7MX2

Cryo-EM structure of human ternary NatC complex with a Bisubstrate inhibitor


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.64 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 role of NAA38 in thermostability and catalytic activity of the human NatC N-terminal acetyltransferase.

Deng, S.Gardner, S.M.Gottlieb, L.Pan, B.Petersson, E.J.Marmorstein, R.

(2023) Structure 31: 166-173.e4

  • DOI: https://doi.org/10.1016/j.str.2022.12.008
  • Primary Citation of Related Structures:  
    7MX2, 7RB3

  • PubMed Abstract: 

    N-terminal acetylation occurs on over 80% of human proteins and is catalyzed by a family of N-terminal acetyltransferases (NATs). All NATs contain a small catalytic subunit, while some also contain a large auxiliary subunit that facilitates catalysis and ribosome targeting for co-translational acetylation. NatC is one of the major NATs containing an NAA30 catalytic subunit, but uniquely contains two auxiliary subunits, large NAA35 and small NAA38. Here, we report the cryo-EM structures of human NatC (hNatC) complexes with and without NAA38, together with biochemical studies, to reveal that NAA38 increases the thermostability and broadens the substrate-specificity profile of NatC by ordering an N-terminal segment of NAA35 and reorienting an NAA30 N-terminal peptide binding loop for optimal catalysis, respectively. We also note important differences in engagement with a stabilizing inositol hexaphosphate molecule between human and yeast NatC. These studies provide new insights for the function and evolution of the NatC complex.


  • Organizational Affiliation

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


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
N-alpha-acetyltransferase 35, NatC auxiliary subunitA [auth B]725Homo sapiensMutation(s): 0 
Gene Names: NAA35EGAPMAK10
UniProt & NIH Common Fund Data Resources
Find proteins for Q5VZE5 (Homo sapiens)
Explore Q5VZE5 
Go to UniProtKB:  Q5VZE5
PHAROS:  Q5VZE5
GTEx:  ENSG00000135040 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5VZE5
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
N-alpha-acetyltransferase 38, NatC auxiliary subunitB [auth C]125Homo sapiensMutation(s): 0 
Gene Names: NAA38LSMD1MAK31PFAAP2
UniProt & NIH Common Fund Data Resources
Find proteins for Q9BRA0 (Homo sapiens)
Explore Q9BRA0 
Go to UniProtKB:  Q9BRA0
PHAROS:  Q9BRA0
GTEx:  ENSG00000183011 
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Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9BRA0
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
N-alpha-acetyltransferase 30C [auth A]152Homo sapiensMutation(s): 0 
Gene Names: NAA30C14orf35MAK3NAT12
EC: 2.3.1.256
UniProt & NIH Common Fund Data Resources
Find proteins for Q147X3 (Homo sapiens)
Explore Q147X3 
Go to UniProtKB:  Q147X3
PHAROS:  Q147X3
GTEx:  ENSG00000139977 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ147X3
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  • Reference Sequence

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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
peptide portion of bisubstrate inhibitor4Homo sapiensMutation(s): 0 
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CMC (Subject of Investigation/LOI)
Query on CMC

Download Ideal Coordinates CCD File 
E [auth D]CARBOXYMETHYL COENZYME *A
C23 H38 N7 O18 P3 S
OBUOSIHPWVNVJN-GRFIIANRSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.64 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: 2022-12-14
    Type: Initial release
  • Version 1.1: 2023-06-28
    Changes: Data collection, Database references
  • Version 1.2: 2024-11-06
    Changes: Data collection, Structure summary