4KVO | pdb_00004kvo

The NatA (Naa10p/Naa15p) amino-terminal acetyltrasferase complex bound to AcCoA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.15 Å
  • R-Value Free: 
    0.246 (Depositor), 0.248 (DCC) 
  • R-Value Work: 
    0.217 (Depositor), 0.220 (DCC) 
  • R-Value Observed: 
    0.218 (Depositor) 

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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history

Literature

Molecular basis for N-terminal acetylation by the heterodimeric NatA complex.

Liszczak, G.Goldberg, J.M.Foyn, H.Petersson, E.J.Arnesen, T.Marmorstein, R.

(2013) Nat Struct Mol Biol 20: 1098-1105

  • DOI: https://doi.org/10.1038/nsmb.2636
  • Primary Citation Related Structures: 
    4KVM, 4KVO, 4KVX

  • PubMed Abstract: 

    N-terminal acetylation is ubiquitous among eukaryotic proteins and controls a myriad of biological processes. Of the N-terminal acetyltransferases (NATs) that facilitate this cotranslational modification, the heterodimeric NatA complex has the most diversity for substrate selection and modifies the majority of all N-terminally acetylated proteins. Here, we report the X-ray crystal structure of the 100-kDa holo-NatA complex from Schizosaccharomyces pombe, in the absence and presence of a bisubstrate peptide-CoA-conjugate inhibitor, as well as the structure of the uncomplexed Naa10p catalytic subunit. The NatA-Naa15p auxiliary subunit contains 13 tetratricopeptide motifs and adopts a ring-like topology that wraps around the NatA-Naa10p subunit, an interaction that alters the Naa10p active site for substrate-specific acetylation. These studies have implications for understanding the mechanistic details of other NAT complexes and how regulatory subunits modulate the activity of the broader family of protein acetyltransferases.


  • Organizational Affiliation
    • 1] Program in Gene Expression and Regulation, Wistar Institute, Philadelphia, Pennsylvania, USA. [2] Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania, USA.

Macromolecule Content 

  • Total Structure Weight: 413.67 kDa 
  • Atom Count: 28,430 
  • Modeled Residue Count: 3,486 
  • Deposited Residue Count: 3,548 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
N-terminal acetyltransferase A complex subunit nat1
A, B, C, D
731Schizosaccharomyces pombe 972h-Mutation(s): 0 
Gene Names: nat1SPCC338.07c
UniProt
Find proteins for O74985 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
Explore O74985 
Go to UniProtKB:  O74985
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO74985
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
N-terminal acetyltransferase A complex catalytic subunit ard1
E, F, G, H
156Schizosaccharomyces pombe 972h-Mutation(s): 0 
Gene Names: ard1SPAC15E1.08
EC: 2.3.1.88 (PDB Primary Data), 2.3.1.255 (UniProt)
UniProt
Find proteins for Q9UTI3 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
Explore Q9UTI3 
Go to UniProtKB:  Q9UTI3
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9UTI3
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ACO

Query on ACO



Download:Ideal Coordinates CCD File
AC [auth H],
JB [auth E],
TB [auth F],
WB [auth G]
ACETYL COENZYME *A
C23 H38 N7 O17 P3 S
ZSLZBFCDCINBPY-ZSJPKINUSA-N
SO4

Query on SO4



Download:Ideal Coordinates CCD File
IB [auth D],
T [auth A]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
CL

Query on CL



Download:Ideal Coordinates CCD File
AA [auth B]
AB [auth D]
BA [auth B]
BB [auth D]
BC [auth H]
AA [auth B],
AB [auth D],
BA [auth B],
BB [auth D],
BC [auth H],
CA [auth B],
CB [auth D],
CC [auth H],
DA [auth B],
DB [auth D],
DC [auth H],
EA [auth B],
EB [auth D],
FA [auth B],
FB [auth D],
GA [auth B],
GB [auth D],
HA [auth B],
HB [auth D],
IA [auth C],
J [auth A],
JA [auth C],
K [auth A],
KA [auth C],
L [auth A],
LA [auth C],
M [auth A],
MA [auth C],
MB [auth E],
N [auth A],
NA [auth C],
NB [auth E],
O [auth A],
OA [auth C],
OB [auth E],
P [auth A],
PA [auth C],
PB [auth E],
Q [auth A],
QA [auth C],
QB [auth E],
R [auth A],
RA [auth C],
RB [auth E],
S [auth A],
SA [auth C],
SB [auth E],
TA [auth C],
U [auth B],
UA [auth C],
UB [auth F],
V [auth B],
VA [auth C],
VB [auth F],
W [auth B],
WA [auth C],
X [auth B],
Y [auth B],
YA [auth D],
YB [auth G],
Z [auth B],
ZA [auth D],
ZB [auth G]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA

Query on NA



Download:Ideal Coordinates CCD File
I [auth A],
KB [auth E],
LB [auth E],
XA [auth D],
XB [auth G]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.15 Å
  • R-Value Free:  0.246 (Depositor), 0.248 (DCC) 
  • R-Value Work:  0.217 (Depositor), 0.220 (DCC) 
  • R-Value Observed: 0.218 (Depositor) 
Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 80.739α = 80.28
b = 119.692β = 76.85
c = 132.024γ = 70.65
Software Package:
Software NamePurpose
HKL-2000data collection
SOLVEphasing
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-07-31
    Type: Initial release
  • Version 1.1: 2013-08-28
    Changes: Database references
  • Version 1.2: 2013-10-09
    Changes: Database references
  • Version 1.3: 2024-02-28
    Changes: Data collection, Database references, Derived calculations