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- EMDB-24070: Cryo-EM structure of human ternary NatC complex with a Bisubstrat... -

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Basic information

Entry
Database: EMDB / ID: EMD-24070
TitleCryo-EM structure of human ternary NatC complex with a Bisubstrate inhibitor
Map data
Sample
  • Complex: heterotimeric human NatC complex with a bisubstrate inhibitor
    • Complex: N-alpha-acetyltransferase NatC complex
      • Protein or peptide: N-alpha-acetyltransferase 35, NatC auxiliary subunit
      • Protein or peptide: N-alpha-acetyltransferase 38, NatC auxiliary subunit
      • Protein or peptide: N-alpha-acetyltransferase 30
    • Complex: bisubstrate inhibitor
      • Protein or peptide: peptide portion of bisubstrate inhibitor
  • Ligand: CARBOXYMETHYL COENZYME *A
KeywordsNatC / NAA30 / NAA35 / NAA38 / TRANSFERASE
Function / homology
Function and homology information


N-terminal methionine Nalpha-acetyltransferase NatC / NatC complex / smooth muscle cell proliferation / Retrograde transport at the Trans-Golgi-Network / peptide alpha-N-acetyltransferase activity / protein stabilization / negative regulation of apoptotic process / RNA binding / nucleoplasm / nucleus ...N-terminal methionine Nalpha-acetyltransferase NatC / NatC complex / smooth muscle cell proliferation / Retrograde transport at the Trans-Golgi-Network / peptide alpha-N-acetyltransferase activity / protein stabilization / negative regulation of apoptotic process / RNA binding / nucleoplasm / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
LSM domain containing 1 / -alpha-acetyltransferase 35, NatC auxiliary subunit / N-alpha-acetyltransferase 30-like / Mak10 subunit, NatC N(alpha)-terminal acetyltransferase / : / LSM domain / LSM domain, eukaryotic/archaea-type / snRNP Sm proteins / : / Sm domain profile. ...LSM domain containing 1 / -alpha-acetyltransferase 35, NatC auxiliary subunit / N-alpha-acetyltransferase 30-like / Mak10 subunit, NatC N(alpha)-terminal acetyltransferase / : / LSM domain / LSM domain, eukaryotic/archaea-type / snRNP Sm proteins / : / Sm domain profile. / LSM domain superfamily / Acetyltransferase (GNAT) family / Gcn5-related N-acetyltransferase (GNAT) domain profile. / GNAT domain / Acyl-CoA N-acyltransferase
Similarity search - Domain/homology
N-alpha-acetyltransferase 30 / N-alpha-acetyltransferase 35, NatC auxiliary subunit / N-alpha-acetyltransferase 38, NatC auxiliary subunit
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.64 Å
AuthorsDeng S / Marmorstein R
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35 GM118090 United States
CitationJournal: Structure / Year: 2023
Title: Molecular role of NAA38 in thermostability and catalytic activity of the human NatC N-terminal acetyltransferase.
Authors: Sunbin Deng / Sarah M Gardner / Leah Gottlieb / Buyan Pan / E James Petersson / Ronen Marmorstein /
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 ...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.
History
DepositionMay 18, 2021-
Header (metadata) releaseDec 14, 2022-
Map releaseDec 14, 2022-
UpdateNov 6, 2024-
Current statusNov 6, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_24070.png

Downloads & links

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Map

FileDownload / File: emd_24070.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.84 Å/pix.
x 200 pix.
= 168. Å		0.84 Å/pix.
x 200 pix.
= 168. Å		0.84 Å/pix.
x 200 pix.
= 168. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.84 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.3
Minimum - Maximum-1.3642398 - 2.0637422
Average (Standard dev.)0.0036807535 (±0.09273529)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-100-100-100
Dimensions200200200
Spacing200200200
CellA=B=C: 168.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : heterotimeric human NatC complex with a bisubstrate inhibitor

EntireName: heterotimeric human NatC complex with a bisubstrate inhibitor
Components
  • Complex: heterotimeric human NatC complex with a bisubstrate inhibitor
    • Complex: N-alpha-acetyltransferase NatC complex
      • Protein or peptide: N-alpha-acetyltransferase 35, NatC auxiliary subunit
      • Protein or peptide: N-alpha-acetyltransferase 38, NatC auxiliary subunit
      • Protein or peptide: N-alpha-acetyltransferase 30
    • Complex: bisubstrate inhibitor
      • Protein or peptide: peptide portion of bisubstrate inhibitor
  • Ligand: CARBOXYMETHYL COENZYME *A

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Supramolecule #1: heterotimeric human NatC complex with a bisubstrate inhibitor

SupramoleculeName: heterotimeric human NatC complex with a bisubstrate inhibitor
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Molecular weightTheoretical: 114 KDa

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Supramolecule #2: N-alpha-acetyltransferase NatC complex

SupramoleculeName: N-alpha-acetyltransferase NatC complex / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#3
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #3: bisubstrate inhibitor

SupramoleculeName: bisubstrate inhibitor / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #4
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: N-alpha-acetyltransferase 35, NatC auxiliary subunit

