7D8D

The crystal structure of ScNTM1 in complex with SAH and Rps25a hexapeptide

• PDB DOI: https://doi.org/10.2210/pdb7D8D/pdb

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


• Deposited: 2020-10-08 Released: 2021-05-26 
• Deposition Author(s): Zhang, H.Y., Yue, J.
• Funding Organization(s): National Natural Science Foundation of China (NSFC), Ministry of Science and Technology (MoST, China)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.05 Å
• R-Value Free: 0.136 
• R-Value Work: 0.118 
• R-Value Observed: 0.119 

Starting Model: experimental

Literature

Structural Basis for Peptide Binding of Alpha-N Terminal Methyltransferase from Saccharomyces cerevisiae

Zhang, H.Y., Kuang, Z., Xue, L., Yue, J., Khan, M.H., Zhu, Z., Niu, L.

(2021) Crystallogr Rep 66: 1316-1321

• DOI: https://doi.org/10.1134/S1063774521070257

Biological Assembly 1  

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

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

Macromolecule Content

• Total Structure Weight: 27.19 kDa 
• Atom Count: 2,305 
• Modelled Residue Count: 238 
• Deposited Residue Count: 238 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Alpha N-terminal protein methyltransferase 1	A	232	Saccharomyces cerevisiae	Mutation(s): 0  Gene Names: TAE1, NTM1, YBR261C, YBR1729 EC: 2.1.1.244
UniProt
Find proteins for P38340 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P38340  Go to UniProtKB:  P38340

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Rps25A-peptide	B [auth D]	6	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for Q3E792 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore Q3E792  Go to UniProtKB:  Q3E792

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SAH (Subject of Investigation/LOI)	C [auth A]	S-ADENOSYL-L-HOMOCYSTEINE C14 H20 N6 O5 S ZJUKTBDSGOFHSH-WFMPWKQPSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.05 Å
• R-Value Free: 0.136 
• R-Value Work: 0.118 
• R-Value Observed: 0.119 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 38.692	α = 90
b = 52.014	β = 90
c = 127.723	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2021-05-26 
Deposition Author(s): Zhang, H.Y., Yue, J.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	U1632124 to L.N.
Ministry of Science and Technology (MoST, China)	China	2017YFA0503600 to L.N.

Revision History  

• Version 1.0: 2021-05-26
  Type: Initial release
  
• Version 1.1: 2021-12-29
  Changes: Database references
• Version 1.2: 2023-11-29
  Changes: Data collection, Refinement description