[English] 日本語
Yorodumi
- EMDB-29657: Semi-synthetic CoA-alpha-Synuclein Constructs Trap N-terminal Ace... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-29657
TitleSemi-synthetic CoA-alpha-Synuclein Constructs Trap N-terminal Acetyltransferase NatB for Binding Mechanism Studies
Map data
Sample
  • Complex: Ternary complex of NAA20, NAA25 and CoA-alpha-Synuclein
    • Protein or peptide: N-alpha-acetyltransferase 20
    • Protein or peptide: N-alpha-acetyltransferase 25, NatB auxiliary subunit
    • Protein or peptide: Alpha-synuclein
  • Ligand: CARBOXYMETHYL COENZYME *A
KeywordsN-terminal acetyltransferase / 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 / 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: 3.39 Å
AuthorsGardner SM / Marmorstein R
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM118090-07 United States
CitationJournal: bioRxiv / Year: 2023
Title: Semi-synthetic CoA-α-Synuclein Constructs Trap N-terminal Acetyltransferase NatB for Binding Mechanism Studies.
Authors: Buyan Pan / Sarah Gardner / Kollin Schultz / Ryann M Perez / Sunbin Deng / Marie Shimogawa / Kohei Sato / Elizabeth Rhoades / Ronen Marmorstein / E James Petersson
Abstract: N-terminal acetylation is a chemical modification carried out by N-terminal acetyltransferases (NATs). A major member of this enzyme family, NatB, acts on much of the human proteome, including α- ...N-terminal acetylation is a chemical modification carried out by N-terminal acetyltransferases (NATs). A major member of this enzyme family, NatB, acts on much of the human proteome, including α-synuclein (αS), a synaptic protein that mediates vesicle trafficking. NatB acetylation of αS modulates its lipid vesicle binding properties and amyloid fibril formation, which underlies its role in the pathogenesis of Parkinson's disease. Although the molecular details of the interaction between human NatB (hNatB) and the N-terminus of αS have been resolved, whether the remainder of the protein plays a role in interacting with the enzyme is unknown. Here we execute the first synthesis, by native chemical ligation, of a bisubstrate inhibitor of NatB consisting of coenzyme A and full-length human αS, additionally incorporating two fluorescent probes for studies of conformational dynamics. We use cryo-electron microscopy (cryo-EM) to characterize the structural features of the hNatB/inhibitor complex and show that, beyond the first few residues, αS remains disordered when in complex with hNatB. We further probe changes in the αS conformation by single molecule Förster resonance energy transfer (smFRET) to reveal that the C-terminus expands when bound to hNatB. Computational models based on the cryo-EM and smFRET data help to explain the conformational changes and their implications for hNatB substrate recognition and specific inhibition of the interaction with αS. Beyond the study of αS and NatB, these experiments illustrate valuable strategies for the study of challenging structural biology targets through a combination of protein semi-synthesis, cryo-EM, smFRET, and computational modeling.
History
DepositionJan 31, 2023-
Header (metadata) releaseMay 3, 2023-
Map releaseMay 3, 2023-
UpdateOct 23, 2024-
Current statusOct 23, 2024Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_29657.png

Downloads & links

-
Map

FileDownload / File: emd_29657.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.86 Å/pix.
x 300 pix.
= 258. Å		0.86 Å/pix.
x 300 pix.
= 258. Å		0.86 Å/pix.
x 300 pix.
= 258. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.86 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.2
Minimum - Maximum-0.24982624 - 0.78872156
Average (Standard dev.)0.0017144546 (±0.028970562)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 258.0 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: #1

Fileemd_29657_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_29657_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Ternary complex of NAA20, NAA25 and CoA-alpha-Synuclein

EntireName: Ternary complex of NAA20, NAA25 and CoA-alpha-Synuclein
Components
  • Complex: Ternary complex of NAA20, NAA25 and CoA-alpha-Synuclein
    • Protein or peptide: N-alpha-acetyltransferase 20
    • Protein or peptide: N-alpha-acetyltransferase 25, NatB auxiliary subunit
    • Protein or peptide: Alpha-synuclein
  • Ligand: CARBOXYMETHYL COENZYME *A

-
Supramolecule #1: Ternary complex of NAA20, NAA25 and CoA-alpha-Synuclein

SupramoleculeName: Ternary complex of NAA20, NAA25 and CoA-alpha-Synuclein
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Homo sapiens (human)

-
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

-
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: 112.444258 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: 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: 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: 641.799 Da
Recombinant expressionOrganism: Escherichia coli BL21 (bacteria)
SequenceString:
MDVFM

UniProtKB: Alpha-synuclein

-
Macromolecule #4: CARBOXYMETHYL COENZYME *A

MacromoleculeName: CARBOXYMETHYL COENZYME *A / type: ligand / ID: 4 / Number of copies: 1 / Formula: CMC
Molecular weightTheoretical: 825.57 Da
Chemical component information

ChemComp-CMC:
CARBOXYMETHYL COENZYME *A

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration4 mg/mL
BufferpH: 7.5
VitrificationCryogen name: ETHANE / Chamber humidity: 100 %

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Number real images: 5470 / Average electron dose: 43.9 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

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

6vp9

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.39 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 192518
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more