8Q9W

Crystal structure of HsRNMT complexed with sinefungin and GMP-PnP

• PDB DOI: https://doi.org/10.2210/pdb8Q9W/pdb

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


• Deposited: 2023-08-21 Released: 2024-09-11 
• Deposition Author(s): Petit, A.P., Fyfe, P.K.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.229 
• R-Value Work: 0.174 
• R-Value Observed: 0.177 

Starting Model: experimental

Literature

Structure-Guided Design of HsRNMT inhibitors

Petit, A.P., Fyfe, P.K.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 66.48 kDa 
• Atom Count: 4,635 
• Modelled Residue Count: 545 
• Deposited Residue Count: 552 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
mRNA cap guanine-N7 methyltransferase	A, B	276	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
PHAROS:  O43148 GTEx:  ENSG00000101654

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GNP (Subject of Investigation/LOI)	F [auth B]	PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER C10 H17 N6 O13 P3 UQABYHGXWYXDTK-UUOKFMHZSA-N
SFG (Subject of Investigation/LOI)	C [auth A], E [auth B]	SINEFUNGIN C15 H23 N7 O5 LMXOHSDXUQEUSF-YECHIGJVSA-N
SO4	D [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.229 
• R-Value Work: 0.174 
• R-Value Observed: 0.177 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 40.463	α = 90
b = 84.086	β = 99.67
c = 85.344	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-09-11 
Deposition Author(s): Petit, A.P., Fyfe, P.K.

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Funding Organization	Location	Grant Number
Not funded	United Kingdom	--

Revision History  

• Version 1.0: 2024-09-11
  Type: Initial release