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- PDB-6pw9: Cryo-EM structure of human NatE/HYPK complex -

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Basic information

Entry
Database: PDB / ID: 6pw9
TitleCryo-EM structure of human NatE/HYPK complex
Components
  • (N-alpha-acetyltransferase ...) x 3
  • Huntingtin-interacting protein K
KeywordsTRANSFERASE / NatA / Naa50 / NatE / HYPK
Function / homology
Function and homology information


negative regulation of maintenance of mitotic sister chromatid cohesion, centromeric / peptidyl-lysine acetyltransferase activity / mitotic sister chromatid cohesion, centromeric / peptide-glutamate-alpha-N-acetyltransferase activity / N-terminal amino-acid Nalpha-acetyltransferase NatA / N-terminal methionine Nalpha-acetyltransferase NatE / peptide-serine-alpha-N-acetyltransferase activity / NatA complex / N-terminal protein amino acid acetylation / peptide alpha-N-acetyltransferase activity ...negative regulation of maintenance of mitotic sister chromatid cohesion, centromeric / peptidyl-lysine acetyltransferase activity / mitotic sister chromatid cohesion, centromeric / peptide-glutamate-alpha-N-acetyltransferase activity / N-terminal amino-acid Nalpha-acetyltransferase NatA / N-terminal methionine Nalpha-acetyltransferase NatE / peptide-serine-alpha-N-acetyltransferase activity / NatA complex / N-terminal protein amino acid acetylation / peptide alpha-N-acetyltransferase activity / : / histone H4 acetyltransferase activity / establishment of mitotic sister chromatid cohesion / N-acetyltransferase activity / mitotic sister chromatid cohesion / internal protein amino acid acetylation / protein acetylation / chromosome organization / protein folding chaperone / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / microtubule cytoskeleton / ribosome binding / angiogenesis / transcription regulator complex / cell differentiation / nuclear body / protein stabilization / intracellular membrane-bounded organelle / nucleolus / negative regulation of apoptotic process / positive regulation of DNA-templated transcription / protein-containing complex / RNA binding / extracellular exosome / nucleoplasm / membrane / nucleus / cytosol / cytoplasm
Similarity search - Function
Huntingtin-interacting protein K, UBA-like domain / Nascent polypeptide-associated complex subunit alpha-like, UBA domain / HYPK UBA domain / N-terminal acetyltransferase A, auxiliary subunit / N-terminal acetyltransferase A, auxiliary subunit / N-acetyltransferase Ard1-like / Tetratricopeptide repeat / Acetyltransferase (GNAT) family / Gcn5-related N-acetyltransferase (GNAT) domain profile. / GNAT domain ...Huntingtin-interacting protein K, UBA-like domain / Nascent polypeptide-associated complex subunit alpha-like, UBA domain / HYPK UBA domain / N-terminal acetyltransferase A, auxiliary subunit / N-terminal acetyltransferase A, auxiliary subunit / N-acetyltransferase Ard1-like / Tetratricopeptide repeat / Acetyltransferase (GNAT) family / Gcn5-related N-acetyltransferase (GNAT) domain profile. / GNAT domain / TPR repeat region circular profile. / TPR repeat profile. / Acyl-CoA N-acyltransferase / Tetratricopeptide repeats / Tetratricopeptide repeat / Tetratricopeptide-like helical domain superfamily
Similarity search - Domain/homology
ACETYL COENZYME *A / INOSITOL HEXAKISPHOSPHATE / N-alpha-acetyltransferase 10 / N-alpha-acetyltransferase 15, NatA auxiliary subunit / N-alpha-acetyltransferase 50 / Huntingtin-interacting protein K
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.03 Å
AuthorsDeng, S. / Marmorstein, R.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35 GM118090 United States
CitationJournal: Nat Commun / Year: 2020
Title: Molecular basis for N-terminal acetylation by human NatE and its modulation by HYPK.
Authors: Sunbin Deng / Nina McTiernan / Xuepeng Wei / Thomas Arnesen / Ronen Marmorstein /
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- ...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.
History
DepositionJul 22, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 19, 2020Provider: repository / Type: Initial release
Revision 1.1Feb 26, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Oct 14, 2020Group: Structure summary / Category: chem_comp / Item: _chem_comp.pdbx_synonyms

