+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-21307 | |||||||||
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Title | Cryo-EM structure of human NatB complex | |||||||||
Map data | NatB complex | |||||||||
Sample |
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Keywords | NatB / NAA20 / NAA25 / TRANSFERASE | |||||||||
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 / peptide alpha-N-acetyltransferase activity / Golgi apparatus / nucleus / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) / Escherichia coli (E. coli) / Escherichia coli K-12 (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.46 Å | |||||||||
Authors | Deng S / Marmorstein R | |||||||||
Funding support | United States, 1 items
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Citation | Journal: Elife / Year: 2020 Title: Molecular basis for N-terminal alpha-synuclein acetylation by human NatB. Authors: Sunbin Deng / Buyan Pan / Leah Gottlieb / E James Petersson / Ronen Marmorstein / Abstract: NatB is one of three major N-terminal acetyltransferase (NAT) complexes (NatA-NatC), which co-translationally acetylate the N-termini of eukaryotic proteins. Its substrates account for about 21% of ...NatB is one of three major N-terminal acetyltransferase (NAT) complexes (NatA-NatC), which co-translationally acetylate the N-termini of eukaryotic proteins. Its substrates account for about 21% of the human proteome, including well known proteins such as actin, tropomyosin, CDK2, and α-synuclein (αSyn). Human NatB (hNatB) mediated N-terminal acetylation of αSyn has been demonstrated to play key roles in the pathogenesis of Parkinson's disease and as a potential therapeutic target for hepatocellular carcinoma. Here we report the cryo-EM structure of hNatB bound to a CoA-αSyn conjugate, together with structure-guided analysis of mutational effects on catalysis. This analysis reveals functionally important differences with human NatA and NatB, resolves key hNatB protein determinants for αSyn N-terminal acetylation, and identifies important residues for substrate-specific recognition and acetylation by NatB enzymes. These studies have implications for developing small molecule NatB probes and for understanding the mode of substrate selection by NAT enzymes. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_21307.map.gz | 7.1 MB | EMDB map data format | |
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Header (meta data) | emd-21307-v30.xml emd-21307.xml | 15.2 KB 15.2 KB | Display Display | EMDB header |
Images | emd_21307.png | 106 KB | ||
Filedesc metadata | emd-21307.cif.gz | 6.2 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-21307 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-21307 | HTTPS FTP |
-Validation report
Summary document | emd_21307_validation.pdf.gz | 395.8 KB | Display | EMDB validaton report |
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Full document | emd_21307_full_validation.pdf.gz | 395.4 KB | Display | |
Data in XML | emd_21307_validation.xml.gz | 5.9 KB | Display | |
Data in CIF | emd_21307_validation.cif.gz | 6.6 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-21307 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-21307 | HTTPS FTP |
-Related structure data
Related structure data | 6vp9MC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | |
EM raw data | EMPIAR-10477 (Title: Cryo-EM structure of Human NatB with an Alpha-Synuclein peptide and CoA conjugate Data size: 2.0 TB Data #1: unaligned raw movies of hNatB with an Alpha-Synuclein peptide and CoA conjugate [micrographs - multiframe]) |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_21307.map.gz / Format: CCP4 / Size: 40.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | NatB complex | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.83 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : human NatB complex
Entire | Name: human NatB complex |
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Components |
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-Supramolecule #1: human NatB complex
Supramolecule | Name: 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 ...
