3BGV

Crystal structure of mRNA cap guanine-N7 methyltransferase in complex with SAH

• PDB DOI: https://doi.org/10.2210/pdb3BGV/pdb

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


• Deposited: 2007-11-27 Released: 2007-12-04 
• Deposition Author(s): Lunin, V.V., Wu, H., Zeng, H., Antoshenko, T., MacKenzie, F., Weigelt, J., Arrowsmith, C.H., Edwards, A.M., Bochkarev, A., Min, J., Plotnikov, A.N., Structural Genomics Consortium (SGC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.294 
• R-Value Work: 0.221 
• R-Value Observed: 0.225 

Starting Model: experimental

Literature

The crystal structure of human RNA (guanine-7-) methyltransferase in complex with SAH.

Wu, H., Lunin, V.V., Zeng, H., Antoshenko, T., MacKenzie, F., Weigelt, J., Arrowsmith, C.H., Edwards, A.M., Bochkarev, A., Min, J., Plotnikov, A.N.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 3 assigned by authors and generated by PISA (software)

Biological Assembly 4  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 4 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 148.63 kDa 
• Atom Count: 9,359 
• Modelled Residue Count: 1,078 
• Deposited Residue Count: 1,252 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
mRNA cap guanine-N7 methyltransferase	A, B, C, D	313	Homo sapiens	Mutation(s): 0  Gene Names: RNMT, KIAA0398 EC: 2.1.1.56
UniProt & NIH Common Fund Data Resources
Find proteins for O43148 (Homo sapiens) Explore O43148  Go to UniProtKB:  O43148
GTEx:  ENSG00000101654

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.294 
• R-Value Work: 0.221 
• R-Value Observed: 0.225 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 77.787	α = 90
b = 99.672	β = 90
c = 167.782	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data collection
HKL-3000	data reduction
HKL-3000	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-12-04 
Deposition Author(s): Lunin, V.V., Wu, H., Zeng, H., Antoshenko, T., MacKenzie, F., Weigelt, J., Arrowsmith, C.H., Edwards, A.M., Bochkarev, A., Min, J., Plotnikov, A.N., Structural Genomics Consortium (SGC)

Revision History  

• Version 1.0: 2007-12-04
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2023-08-30
  Changes: Data collection, Database references, Derived calculations, Refinement description