7YF2

Crystal structure of METTL9 in complex with unmethylated SLC39A5 peptide and SAH

PDB DOI: https://doi.org/10.2210/pdb7YF2/pdb

Classification: TRANSFERASE
Organism(s): Homo sapiens
Expression System: Escherichia coli, synthetic construct
Mutation(s): Yes

Deposited: 2022-07-07 Released: 2023-04-12
Deposition Author(s): Xie, H., Wang, X., Xu, C.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.69 Å
R-Value Free: 0.218
R-Value Work: 0.179
R-Value Observed: 0.180

Starting Model: in silico
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Molecular basis for METTL9-mediated N1-histidine methylation.

Wang, X., Xie, H., Guo, Q., Cao, D., Ru, W., Zhao, S., Zhu, Z., Zhang, J., Pan, W., Yao, X., Xu, C.

(2023) Cell Discov 9: 38-38

PubMed: 37015930 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1038/s41421-023-00548-w
Primary Citation of Related Structures:
7Y9C, 7YF2, 7YF3, 7YF4

Organizational Affiliation

MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, Hefei National Research Center for Interdisciplinary Sciences at the Microscale, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China.

Macromolecule Content

Total Structure Weight: 66.6 kDa
Atom Count: 5,044
Modelled Residue Count: 567
Deposited Residue Count: 576
Unique protein chains: 2

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein-L-histidine N-pros-methyltransferase	A, B	275	Homo sapiens	Mutation(s): 6 Gene Names: METTL9, DREV, CGI-81 EC: 2.1.1
UniProt & NIH Common Fund Data Resources
Find proteins for Q9H1A3 (Homo sapiens) Explore Q9H1A3 Go to UniProtKB: Q9H1A3
PHAROS: Q9H1A3 GTEx: ENSG00000197006
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9H1A3
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
SLC39A5 peptide	C, D	13	Homo sapiens	Mutation(s): 0 Gene Names: METTL9, DREV, CGI-81
UniProt & NIH Common Fund Data Resources
Find proteins for Q6ZMH5 (Homo sapiens) Explore Q6ZMH5 Go to UniProtKB: Q6ZMH5
PHAROS: Q6ZMH5 GTEx: ENSG00000139540
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q6ZMH5
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SAH (Subject of Investigation/LOI) Query on SAH Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth B] MOL2 format, chain E [auth A] MOL2 format, chain F [auth B] mmCIF format, chain E [auth A] mmCIF format, chain F [auth B]	E [auth A], F [auth B]	S-ADENOSYL-L-HOMOCYSTEINE C₁₄ H₂₀ N₆ O₅ S ZJUKTBDSGOFHSH-WFMPWKQPSA-N		Interactions Focus chain E [auth A] Focus chain F [auth B] Interactions & Density Focus chain E [auth A] Focus chain F [auth B]