Supramolecule | Name: N-alpha-acetyltransferase 20, N-alpha-acetyltransferase 25, NatB auxiliary subunit type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#2 |
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Source (natural) | Organism: Homo sapiens (human) |
-Supramolecule #3: MDVFM peptide
Supramolecule | Name: MDVFM peptide / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #3 |
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Source (natural) | Organism: Escherichia coli (E. coli) |
-Macromolecule #1: N-alpha-acetyltransferase 20
Macromolecule | Name: N-alpha-acetyltransferase 20 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO EC number: N-terminal methionine Nalpha-acetyltransferase NatB |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 18.694168 KDa |
Recombinant expression | Organism: Spodoptera frugiperda (fall armyworm) |
Sequence | String: MTTLRAFTCD DLFRFNNINL DPLTETYGIP FYLQYLAHWP EYFIVAEAPG GELMGYIMGK AEGSVAREEW HGHVTALSVA PEFRRLGLA AKLMELLEEI SERKGGFFVD LFVRVSNQVA VNMYKQLGYS VYRTVIEYYS ASNGEPDEDA YDMRKALSRD T EKK UniProtKB: N-alpha-acetyltransferase 20 |
-Macromolecule #2: N-alpha-acetyltransferase 25, NatB auxiliary subunit
Macromolecule | Name: N-alpha-acetyltransferase 25, NatB auxiliary subunit / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 112.444258 KDa |
Recombinant expression | Organism: Spodoptera frugiperda (fall armyworm) |
Sequence | String: MATRGHVQDP NDRRLRPIYD YLDNGNNKMA IQQADKLLKK HKDLHCAKVL KAIGLQRTGK QEEAFTLAQE VAALEPTDDN SLQALTILY REMHRPELVT KLYEAAVKKV PNSEEYHSHL FMAYARVGEY KKMQQAGMAL YKIVPKNPYY FWSVMSLIMQ S ISAQDENL ...String: MATRGHVQDP NDRRLRPIYD YLDNGNNKMA IQQADKLLKK HKDLHCAKVL KAIGLQRTGK QEEAFTLAQE VAALEPTDDN SLQALTILY REMHRPELVT KLYEAAVKKV PNSEEYHSHL FMAYARVGEY KKMQQAGMAL YKIVPKNPYY FWSVMSLIMQ S ISAQDENL SKTMFLPLAE RMVEKMVKED KIEAEAEVEL YYMILERLGK YQEALDVIRG KLGEKLTSEI QSRENKCMAM YK KLSRWPE CNALSRRLLL KNSDDWQFYL TYFDSVFRLI EEAWSPPAEG EHSLEGEVHY SAEKAVKFIE DRITEESKSS RHL RGPHLA KLELIRRLRS QGCNDEYKLG DPEELMFQYF KKFGDKPCCF TDLKVFVDLL PATQCTKFIN QLLGVVPLST PTED KLALP ADIRALQQHL CVVQLTRLLG LYHTMDKNQK LSVVRELMLR YQHGLEFGKT CLKTELQFSD YYCLLAVHAL IDVWR ETGD ETTVWQALTL LEEGLTHSPS NAQFKLLLVR IYCMLGAFEP VVDLYSSLDA KHIQHDTIGY LLTRYAESLG QYAAAS QSC NFALRFFHSN QKDTSEYIIQ AYKYGAFEKI PEFIAFRNRL NNSLHFAQVR TERMLLDLLL EANISTSLAE SIKSMNL RP EEDDIPWEDL RDNRDLNVFF SWDPKDRDVS EEHKKLSLEE ETLWLRIRSL TLRLISGLPS LNHPVEPKNS EKTAENGV S SRIDILRLLL QQLEATLETG KRFIEKDIQY PFLGPVPTRM GGFFNSGCSQ CQISSFYLVN DIYELDTSGL EDTMEIQER IENSFKSLLD QLKDVFSKCK GDLLEVKDGN LKTHPTLLEN LVFFVETISV ILWVSSYCES VLRPYKLNLQ KKKKKKKETS IIMPPVFTS FQDYVTGLQT LISNVVDHIK GLETHLIALK LEELILEDTS LSPEERKFSK TVQGKVQSSY LHSLLEMGEL L KKRLETTK KLKI UniProtKB: N-alpha-acetyltransferase 25, NatB auxiliary subunit |
-Macromolecule #3: MDVFM peptide
Macromolecule | Name: MDVFM peptide / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Escherichia coli K-12 (bacteria) |
Molecular weight | Theoretical: 641.799 Da |
Sequence | String: MDVFM |
-Macromolecule #4: CARBOXYMETHYL COENZYME *A
Macromolecule | Name: CARBOXYMETHYL COENZYME *A / type: ligand / ID: 4 / Number of copies: 1 / Formula: CMC |
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Molecular weight | Theoretical: 825.57 Da |
Chemical component information | ChemComp-CMC: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 1.0 mg/mL | ||||||||||||
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Buffer | pH: 7 Component:
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Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 289 K / Instrument: FEI VITROBOT MARK II |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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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 beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
+Image processing
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: AB INITIO MODEL |
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Output model | PDB-6vp9: |