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- EMDB-20501: Cryo-EM structure of human NatE/HYPK complex -

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Basic information

Entry
Database: EMDB / ID: EMD-20501
TitleCryo-EM structure of human NatE/HYPK complex
Map dataNatE/HYPK complex
Sample
  • Complex: human NatE complex
    • Complex: N-alpha-acetyltransferase 50
      • Protein or peptide: N-alpha-acetyltransferase 50
    • Complex: N-alpha-acetyltransferase 15, NatA auxiliary subunit, N-alpha-acetyltransferase 10, Huntingtin-interacting protein K
      • Protein or peptide: N-alpha-acetyltransferase 15, NatA auxiliary subunit
      • Protein or peptide: N-alpha-acetyltransferase 10
      • Protein or peptide: Huntingtin-interacting protein K
  • Ligand: INOSITOL HEXAKISPHOSPHATE
  • Ligand: ACETYL COENZYME *A
Function / homology
Function and homology information


negative regulation of maintenance of mitotic sister chromatid cohesion, centromeric / : / mitotic sister chromatid cohesion, centromeric / N-terminal methionine Nalpha-acetyltransferase NatE / N-terminal amino-acid Nalpha-acetyltransferase NatA / peptide-glutamate-alpha-N-acetyltransferase activity / NatA complex / peptide-serine-alpha-N-acetyltransferase activity / N-terminal protein amino acid acetylation / peptide alpha-N-acetyltransferase activity ...negative regulation of maintenance of mitotic sister chromatid cohesion, centromeric / : / mitotic sister chromatid cohesion, centromeric / N-terminal methionine Nalpha-acetyltransferase NatE / N-terminal amino-acid Nalpha-acetyltransferase NatA / peptide-glutamate-alpha-N-acetyltransferase activity / NatA complex / peptide-serine-alpha-N-acetyltransferase activity / 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 / cytoplasm / cytosol
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
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)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.03 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: 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, 2019-
Header (metadata) releaseNov 27, 2019-
Map releaseFeb 19, 2020-
UpdateOct 14, 2020-
Current statusOct 14, 2020Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.02
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.02
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6pw9
  • Surface level: 0.018
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_20501.png

Downloads & links

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Map

FileDownload / File: emd_20501.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationNatE/HYPK complex
Voxel sizeX=Y=Z: 1.169 Å
Density
Contour LevelBy AUTHOR: 0.015 / Movie #1: 0.02
Minimum - Maximum-0.08190348 - 0.14458595
Average (Standard dev.)-0.0000082558 (±0.0050283438)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-100-100-100
Dimensions200200200
Spacing200200200
CellA=B=C: 233.8 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.1691.1691.169
M x/y/z200200200
origin x/y/z0.0000.0000.000
length x/y/z233.800233.800233.800
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS-100-100-100
NC/NR/NS200200200
D min/max/mean-0.0820.145-0.000

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Supplemental data

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Sample components

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Entire : human NatE complex

EntireName: human NatE complex
Components
  • Complex: human NatE complex
    • Complex: N-alpha-acetyltransferase 50
      • Protein or peptide: N-alpha-acetyltransferase 50
    • Complex: N-alpha-acetyltransferase 15, NatA auxiliary subunit, N-alpha-acetyltransferase 10, Huntingtin-interacting protein K
      • Protein or peptide: N-alpha-acetyltransferase 15, NatA auxiliary subunit
      • Protein or peptide: N-alpha-acetyltransferase 10
      • Protein or peptide: Huntingtin-interacting protein K
  • Ligand: INOSITOL HEXAKISPHOSPHATE
  • Ligand: ACETYL COENZYME *A

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Supramolecule #1: human NatE complex

SupramoleculeName: human NatE complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4

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Supramolecule #2: N-alpha-acetyltransferase 50

SupramoleculeName: N-alpha-acetyltransferase 50 / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Escherichia coli (E. coli)

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Supramolecule #3: N-alpha-acetyltransferase 15, NatA auxiliary subunit, N-alpha-ace...

SupramoleculeName: N-alpha-acetyltransferase 15, NatA auxiliary subunit, N-alpha-acetyltransferase 10, Huntingtin-interacting protein K
type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2-#4
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)

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Macromolecule #1: N-alpha-acetyltransferase 50

MacromoleculeName: N-alpha-acetyltransferase 50 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
EC number: N-terminal methionine Nalpha-acetyltransferase NatE
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 19.427373 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MKGSRIELGD VTPHNIKQLK RLNQVIFPVS YNDKFYKDVL EVGELAKLAY FNDIAVGAVC CRVDHSQNQK RLYIMTLGCL APYRRLGIG TKMLNHVLNI CEKDGTFDNI YLHVQISNES AIDFYRKFGF EIIETKKNYY KRIEPADAHV LQKNLKVPSG Q NADVQKTD N

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Macromolecule #2: N-alpha-acetyltransferase 15, NatA auxiliary subunit

