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- EMDB-25438: Cryo-EM structure of human NatB in complex with CoA-Alpha-Synuclein -

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Basic information

Entry
Database: EMDB / ID: EMD-25438
TitleCryo-EM structure of human NatB in complex with CoA-Alpha-Synuclein
Map data
Sample
  • Complex: human NatB complex
    • Complex: N-alpha-acetyltransferase 20, N-alpha-acetyltransferase 25, NatB auxiliary subunit
      • Protein or peptide: N-alpha-acetyltransferase 20
      • Protein or peptide: N-alpha-acetyltransferase 25, NatB auxiliary subunit
    • Complex: MDVFM peptide
      • Protein or peptide: Alpha-synuclein
  • Ligand: COENZYME A
KeywordsNatB / NAA20 / NAA25 / TRANSFERASE / alpha Synuclein
Function / homology
Function and homology information


N-terminal peptidyl-glutamine acetylation / N-terminal methionine Nalpha-acetyltransferase NatB / N-terminal peptidyl-aspartic acid acetylation / N-terminal peptidyl-glutamic acid acetylation / NatB complex / N-terminal protein amino acid acetylation / protein N-terminal-methionine acetyltransferase activity / protein-N-terminal amino-acid acetyltransferase activity / acetyltransferase activator activity / negative regulation of mitochondrial electron transport, NADH to ubiquinone ...N-terminal peptidyl-glutamine acetylation / N-terminal methionine Nalpha-acetyltransferase NatB / N-terminal peptidyl-aspartic acid acetylation / N-terminal peptidyl-glutamic acid acetylation / NatB complex / N-terminal protein amino acid acetylation / protein N-terminal-methionine acetyltransferase activity / protein-N-terminal amino-acid acetyltransferase activity / acetyltransferase activator activity / negative regulation of mitochondrial electron transport, NADH to ubiquinone / : / neutral lipid metabolic process / regulation of acyl-CoA biosynthetic process / negative regulation of dopamine uptake involved in synaptic transmission / negative regulation of norepinephrine uptake / response to desipramine / positive regulation of SNARE complex assembly / positive regulation of hydrogen peroxide catabolic process / supramolecular fiber / regulation of synaptic vesicle recycling / negative regulation of chaperone-mediated autophagy / mitochondrial membrane organization / regulation of reactive oxygen species biosynthetic process / negative regulation of platelet-derived growth factor receptor signaling pathway / positive regulation of protein localization to cell periphery / negative regulation of exocytosis / regulation of glutamate secretion / dopamine biosynthetic process / response to iron(II) ion / SNARE complex assembly / regulation of locomotion / positive regulation of neurotransmitter secretion / negative regulation of dopamine metabolic process / regulation of macrophage activation / positive regulation of inositol phosphate biosynthetic process / regulation of norepinephrine uptake / negative regulation of microtubule polymerization / synaptic vesicle transport / transporter regulator activity / synaptic vesicle priming / dopamine uptake involved in synaptic transmission / protein kinase inhibitor activity / regulation of dopamine secretion / dynein complex binding / mitochondrial ATP synthesis coupled electron transport / negative regulation of thrombin-activated receptor signaling pathway / positive regulation of receptor recycling / cuprous ion binding / nuclear outer membrane / response to magnesium ion / positive regulation of endocytosis / positive regulation of exocytosis / synaptic vesicle exocytosis / kinesin binding / synaptic vesicle endocytosis / enzyme inhibitor activity / cysteine-type endopeptidase inhibitor activity / negative regulation of serotonin uptake / response to type II interferon / regulation of presynapse assembly / alpha-tubulin binding / beta-tubulin binding / phospholipase binding / behavioral response to cocaine / supramolecular fiber organization / phospholipid metabolic process / cellular response to fibroblast growth factor stimulus / inclusion body / cytoskeleton organization / axon terminus / Hsp70 protein binding / cellular response to epinephrine stimulus / response to interleukin-1 / regulation of microtubule cytoskeleton organization / cellular response to copper ion / positive regulation of release of sequestered calcium ion into cytosol / adult locomotory behavior / SNARE binding / regulation of actin cytoskeleton organization / excitatory postsynaptic potential / protein tetramerization / phosphoprotein binding / microglial cell activation / ferrous iron binding / fatty acid metabolic process / regulation of long-term neuronal synaptic plasticity / synapse organization / protein destabilization / PKR-mediated signaling / phospholipid binding / receptor internalization / tau protein binding / long-term synaptic potentiation / terminal bouton / positive regulation of inflammatory response / synaptic vesicle membrane / actin cytoskeleton / growth cone / actin binding / cellular response to oxidative stress
Similarity search - Function
N-acetyltransferase B complex, non-catalytic subunit / N-acetyltransferase B complex (NatB) non catalytic subunit / : / Synuclein / Alpha-synuclein / Synuclein / Acetyltransferase (GNAT) family / Gcn5-related N-acetyltransferase (GNAT) domain profile. / GNAT domain / TPR repeat region circular profile. ...N-acetyltransferase B complex, non-catalytic subunit / N-acetyltransferase B complex (NatB) non catalytic subunit / : / Synuclein / Alpha-synuclein / Synuclein / Acetyltransferase (GNAT) family / Gcn5-related N-acetyltransferase (GNAT) domain profile. / GNAT domain / TPR repeat region circular profile. / Acyl-CoA N-acyltransferase / Tetratricopeptide-like helical domain superfamily
Similarity search - Domain/homology
Alpha-synuclein / N-alpha-acetyltransferase 20 / N-alpha-acetyltransferase 25, NatB auxiliary subunit
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.14 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: Not Published
Title: Cryo-EM structure of human NatB in complex with CoA-Alpha-Synuclein
Authors: Deng S / Marmorstein R
History
DepositionNov 15, 2021-
Header (metadata) releaseDec 22, 2021-
Map releaseDec 22, 2021-
UpdateDec 25, 2024-
Current statusDec 25, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.015
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.015
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7stx
  • Surface level: 0.015
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_25438.png

