6KDQ

Crystal structure of human NRMT1 in complex with alpha-N-monomethylated human CENP-A peptide

• PDB DOI: https://doi.org/10.2210/pdb6KDQ/pdb

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


• Deposited: 2019-07-02 Released: 2020-07-08 
• Deposition Author(s): Yue, Y., Li, H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 0.180 
• R-Value Work: 0.158 
• R-Value Observed: 0.159 

Starting Model: experimental

Literature

Substrate engagement regulates state-specific alpha-N methylation of CENP-A by NRMT2

Wu, R., Yue, Y., Zheng, X., Li, H.

To be published.

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

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Macromolecule Content

• Total Structure Weight: 57.75 kDa 
• Atom Count: 4,522 
• Modelled Residue Count: 468 
• Deposited Residue Count: 500 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
N-terminal Xaa-Pro-Lys N-methyltransferase 1	A, B	243	Homo sapiens	Mutation(s): 0  Gene Names: NTMT1, NRMT1 EC: 2.1.1.244
UniProt & NIH Common Fund Data Resources
Find proteins for Q9BV86 (Homo sapiens) Explore Q9BV86  Go to UniProtKB:  Q9BV86
PHAROS:  Q9BV86 GTEx:  ENSG00000148335

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
CENP-A peptide	C [auth E], D [auth F]	7	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P49450 (Homo sapiens) Explore P49450  Go to UniProtKB:  P49450
PHAROS:  P49450 GTEx:  ENSG00000115163

Small Molecules

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

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
SAR	C [auth E], D [auth F]	PEPTIDE LINKING	C3 H7 N O2		GLY

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 0.180 
• R-Value Work: 0.158 
• R-Value Observed: 0.159 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 114.724	α = 90
b = 65.79	β = 106.54
c = 69.003	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
HKL-2000	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2020-07-08 
Deposition Author(s): Yue, Y., Li, H.

Revision History  

• Version 1.0: 2020-07-08
  Type: Initial release
  
• Version 1.1: 2023-11-22
  Changes: Data collection, Database references, Refinement description
• Version 1.2: 2024-10-30
  Changes: Data collection, Structure summary