MacromoleculeName: N-alpha-acetyltransferase 15, NatA auxiliary subunit / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 101.427562 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MPAVSLPPKE NALFKRILRC YEHKQYRNGL KFCKQILSNP KFAEHGETLA MKGLTLNCLG KKEEAYELVR RGLRNDLKSH VCWHVYGLL QRSDKKYDEA IKCYRNALKW DKDNLQILRD LSLLQIQMRD LEGYRETRYQ LLQLRPAQRA SWIGYAIAYH L LEDYEMAA ...String:
MPAVSLPPKE NALFKRILRC YEHKQYRNGL KFCKQILSNP KFAEHGETLA MKGLTLNCLG KKEEAYELVR RGLRNDLKSH VCWHVYGLL QRSDKKYDEA IKCYRNALKW DKDNLQILRD LSLLQIQMRD LEGYRETRYQ LLQLRPAQRA SWIGYAIAYH L LEDYEMAA KILEEFRKTQ QTSPDKVDYE YSELLLYQNQ VLREAGLYRE ALEHLCTYEK QICDKLAVEE TKGELLLQLC RL EDAADVY RGLQERNPEN WAYYKGLEKA LKPANMLERL KIYEEAWTKY PRGLVPRRLP LNFLSGEKFK ECLDKFLRMN FSK GCPPVF NTLRSLYKDK EKVAIIEELV VGYETSLKSC RLFNPNDDGK EEPPTTLLWV QYYLAQHYDK IGQPSIALEY INTA IESTP TLIELFLVKA KIYKHAGNIK EAARWMDEAQ ALDTADRFIN SKCAKYMLKA NLIKEAEEMC SKFTREGTSA VENLN EMQC MWFQTECAQA YKAMNKFGEA LKKCHEIERH FIEITDDQFD FHTYCMRKIT LRSYVDLLKL EDVLRQHPFY FKAARI AIE IYLKLHDNPL TDENKEHEAD TANMSDKELK KLRNKQRRAQ KKAQIEEEKK NAEKEKQQRN QKKKKDDDDE EIGGPKE EL IPEKLAKVET PLEEAIKFLT PLKNLVKNKI ETHLFAFEIY FRKEKFLLML QSVKRAFAID SSHPWLHECM IRLFNTAV C ESKDLSDTVR TVLKQEMNRL FGATNPKNFN ETFLKRNSDS LPHRLSAAKM VYYLDPSSQK RAIELATTLD ESLTNRNLQ TCMEVLEALY DGSLGDCKEA AEIYRANCHK LFPYALAFMP PGYEEDMKIT VNGDSSAEAE ELANEI

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Macromolecule #3: N-alpha-acetyltransferase 10

MacromoleculeName: N-alpha-acetyltransferase 10 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
EC number: N-terminal amino-acid Nalpha-acetyltransferase NatA
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 26.522602 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: (ACE)MNIRNARPE DLMNMQHCNL LCLPENYQMK YYFYHGLSWP QLSYIAEDEN GKIVGYVLAK MEEDPDDVPH GHITSL AVK RSHRRLGLAQ KLMDQASRAM IENFNAKYVS LHVRKSNRAA LHLYSNTLNF QISEVEPKYY ADGEDAYAMK RDLTQMA DE LRRHLELKEK ...String:
(ACE)MNIRNARPE DLMNMQHCNL LCLPENYQMK YYFYHGLSWP QLSYIAEDEN GKIVGYVLAK MEEDPDDVPH GHITSL AVK RSHRRLGLAQ KLMDQASRAM IENFNAKYVS LHVRKSNRAA LHLYSNTLNF QISEVEPKYY ADGEDAYAMK RDLTQMA DE LRRHLELKEK GRHVVLGAIE NKVESKGNSP PSSGEACREE KGLAAEDSGG DSKDLSEVSE TTESTDVKDS SEASDSAS

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Macromolecule #4: Huntingtin-interacting protein K

MacromoleculeName: Huntingtin-interacting protein K / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 14.689457 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString:
MRRRGEIDMA TEGDVELELE TETSGPERPP EKPRKHDSGA ADLERVTDYA EEKEIQSSNL ETAMSVIGDR RSREQKAKQE REKELAKVT IKKEDLELIM TEMEISRAAA ERSLREHMGN VVEALIALTN

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Macromolecule #5: INOSITOL HEXAKISPHOSPHATE

MacromoleculeName: INOSITOL HEXAKISPHOSPHATE / type: ligand / ID: 5 / Number of copies: 1 / Formula: IHP
Molecular weightTheoretical: 660.035 Da
Chemical component information

ChemComp-IHP:
INOSITOL HEXAKISPHOSPHATE

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Macromolecule #6: ACETYL COENZYME *A

MacromoleculeName: ACETYL COENZYME *A / type: ligand / ID: 6 / Number of copies: 1 / Formula: ACO
Molecular weightTheoretical: 809.571 Da
Chemical component information

ChemComp-ACO:
ACETYL 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 cloride
25.0 mMHepes4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid
1.0 mMDTTDithiothreitol
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 recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 1.6 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

6c95

Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 4.03 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 168536
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

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

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