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Assembly

Deposited unit
A: N-alpha-acetyltransferase 50
B: N-alpha-acetyltransferase 15, NatA auxiliary subunit
C: N-alpha-acetyltransferase 10
D: Huntingtin-interacting protein K
hetero molecules


Theoretical massNumber of molelcules
Total (without water)163,5376
Polymers162,0674
Non-polymers1,4702
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area12860 Å2
ΔGint-50 kcal/mol
Surface area54100 Å2

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Components

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N-alpha-acetyltransferase ... , 3 types, 3 molecules ABC

#1: Protein N-alpha-acetyltransferase 50 / hNaa50p / N-acetyltransferase 13 / N-acetyltransferase 5 / hNAT5 / N-acetyltransferase san homolog ...hNaa50p / N-acetyltransferase 13 / N-acetyltransferase 5 / hNAT5 / N-acetyltransferase san homolog / hSAN / N-epsilon-acetyltransferase 50 / NatE catalytic subunit


Mass: 19427.373 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NAA50, MAK3, NAT13, NAT5 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9GZZ1, N-terminal methionine Nalpha-acetyltransferase NatE, Transferases; Acyltransferases; Transferring groups other than aminoacyl groups
#2: Protein N-alpha-acetyltransferase 15, NatA auxiliary subunit / Gastric cancer antigen Ga19 / N-terminal acetyltransferase / NMDA receptor-regulated protein 1 / ...Gastric cancer antigen Ga19 / N-terminal acetyltransferase / NMDA receptor-regulated protein 1 / Protein tubedown-1 / Tbdn100


Mass: 101427.562 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NAA15, GA19, NARG1, NATH, TBDN100 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q9BXJ9
#3: Protein N-alpha-acetyltransferase 10 / / N-terminal acetyltransferase complex ARD1 subunit homolog A / hARD1 / NatA catalytic subunit Naa10


Mass: 26522.602 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NAA10, ARD1, ARD1A, TE2 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: P41227, N-terminal amino-acid Nalpha-acetyltransferase NatA

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Protein , 1 types, 1 molecules D

#4: Protein Huntingtin-interacting protein K / Huntingtin yeast partner K


Mass: 14689.457 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HYPK, C15orf63, HSPC136 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q9NX55

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Non-polymers , 2 types, 2 molecules

#5: Chemical ChemComp-IHP / INOSITOL HEXAKISPHOSPHATE / MYO-INOSITOL HEXAKISPHOSPHATE / INOSITOL 1,2,3,4,5,6-HEXAKISPHOSPHATE / Phytic acid


Mass: 660.035 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H18O24P6
#6: Chemical ChemComp-ACO / ACETYL COENZYME *A / Acetyl-CoA


Mass: 809.571 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H38N7O17P3S / Feature type: SUBJECT OF INVESTIGATION

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Details

Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

Component
IDNameTypeEntity IDParent-IDSource
1human NatE complexCOMPLEX#1-#40RECOMBINANT
2N-alpha-acetyltransferase 50COMPLEX#11RECOMBINANT
3N-alpha-acetyltransferase 15, NatA auxiliary subunit, N-alpha-acetyltransferase 10, Huntingtin-interacting protein KCOMPLEX#2-#41RECOMBINANT
Molecular weightUnits: MEGADALTONS / Experimental value: NO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
23Homo sapiens (human)9606
12Homo sapiens (human)9606
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-ID
23Spodoptera frugiperda (fall armyworm)7108
12Escherichia coli (E. coli)562
Buffer solutionpH: 7
Buffer component
IDConc.NameFormulaBuffer-ID
1200 mMsodium clorideNaClSodium chloride1
225 mM4-(2-hydroxyethyl)-1-piperazineethanesulfonic acidHepes1
31 mMDithiothreitolDTT1
SpecimenConc.: 1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK II / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 289 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingElectron dose: 1.6 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 4.03 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 168536 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL

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