7DPE | pdb_00007dpe

RNA methyltransferase METTL4

• PDB DOI: https://doi.org/10.2210/pdb7DPE/pdb
• NAKB: 7DPE

• Classification: TRANSFERASE/DNA
• Organism(s): Arabidopsis thaliana
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2020-12-18 Released: 2021-12-22 
• Deposition Author(s): Luo, Q., Ma, J.B.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.75 Å
• R-Value Free: 
  0.262 (Depositor), 0.260 (DCC) 
• R-Value Work: 
  0.210 (Depositor), 0.210 (DCC) 
• R-Value Observed: 
  0.213 (Depositor) 

Literature

Structure of RNA m6A methyltransferase METTL4 in complex with DNA at 2.75 Angstroms resolutioon

Luo, Q., Ma, J.B.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content 

• Total Structure Weight: 54.23 kDa 
• Atom Count: 3,246 
• Modeled Residue Count: 354 
• Deposited Residue Count: 432 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Methyltransferase-like protein 2	B [auth A]	414	Arabidopsis thaliana	Mutation(s): 0  Gene Names: At1g19340, F18O14.6 EC: 2.1.1
UniProt
Find proteins for Q8LFA9 (Arabidopsis thaliana) Explore Q8LFA9  Go to UniProtKB:  Q8LFA9

Entity ID: 1
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*GP*CP*CP*GP*CP*GP*TP*GP*AP*TP*CP*AP*CP*GP*CP*GP*GP*C)-3')	A [auth B]	18	Arabidopsis thaliana

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SAH	C [auth A]	S-ADENOSYL-L-HOMOCYSTEINE C14 H20 N6 O5 S ZJUKTBDSGOFHSH-WFMPWKQPSA-N
GOL	D [auth A], E [auth A], F [auth A], G [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.75 Å
• R-Value Free:  0.262 (Depositor), 0.260 (DCC) 
• R-Value Work:  0.210 (Depositor), 0.210 (DCC) 
• R-Value Observed: 0.213 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 90.655	α = 90
b = 93.494	β = 107.19
c = 70.885	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-3000	data reduction
REFMAC	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2021-12-22 
Deposition Author(s): Luo, Q., Ma, J.B.

Revision History  

• Version 1.0: 2021-12-22
  Type: Initial release
  
• Version 1.1: 2024-05-29
  Changes: Data collection