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Yorodumi- EMDB-25438: Cryo-EM structure of human NatB in complex with CoA-Alpha-Synuclein -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-25438 | |||||||||
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Title | Cryo-EM structure of human NatB in complex with CoA-Alpha-Synuclein | |||||||||
Map data | ||||||||||
Sample |
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Keywords | NatB / 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 / peptide alpha-N-acetyltransferase activity / negative regulation of mitochondrial electron transport, NADH to ubiquinone / neutral lipid metabolic process / regulation of phospholipase activity ...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 / negative regulation of mitochondrial electron transport, NADH to ubiquinone / neutral lipid metabolic process / regulation of phospholipase activity / negative regulation of monooxygenase activity / regulation of acyl-CoA biosynthetic process / negative regulation of dopamine uptake involved in synaptic transmission / negative regulation of norepinephrine uptake / positive regulation of glutathione peroxidase activity / positive regulation of SNARE complex assembly / positive regulation of hydrogen peroxide catabolic process / supramolecular fiber / negative regulation of transporter activity / mitochondrial membrane organization / negative regulation of chaperone-mediated autophagy / regulation of reactive oxygen species biosynthetic process / positive regulation of protein localization to cell periphery / regulation of synaptic vesicle recycling / negative regulation of platelet-derived growth factor receptor signaling pathway / negative regulation of exocytosis / regulation of glutamate secretion / regulation of norepinephrine uptake / response to iron(II) ion / SNARE complex assembly / positive regulation of neurotransmitter secretion / dopamine biosynthetic process / regulation of locomotion / positive regulation of inositol phosphate biosynthetic process / synaptic vesicle priming / regulation of macrophage activation / negative regulation of microtubule polymerization / synaptic vesicle transport / dopamine uptake involved in synaptic transmission / dynein complex binding / positive regulation of receptor recycling / regulation of dopamine secretion / protein kinase inhibitor activity / negative regulation of thrombin-activated receptor signaling pathway / response to type II interferon / cuprous ion binding / synaptic vesicle exocytosis / positive regulation of exocytosis / kinesin binding / positive regulation of endocytosis / mitochondrial ATP synthesis coupled electron transport / cysteine-type endopeptidase inhibitor activity involved in apoptotic process / response to magnesium ion / regulation of presynapse assembly / synaptic vesicle endocytosis / negative regulation of serotonin uptake / alpha-tubulin binding / localization / phospholipid metabolic process / supramolecular fiber organization / axon terminus / inclusion body / cellular response to copper ion / cellular response to epinephrine stimulus / Hsp70 protein binding / excitatory postsynaptic potential / response to interleukin-1 / adult locomotory behavior / negative regulation of cysteine-type endopeptidase activity involved in apoptotic process / positive regulation of release of sequestered calcium ion into cytosol / SNARE binding / fatty acid metabolic process / long-term synaptic potentiation / phosphoprotein binding / protein tetramerization / regulation of transmembrane transporter activity / microglial cell activation / synapse organization / negative regulation of protein kinase activity / regulation of long-term neuronal synaptic plasticity / protein destabilization / ferrous iron binding / tau protein binding / PKR-mediated signaling / positive regulation of protein serine/threonine kinase activity / receptor internalization / phospholipid binding / synaptic vesicle membrane / positive regulation of inflammatory response / activation of cysteine-type endopeptidase activity involved in apoptotic process / actin cytoskeleton / positive regulation of peptidyl-serine phosphorylation / actin binding / cell cortex / cellular response to oxidative stress / histone binding / growth cone / postsynapse / chemical synaptic transmission / neuron apoptotic process Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.14 Å | |||||||||
Authors | Deng S / Marmorstein R | |||||||||
Funding support | United States, 1 items
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Citation | Journal: Not Published Title: Cryo-EM structure of human NatB in complex with CoA-Alpha-Synuclein Authors: Deng S / Marmorstein R | |||||||||
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_25438.map.gz | 9.8 MB | EMDB map data format | |
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Header (meta data) | emd-25438-v30.xml emd-25438.xml | 15.4 KB 15.4 KB | Display Display | EMDB header |
Images | emd_25438.png | 168.9 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-25438 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-25438 | HTTPS FTP |
-Validation report
Summary document | emd_25438_validation.pdf.gz | 373.1 KB | Display | EMDB validaton report |
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Full document | emd_25438_full_validation.pdf.gz | 372.7 KB | Display | |
Data in XML | emd_25438_validation.xml.gz | 6.2 KB | Display | |
Data in CIF | emd_25438_validation.cif.gz | 7.2 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-25438 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-25438 | HTTPS FTP |
-Related structure data
Related structure data | 7stxMC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_25438.map.gz / Format: CCP4 / Size: 91.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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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-#3 |
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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: Homo sapiens (human) |
-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: 20.390133 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 EKKSIIPL PHPVRPEDIE |
-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: 109.64225 KDa |
Recombinant expression | Organism: Spodoptera frugiperda (fall armyworm) |
Sequence | 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 ...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 |
-Macromolecule #3: Alpha-synuclein
Macromolecule | Name: Alpha-synuclein / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 641.799 Da |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MDVFM |
-Macromolecule #4: COENZYME A
Macromolecule | Name: COENZYME A / type: ligand / ID: 4 / Number of copies: 1 / Formula: COA |
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Molecular weight | Theoretical: 767.534 Da |
Chemical component information | ChemComp-COA: |
-Macromolecule #5: ACETYL GROUP
Macromolecule | Name: ACETYL GROUP / type: ligand / ID: 5 / Number of copies: 1 / Formula: ACE |
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Molecular weight | Theoretical: 44.053 Da |
Chemical component information | ChemComp-ACE: |
-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-7stx: |