8H0N | pdb_00008h0n

Crystal structure of the human METTL1-WDR4 complex

• PDB DOI: https://doi.org/10.2210/pdb8H0N/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2022-09-30 Released: 2023-07-05 
• Deposition Author(s): Jin, X.H., Guan, Z.Y., Gong, Z., Zhang, D.L.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.227 (Depositor), 0.226 (DCC) 
• R-Value Work: 
  0.193 (Depositor), 0.193 (DCC) 
• R-Value Observed: 
  0.195 (Depositor) 

Starting Model: experimental

Literature

Structural insight into how WDR4 promotes the tRNA N7-methylguanosine methyltransferase activity of METTL1.

Jin, X., Guan, Z., Hu, N., He, C., Yin, P., Gong, Z., Zhang, D.

(2023) Cell Discov 9: 65-65

• PubMed: 37369656 
• DOI: https://doi.org/10.1038/s41421-023-00562-y
• Primary Citation Related Structures: 
  8H0N

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Organizational Affiliation: 
• National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, Hubei, China.
State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, Innovation Academy for Precision Measurement Science and Technology Chinese Academy of Sciences, Wuhan, Hubei, China. [e-mail].
National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, Hubei, China. [e-mail].

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

Macromolecule Content 

• Total Structure Weight: 68.58 kDa 
• Atom Count: 4,751 
• Modeled Residue Count: 540 
• Deposited Residue Count: 611 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
tRNA (guanine-N(7)-)-methyltransferase non-catalytic subunit WDR4	A	367	Homo sapiens	Mutation(s): 0  Gene Names: WDR4
UniProt & NIH Common Fund Data Resources
Find proteins for P57081 (Homo sapiens) Explore P57081  Go to UniProtKB:  P57081
PHAROS:  P57081 GTEx:  ENSG00000160193

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
tRNA (guanine-N(7)-)-methyltransferase	B	244	Homo sapiens	Mutation(s): 0  Gene Names: METTL1, C12orf1 EC: 2.1.1.33 (PDB Primary Data), 2.1.1 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UBP6 (Homo sapiens) Explore Q9UBP6  Go to UniProtKB:  Q9UBP6
PHAROS:  Q9UBP6 GTEx:  ENSG00000037897

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.227 (Depositor), 0.226 (DCC) 
• R-Value Work:  0.193 (Depositor), 0.193 (DCC) 
• R-Value Observed: 0.195 (Depositor) 

Space Group: P 2 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 84.465	α = 90
b = 87.03	β = 90
c = 95.915	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2023-07-05 
Deposition Author(s): Jin, X.H., Guan, Z.Y., Gong, Z., Zhang, D.L.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	2017YFD0200400

Revision History  

• Version 1.0: 2023-07-05
  Type: Initial release
  
• Version 1.1: 2023-07-12
  Changes: Database references
• Version 1.2: 2023-11-08
  Changes: Data collection, Refinement description