MacromoleculeName: N-alpha-acetyltransferase 35, NatC auxiliary subunit / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 83.754031 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MVMKASVDDD DSGWELSMPE KMEKSNTNWV DITQDFEEAC RELKLGELLH DKLFGLFEAM SAIEMMDPKM DAGMIGNQVN RKVLNFEQA IKDGTIKIKD LTLPELIGIM DTCFCCLITW LEGHSLAQTV FTCLYIHNPD FIEDPAMKAF ALGILKICDI A REKVNKAA ...String:
MVMKASVDDD DSGWELSMPE KMEKSNTNWV DITQDFEEAC RELKLGELLH DKLFGLFEAM SAIEMMDPKM DAGMIGNQVN RKVLNFEQA IKDGTIKIKD LTLPELIGIM DTCFCCLITW LEGHSLAQTV FTCLYIHNPD FIEDPAMKAF ALGILKICDI A REKVNKAA VFEEEDFQSM TYGFKMANSV TDLRVTGMLK DVEDDMQRRV KSTRSRQGEE RDPEVELEHQ QCLAVFSRVK FT RVLLTVL IAFTKKETSA VAEAQKLMVQ AADLLSAIHN SLHHGIQAQN DTTKGDHPIM MGFEPLVNQR LLPPTFPRYA KII KREEMV NYFARLIDRI KTVCEVVNLT NLHCILDFFC EFSEQSPCVL SRSLLQTTFL VDNKKVFGTH LMQDMVKDAL RSFV SPPVL SPKCYLYNNH QAKDCIDSFV THCVRPFCSL IQIHGHNRAR QRDKLGHILE EFATLQDEAE KVDAALHTML LKQEP QRQH LACLGTWVLY HNLRIMIQYL LSGFELELYS MHEYYYIYWY LSEFLYAWLM STLSRADGSQ MAEERIMEEQ QKGRSS KKT KKKKKVRPLS REITMSQAYQ NMCAGMFKTM VAFDMDGKVR KPKFELDSEQ VRYEHRFAPF NSVMTPPPVH YLQFKEM SD LNKYSPPPQS PELYVAASKH FQQAKMILEN IPNPDHEVNR ILKVAKPNFV VMKLLAGGHK KESKVPPEFD FSAHKYFP V VKLV

UniProtKB: N-alpha-acetyltransferase 35, NatC auxiliary subunit

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Macromolecule #2: N-alpha-acetyltransferase 38, NatC auxiliary subunit

MacromoleculeName: N-alpha-acetyltransferase 38, NatC auxiliary subunit / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 13.530276 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString:
MAGAGPTMLL REENGCCSRR QSSSSAGDSD GEREDSAAER ARQQLEALLN KTMRIRMTDG RTLVGCFLCT DRDCNVILGS AQEFLKPSD SFSAGEPRVL GLAMVPGHHI VSIEVQRESL TGPPYL

UniProtKB: N-alpha-acetyltransferase 38, NatC auxiliary subunit

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Macromolecule #3: N-alpha-acetyltransferase 30

MacromoleculeName: N-alpha-acetyltransferase 30 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
EC number: N-terminal methionine Nalpha-acetyltransferase NatC
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 18.083293 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString:
RTIRYVRYES ELQMPDIMRL ITKDLSEPYS IYTYRYFIHN WPQLCFLAMV GEECVGAIVC KLDMHKKMFR RGYIAMLAVD SKYRRNGIG TNLVKKAIYA MVEGDCDEVV LETEITNKSA LKLYENLGFV RDKRLFRYYL NGVDALRLKL WLR

UniProtKB: N-alpha-acetyltransferase 30

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Macromolecule #4: peptide portion of bisubstrate inhibitor

MacromoleculeName: peptide portion of bisubstrate inhibitor / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 416.535 Da
SequenceString:
MLGP

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Macromolecule #5: CARBOXYMETHYL COENZYME *A

MacromoleculeName: CARBOXYMETHYL COENZYME *A / type: ligand / ID: 5 / Number of copies: 1 / Formula: CMC
Molecular weightTheoretical: 825.57 Da
Chemical component information

ChemComp-CMC:
CARBOXYMETHYL COENZYME *A

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration1.0 mg/mL
BufferpH: 7
Component:
ConcentrationFormulaName
200.0 mMNaClsodium chloride
25.0 mM4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid
1.0 mMDithiothreitol
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 289 K / Instrument: FEI VITROBOT MARK II

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recording#0 - Image recording ID: 1 / #0 - Film or detector model: GATAN K3 (6k x 4k) / #0 - Average electron dose: 1.6 e/Å2 / #1 - Image recording ID: 2 / #1 - Film or detector model: GATAN K3 (6k x 4k) / #1 - Average electron dose: 1.3 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Image recording ID1
Details5372 images
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

6c95

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.64 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. v2) / Number images used: 172041
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. v2)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. v2)
Final 3D classificationNumber classes: 4 / Software - Name: cryoSPARC (ver. v2)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: AB INITIO MODEL
Output model

PDB-7mx2:
Cryo-EM structure of human ternary NatC complex with a Bisubstrate inhibitor

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