Content

Total Structure Weight: 39.68 kDa
Atom Count: 2,723
Modelled Residue Count: 297
Deposited Residue Count: 334
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
YTH domain-containing family protein 2	A, B	167	Homo sapiens	Mutation(s): 0 Gene Names: YTHDF2, HGRG8
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y5A9 (Homo sapiens) Explore Q9Y5A9 Go to UniProtKB: Q9Y5A9
PHAROS: Q9Y5A9 GTEx: ENSG00000198492
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9Y5A9
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
6MD Query on 6MD Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain F [auth B] MOL2 format, chain C [auth A] MOL2 format, chain F [auth B]	C [auth A], F [auth B]	N-methyladenosine C₁₁ H₁₅ N₅ O₄ VQAYFKKCNSOZKM-IOSLPCCCSA-N		Interactions Focus chain C [auth A] Focus chain F [auth B] Interactions & Density Focus chain C [auth A] Focus chain F [auth B]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain D [auth A] SDF format, chain G [auth B] SDF format, chain H [auth B] MOL2 format, chain E [auth A] MOL2 format, chain D [auth A] MOL2 format, chain G [auth B] MOL2 format, chain H [auth B]	D [auth A], E [auth A], G [auth B], H [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain G [auth B] Focus chain H [auth B] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain G [auth B] Focus chain H [auth B]