7Y9C

Crystal structure of METTL9 in complex with SLC39A5 peptide and SAH

• PDB DOI: https://doi.org/10.2210/pdb7Y9C/pdb

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


• Deposited: 2022-06-24 Released: 2023-04-12 
• Deposition Author(s): Xie, H., Wang, X., Xu, C.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.243 
• R-Value Work: 0.192 
• R-Value Observed: 0.195 

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

• DOI: https://doi.org/10.1038/s41421-023-00548-w

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 66.63 kDa 
• Atom Count: 4,940 
• Modelled Residue Count: 563 
• Deposited Residue Count: 576 
• Unique protein chains: 2

Macromolecules

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 ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
SLC39A5	C, D	13	synthetic construct	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for Q6ZMH5 (Homo sapiens) Explore Q6ZMH5  Go to UniProtKB:  Q6ZMH5
PHAROS:  Q6ZMH5 GTEx:  ENSG00000139540

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SAH	E [auth A], F [auth B]	S-ADENOSYL-L-HOMOCYSTEINE C14 H20 N6 O5 S ZJUKTBDSGOFHSH-WFMPWKQPSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MHS	C, D	L-PEPTIDE LINKING	C7 H11 N3 O2		HIS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.243 
• R-Value Work: 0.192 
• R-Value Observed: 0.195 
• Space Group: I 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 106.28	α = 90
b = 46.046	β = 103.35
c = 124.78	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-04-12 
Deposition Author(s): Xie, H., Wang, X., Xu, C.

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

Revision History  

• Version 1.0: 2023-04-12
  Type: Initial release
  
• Version 1.1: 2024-04-03
  Changes: Data collection, Refinement description