6KDS | pdb_00006kds

Crystal structure of human NRMT2 in complex with alpha-N-monomethylated human CENP-A peptide

• PDB DOI: https://doi.org/10.2210/pdb6KDS/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: 1.84 Å
• R-Value Free: 
  0.205 (Depositor), 0.209 (DCC) 
• R-Value Work: 
  0.178 (Depositor), 0.179 (DCC) 
• R-Value Observed: 
  0.180 (Depositor) 

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

Macromolecule Content 

• Total Structure Weight: 28.65 kDa 
• Atom Count: 2,019 
• Modeled Residue Count: 227 
• Deposited Residue Count: 250 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Alpha N-terminal protein methyltransferase 1B	A	244	Homo sapiens	Mutation(s): 0  Gene Names: METTL11B, C1orf184, NRMT2 EC: 2.1.1.299
UniProt & NIH Common Fund Data Resources
Find proteins for Q5VVY1 (Homo sapiens) Explore Q5VVY1  Go to UniProtKB:  Q5VVY1
GTEx:  ENSG00000203740

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
CENP-A peptide	B [auth E]	6	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	C [auth A]	S-ADENOSYL-L-HOMOCYSTEINE C14 H20 N6 O5 S ZJUKTBDSGOFHSH-WFMPWKQPSA-N

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.84 Å
• R-Value Free:  0.205 (Depositor), 0.209 (DCC) 
• R-Value Work:  0.178 (Depositor), 0.179 (DCC) 
• R-Value Observed: 0.180 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 62.603	α = 90
b = 108.191	β = 90
c = 38.799	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: 2024-10-09
  Changes: Data collection, Structure summary