6VP9

Cryo-EM structure of human NatB complex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.46 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


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Literature

Molecular basis for N-terminal alpha-synuclein acetylation by human NatB.

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

(2020) Elife 9

  • DOI: 10.7554/eLife.57491
  • Primary Citation of Related Structures:  
    6VP9

  • PubMed Abstract: 
  • NatB is one of three major N-terminal acetyltransferase (NAT) complexes (NatA-NatC), which co-translationally acetylate the N-termini of eukaryotic proteins. Its substrates account for about 21% of the human proteome, including well known proteins such as actin, tropomyosin, CDK2, and α-synuclein (αSyn) ...

    NatB is one of three major N-terminal acetyltransferase (NAT) complexes (NatA-NatC), which co-translationally acetylate the N-termini of eukaryotic proteins. Its substrates account for about 21% of the human proteome, including well known proteins such as actin, tropomyosin, CDK2, and α-synuclein (αSyn). Human NatB (hNatB) mediated N-terminal acetylation of αSyn has been demonstrated to play key roles in the pathogenesis of Parkinson's disease and as a potential therapeutic target for hepatocellular carcinoma. Here we report the cryo-EM structure of hNatB bound to a CoA-αSyn conjugate, together with structure-guided analysis of mutational effects on catalysis. This analysis reveals functionally important differences with human NatA and Candida albicans NatB, resolves key hNatB protein determinants for αSyn N-terminal acetylation, and identifies important residues for substrate-specific recognition and acetylation by NatB enzymes. These studies have implications for developing small molecule NatB probes and for understanding the mode of substrate selection by NAT enzymes.


    Organizational Affiliation

    Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, United States.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
N-alpha-acetyltransferase 20 A163Homo sapiensMutation(s): 0 
Gene Names: NAA20NAT5
EC: 2.3.1.254
Find proteins for P61599 (Homo sapiens)
Explore P61599 
Go to UniProtKB:  P61599
NIH Common Fund Data Resources
PHAROS:  P61599
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
N-alpha-acetyltransferase 25, NatB auxiliary subunit B972Homo sapiensMutation(s): 0 
Gene Names: NAA25C12orf30MDM20NAP1
Find proteins for Q14CX7 (Homo sapiens)
Explore Q14CX7 
Go to UniProtKB:  Q14CX7
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PHAROS:  Q14CX7
Protein Feature View
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
MDVFM peptide C5Escherichia coli K-12Mutation(s): 0 
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CMC
Query on CMC

Download Ideal Coordinates CCD File 
A
CARBOXYMETHYL COENZYME *A
C23 H38 N7 O18 P3 S
OBUOSIHPWVNVJN-GRFIIANRSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.46 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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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: 2020-09-23
    Type: Initial release