6PW9

Cryo-EM structure of human NatE/HYPK complex

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.03 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 basis for N-terminal acetylation by human NatE and its modulation by HYPK.

Deng, S., McTiernan, N., Wei, X., Arnesen, T., Marmorstein, R.

(2020) Nat Commun 11: 818-818

  • DOI: 10.1038/s41467-020-14584-7
  • Primary Citation of Related Structures:  
    6PPL, 6PW9

  • PubMed Abstract: 

    • The human N-terminal acetyltransferase E (NatE) contains NAA10 and NAA50 catalytic, and NAA15 auxiliary subunits and associates with HYPK, a protein with intrinsic NAA10 inhibitory activity. NatE co-translationally acetylates the N-terminus of half the proteome to mediate diverse biological processes, including protein half-life, localization, and interaction ...

    The human N-terminal acetyltransferase E (NatE) contains NAA10 and NAA50 catalytic, and NAA15 auxiliary subunits and associates with HYPK, a protein with intrinsic NAA10 inhibitory activity. NatE co-translationally acetylates the N-terminus of half the proteome to mediate diverse biological processes, including protein half-life, localization, and interaction. The molecular basis for how NatE and HYPK cooperate is unknown. Here, we report the cryo-EM structures of human NatE and NatE/HYPK complexes and associated biochemistry. We reveal that NAA50 and HYPK exhibit negative cooperative binding to NAA15 in vitro and in human cells by inducing NAA15 shifts in opposing directions. NAA50 and HYPK each contribute to NAA10 activity inhibition through structural alteration of the NAA10 substrate-binding site. NAA50 activity is increased through NAA15 tethering, but is inhibited by HYPK through structural alteration of the NatE substrate-binding site. These studies reveal the molecular basis for coordinated N-terminal acetylation by NatE and HYPK.

    Organizational Affiliation: 

    Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA. marmor@upenn.edu.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
N-alpha-acetyltransferase 50A169Homo sapiensMutation(s): 0 
Gene Names: NAA50, MAK3, NAT13, NAT5
EC: 2.3.1.258 (PDB Primary Data), 2.3.1 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for Q9GZZ1 (Homo sapiens)
Explore Q9GZZ1 
Go to UniProtKB:  Q9GZZ1
PHAROS:  Q9GZZ1
GTEx:  ENSG00000121579
Protein Feature View
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  • Reference Sequence
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(by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
N-alpha-acetyltransferase 15, NatA auxiliary subunitB866Homo sapiensMutation(s): 0 
Gene Names: NAA15, GA19, NARG1, NATH, TBDN100
UniProt & NIH Common Fund Data Resources
Find proteins for Q9BXJ9 (Homo sapiens)
Explore Q9BXJ9 
Go to UniProtKB:  Q9BXJ9
PHAROS:  Q9BXJ9
GTEx:  ENSG00000164134
Protein Feature View
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
N-alpha-acetyltransferase 10C236Homo sapiensMutation(s): 1 
Gene Names: NAA10, ARD1, ARD1A, TE2
EC: 2.3.1.255
UniProt & NIH Common Fund Data Resources
Find proteins for P41227 (Homo sapiens)
Explore P41227 
Go to UniProtKB:  P41227
PHAROS:  P41227
GTEx:  ENSG00000102030
Protein Feature View
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  • Reference Sequence
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Huntingtin-interacting protein KD129Homo sapiensMutation(s): 0 
Gene Names: HYPK, C15orf63, HSPC136
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NX55 (Homo sapiens)
Explore Q9NX55 
Go to UniProtKB:  Q9NX55
PHAROS:  Q9NX55
GTEx:  ENSG00000242028
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ACO (Subject of Investigation/LOI)
Query on ACO
Download Ideal Coordinates CCD File 
F [auth C]ACETYL COENZYME *A
C23 H38 N7 O17 P3 S
ZSLZBFCDCINBPY-ZSJPKINUSA-N		 Ligand Interaction
IHP (Subject of Investigation/LOI)
Query on IHP
Download Ideal Coordinates CCD File 
E [auth C]INOSITOL HEXAKISPHOSPHATE
C6 H18 O24 P6
IMQLKJBTEOYOSI-GPIVLXJGSA-N		 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
ACO BindingDB:  6PW9 Kd: 18 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.03 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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View more in-depth experimental data

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: 2020-02-19
    Type: Initial release
  • Version 1.1: 2020-02-26
    Changes: Database references
  • Version 1.2: 2020-10-14
    Changes: Structure summary