Downloads & links

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Map

FileDownload / File: emd_25438.map.gz / Format: CCP4 / Size: 91.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 288 pix.
= 239.04 Å		0.83 Å/pix.
x 288 pix.
= 239.04 Å		0.83 Å/pix.
x 288 pix.
= 239.04 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.83 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.015 / Movie #1: 0.015
Minimum - Maximum-0.12117671 - 0.14295562
Average (Standard dev.)0.00007930015 (±0.0027739124)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions288288288
Spacing288288288
CellA=B=C: 239.04 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.830.830.83
M x/y/z288288288
origin x/y/z0.0000.0000.000
length x/y/z239.040239.040239.040
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS288288288
D min/max/mean-0.1210.1430.000

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Supplemental data

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Sample components

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Entire : human NatB complex

EntireName: human NatB complex
Components
  • Complex: human NatB complex
    • Complex: N-alpha-acetyltransferase 20, N-alpha-acetyltransferase 25, NatB auxiliary subunit
      • Protein or peptide: N-alpha-acetyltransferase 20
      • Protein or peptide: N-alpha-acetyltransferase 25, NatB auxiliary subunit
    • Complex: MDVFM peptide
      • Protein or peptide: Alpha-synuclein
  • Ligand: COENZYME A

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Supramolecule #1: human NatB complex

SupramoleculeName: human NatB complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2

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Supramolecule #2: N-alpha-acetyltransferase 20, N-alpha-acetyltransferase 25, NatB ...

