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- EMDB-24393: Cryo-EM structure of human binary NatC complex with a Bisubstrate... -

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Basic information

Entry
Database: EMDB / ID: EMD-24393
TitleCryo-EM structure of human binary NatC complex with a Bisubstrate inhibitor
Map data
Sample
  • Complex: heterotimeric S.pombe NatC complex with a bisubstrate inhibitor and inositol hexaphosphate
    • Protein or peptide: N-alpha-acetyltransferase 35, NatC auxiliary subunit
    • Protein or peptide: N-alpha-acetyltransferase 30
  • Ligand: CARBOXYMETHYL COENZYME *A
  • Ligand: METHIONINE
  • Ligand: LEUCINE
KeywordsNatC / NAA30 / NAA35 / 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 / nucleoplasm / nucleus / plasma membrane ...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 / nucleoplasm / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
-alpha-acetyltransferase 35, NatC auxiliary subunit / N-alpha-acetyltransferase 30-like / Mak10 subunit, NatC N(alpha)-terminal acetyltransferase / 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
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.1 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
DepositionJul 5, 2021-
Header (metadata) releaseJan 11, 2023-
Map releaseJan 11, 2023-
UpdateMay 1, 2024-
Current statusMay 1, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_24393.png

Downloads & links

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Map

FileDownload / File: emd_24393.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: 0.25
Minimum - Maximum-1.0394663 - 2.212717
Average (Standard dev.)-0.0019908915 (±0.07980135)
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 S.pombe NatC complex with a bisubstrate inhibitor a...

EntireName: heterotimeric S.pombe NatC complex with a bisubstrate inhibitor and inositol hexaphosphate
Components
  • Complex: heterotimeric S.pombe NatC complex with a bisubstrate inhibitor and inositol hexaphosphate
    • Protein or peptide: N-alpha-acetyltransferase 35, NatC auxiliary subunit
    • Protein or peptide: N-alpha-acetyltransferase 30
  • Ligand: CARBOXYMETHYL COENZYME *A
  • Ligand: METHIONINE
  • Ligand: LEUCINE

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Supramolecule #1: heterotimeric S.pombe NatC complex with a bisubstrate inhibitor a...

SupramoleculeName: heterotimeric S.pombe NatC complex with a bisubstrate inhibitor and inositol hexaphosphate
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
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: 80.707625 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: NWVDITQDFE EACRELKLGE LLHDKLFGLF EAMSAIEMMD PKMDAGMIGN QVNRKVLNFE QAIKDGTIKI KDLTLPELIG IMDTCFCCL ITWLEGHSLA QTVFTCLYIH NPDFIEDPAM KAFALGILKI CDIAREKVNK AAVFEEEDFQ SMTYGFKMAN S VTDLRVTG ...String:
NWVDITQDFE EACRELKLGE LLHDKLFGLF EAMSAIEMMD PKMDAGMIGN QVNRKVLNFE QAIKDGTIKI KDLTLPELIG IMDTCFCCL ITWLEGHSLA QTVFTCLYIH NPDFIEDPAM KAFALGILKI CDIAREKVNK AAVFEEEDFQ SMTYGFKMAN S VTDLRVTG MLKDVEDDMQ RRVKSTRSRQ GEERDPEVEL EHQQCLAVFS RVKFTRVLLT VLIAFTKKET SAVAEAQKLM VQ AADLLSA IHNSLHHGIQ AQNDTTKGDH PIMMGFEPLV NQRLLPPTFP RYAKIIKREE MVNYFARLID RIKTVCEVVN LTN LHCILD FFCEFSEQSP CVLSRSLLQT TFLVDNKKVF GTHLMQDMVK DALRSFVSPP VLSPKCYLYN NHQAKDCIDS FVTH CVRPF CSLIQIHGHN RARQRDKLGH ILEEFATLQD EAEKVDAALH TMLLKQEPQR QHLACLGTWV LYHNLRIMIQ YLLSG FELE LYSMHEYYYI YWYLSEFLYA WLMSTLSRAD GSQMAEERIM EEQQKGRSSK KTKKKKKVRP LSREITMSQA YQNMCA GMF KTMVAFDMDG KVRKPKFELD SEQVRYEHRF APFNSVMTPP PVHYLQFKEM SDLNKYSPPP QSPELYVAAS KHFQQAK MI LENIPNPDHE VNRILKVAKP NFVVMKLLAG GHKKESKVPP EFDFSAHKYF PVVKLV

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

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Macromolecule #2: N-alpha-acetyltransferase 30

MacromoleculeName: N-alpha-acetyltransferase 30 / type: protein_or_peptide / ID: 2 / 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 #3: CARBOXYMETHYL COENZYME *A

MacromoleculeName: CARBOXYMETHYL COENZYME *A / type: ligand / ID: 3 / Number of copies: 1 / Formula: CMC
Molecular weightTheoretical: 825.57 Da
Chemical component information

ChemComp-CMC:
CARBOXYMETHYL COENZYME *A

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Macromolecule #4: METHIONINE

MacromoleculeName: METHIONINE / type: ligand / ID: 4 / Number of copies: 1 / Formula: MET
Molecular weightTheoretical: 149.211 Da
Chemical component information

ChemComp-MET:
METHIONINE

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Macromolecule #5: LEUCINE

MacromoleculeName: LEUCINE / type: ligand / ID: 5 / Number of copies: 1 / Formula: LEU
Molecular weightTheoretical: 131.173 Da
Chemical component information

ChemComp-LEU:
LEUCINE

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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 cloride
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
Details4222 images
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

6c95

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. v2) / Number images used: 192437
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-7rb3:
Cryo-EM structure of human binary NatC complex with a Bisubstrate inhibitor

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