7YF2 | pdb_00007yf2

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)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.69 Å
• R-Value Free: 
  0.218 (Depositor), 0.220 (DCC) 
• R-Value Work: 
  0.179 (Depositor), 0.180 (DCC) 
• R-Value Observed: 
  0.180 (Depositor) 

Starting Model: in silico

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 
• DOI: https://doi.org/10.1038/s41421-023-00548-w
• Primary Citation of Related Structures:  
  7Y9C, 7YF2, 7YF3, 7YF4

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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.
Institute of Immunology, The CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China.
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. [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 4-mer - A2B2 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 4-mer - A2B1C1 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 66.6 kDa 
• Atom Count: 5,044 
• Modeled Residue Count: 567 
• 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 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

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.69 Å
• R-Value Free:  0.218 (Depositor), 0.220 (DCC) 
• R-Value Work:  0.179 (Depositor), 0.180 (DCC) 
• R-Value Observed: 0.180 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 143.838	α = 90
b = 45.836	β = 122.64
c = 106.415	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-3000	data reduction
HKL-3000	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
• Version 1.2: 2024-05-08
  Changes: Database references