7L1K

Cryo-EM structure of S. Pombe NatC complex with a Bisubstrate inhibitor and inositol hexaphosphate


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.16 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Molecular mechanism of N-terminal acetylation by the ternary NatC complex.

Deng, S.Gottlieb, L.Pan, B.Supplee, J.Wei, X.Petersson, E.J.Marmorstein, R.

(2021) Structure 29: 1094

  • DOI: https://doi.org/10.1016/j.str.2021.05.003
  • Primary Citation of Related Structures:  
    7L1K

  • PubMed Abstract: 

    Protein N-terminal acetylation is predominantly a ribosome-associated modification, with NatA-E serving as the major enzymes. NatC is the most unusual of these enzymes, containing one Naa30 catalytic subunit and two auxiliary subunits, Naa35 and Naa38; and substrate selectivity profile that overlaps with NatE. Here, we report the cryoelectron microscopy structure of S. pombe NatC with a NatE/C-type bisubstrate analog and inositol hexaphosphate (IP 6 ), and associated biochemistry studies. We find that the presence of three subunits is a prerequisite for normal NatC acetylation activity in yeast and that IP 6 binds tightly to NatC to stabilize the complex. We also describe the molecular basis for IP 6 -mediated NatC complex stabilization and the overlapping yet distinct substrate profiles of NatC and NatE.


  • Organizational Affiliation

    Department of Chemistry, 231 South 34(th) Street, University of Pennsylvania, Philadelphia, PA 19104, USA; Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
N-alpha-acetyltransferase 30150Schizosaccharomyces pombe 972h-Mutation(s): 0 
Gene Names: naa30mak3SPBC15D4.06
EC: 2.3.1.256
UniProt
Find proteins for O74311 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
Explore O74311 
Go to UniProtKB:  O74311
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO74311
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
N-alpha-acetyltransferase 35, NatC auxiliary subunit708Schizosaccharomyces pombe 972h-Mutation(s): 0 
Gene Names: mak10naa35SPBC1861.03
UniProt
Find proteins for Q9USY3 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
Explore Q9USY3 
Go to UniProtKB:  Q9USY3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9USY3
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
N-alpha-acetyltransferase 38, NatC auxiliary subunit116Schizosaccharomyces pombe 972h-Mutation(s): 0 
Gene Names: naa38mak31SPBC947.03c
UniProt
Find proteins for O43080 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
Explore O43080 
Go to UniProtKB:  O43080
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO43080
Sequence Annotations
Expand
  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
MLGP peptide4Homo sapiensMutation(s): 0 
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.16 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.17.1-3660
RECONSTRUCTIONcryoSPARCv2

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR35 GM118090

Revision History  (Full details and data files)

  • Version 1.0: 2021-05-12
    Type: Initial release
  • Version 1.1: 2021-06-30
    Changes: Database references
  • Version 1.2: 2021-10-20
    Changes: Database references