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


This is version 1.0 of the entry. See complete history. 


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
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
N-alpha-acetyltransferase 20A163Homo sapiensMutation(s): 0 
Gene Names: NAA20, NAT5
EC: 2.3.1.254
UniProt & NIH Common Fund Data Resources
Find proteins for P61599 (Homo sapiens)
Explore P61599 
Go to UniProtKB:  P61599
PHAROS:  P61599
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UniProt GroupP61599
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
N-alpha-acetyltransferase 25, NatB auxiliary subunitB972Homo sapiensMutation(s): 0 
Gene Names: NAA25, C12orf30, MDM20, NAP1
UniProt & NIH Common Fund Data Resources
Find proteins for Q14CX7 (Homo sapiens)
Explore Q14CX7 
Go to UniProtKB:  Q14CX7
PHAROS:  Q14CX7
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UniProt GroupQ14CX7
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  • Reference Sequence

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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
MDVFM peptideC5Escherichia 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 (Subject of Investigation/LOI)
Query on CMC
Download Ideal Coordinates CCD File 
D [auth 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 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.17.1-3660
RECONSTRUCTIONRELION3.0

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