SupramoleculeName: N-alpha-acetyltransferase 20, N-alpha-acetyltransferase 25, NatB auxiliary subunit
type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#2
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #3: MDVFM peptide

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

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Macromolecule #1: N-alpha-acetyltransferase 20

MacromoleculeName: N-alpha-acetyltransferase 20 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
EC number: N-terminal methionine Nalpha-acetyltransferase NatB
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 20.390133 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString:
MTTLRAFTCD DLFRFNNINL DPLTETYGIP FYLQYLAHWP EYFIVAEAPG GELMGYIMGK AEGSVAREEW HGHVTALSVA PEFRRLGLA AKLMELLEEI SERKGGFFVD LFVRVSNQVA VNMYKQLGYS VYRTVIEYYS ASNGEPDEDA YDMRKALSRD T EKKSIIPL PHPVRPEDIE

UniProtKB: N-alpha-acetyltransferase 20

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Macromolecule #2: N-alpha-acetyltransferase 25, NatB auxiliary subunit

MacromoleculeName: N-alpha-acetyltransferase 25, NatB auxiliary subunit / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 109.64225 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)H CAKVLKAIGL QRTGKQEEA FTLAQEVAAL EPTDDNSLQA ...String:
(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)H CAKVLKAIGL QRTGKQEEA FTLAQEVAAL EPTDDNSLQA LTILYREMHR PELVTKLYEA AVKKVPNSEE YHSHLFMAYA RVGEYKKMQQ AGMALYKIVP KNPYYFWSV MSLIMQSISA QDENLSKTMF LPLAERMVEK MVKEDKIEAE AEVELYYMIL ERLGKYQEAL DVIRGKLGEK L TSEIQSRE NKCMAMYKKL SRWPECNALS RRLLLKNSDD WQFYLTYFDS VFRLIEEAWS PPAEGEHSLE GEVHYSAEKA VK FIEDRIT EESKSSRHLR GPHLAKLELI RRLRSQGCND EYKLGDPEEL MFQYFKKFGD KPCCFTDLKV FVDLLPATQC TKF INQLLG VVPLSTPTED KLALPADIRA LQQHLCVVQL TRLLGLYHTM DKNQKLSVVR ELMLRYQHGL EFGKTCLKTE LQFS DYYCL LAVHALIDVW RETGDETTVW QALTLLEEGL THSPSNAQFK LLLVRIYCML GAFEPVVDLY SSLDAKHIQH DTIGY LLTR YAESLGQYAA ASQSCNFALR FFHSNQKDTS EYIIQAYKYG AFEKIPEFIA FRNRLNNSLH FAQVRTERML LDLLLE ANI STSLAESIKS MNLRPEEDDI PWEDLRDNRD LNVFFSWDPK DRDVSEEHKK LSLEEETLWL RIRSLTLRLI SGLPSLN HP VEPKNSEKTA ENGVSSRIDI LRLLLQQLEA TLETGKRFIE KDIQYPFLGP VPTRMGGFFN SGCSQCQISS FYLVNDIY E LDTSGLEDTM EIQERIENSF KSLLDQLKDV FSKCKGDLLE VKDGNLKTHP TLLENLVFFV ETISVILWVS SYCESVLRP YKLNLQKKKK KKKETSIIMP PVFTSFQDYV TGLQTLISNV VDHIKGLETH LIALKLEELI LEDTSLSPEE RKFSKTVQGK VQSSYLHSL LEMGELLKKR LETTKKLKI

UniProtKB: N-alpha-acetyltransferase 25, NatB auxiliary subunit

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Macromolecule #3: Alpha-synuclein

MacromoleculeName: Alpha-synuclein / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 667.837 Da
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
(ACE)MDVFM

UniProtKB: Alpha-synuclein

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Macromolecule #4: COENZYME A

MacromoleculeName: COENZYME A / type: ligand / ID: 4 / Number of copies: 1 / Formula: COA
Molecular weightTheoretical: 767.534 Da
Chemical component information

ChemComp-COA:
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 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 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
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Image recording ID1
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.14 Å / Resolution method: OTHER / Software - Name: RELION (ver. 3.0) / Details: not sure exactly how many particles were used / Number images used: 726923
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: AB INITIO MODEL
Output model

PDB-7stx:
Cryo-EM structure of human NatB in complex with CoA-Alpha-Synuclein

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