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

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Basic information

Entry
Database: PDB / ID: 7stx
TitleCryo-EM structure of human NatB in complex with CoA-Alpha-Synuclein
Components
  • Alpha-synuclein
  • N-alpha-acetyltransferase 20
  • N-alpha-acetyltransferase 25, NatB auxiliary subunit
KeywordsTRANSFERASE / NatB / NAA20 / NAA25 / 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 / positive regulation of SNARE complex assembly / positive regulation of hydrogen peroxide catabolic process / supramolecular fiber / mitochondrial membrane organization / negative regulation of chaperone-mediated autophagy / regulation of synaptic vesicle recycling / 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 / response to iron(II) ion / SNARE complex assembly / positive regulation of neurotransmitter secretion / dopamine biosynthetic process / regulation of norepinephrine uptake / transporter regulator activity / regulation of locomotion / synaptic vesicle priming / mitochondrial ATP synthesis coupled electron transport / regulation of macrophage activation / positive regulation of inositol phosphate biosynthetic process / negative regulation of microtubule polymerization / synaptic vesicle transport / positive regulation of receptor recycling / dopamine uptake involved in synaptic transmission / protein kinase inhibitor activity / dynein complex binding / regulation of dopamine secretion / negative regulation of thrombin-activated receptor signaling pathway / cuprous ion binding / positive regulation of endocytosis / positive regulation of exocytosis / response to magnesium ion / synaptic vesicle exocytosis / enzyme inhibitor activity / kinesin binding / synaptic vesicle endocytosis / regulation of presynapse assembly / response to type II interferon / cysteine-type endopeptidase inhibitor activity / negative regulation of serotonin uptake / alpha-tubulin binding / supramolecular fiber organization / inclusion body / phospholipid metabolic process / cellular response to copper ion / axon terminus / cellular response to epinephrine stimulus / cytoskeleton organization / Hsp70 protein binding / response to interleukin-1 / regulation of microtubule cytoskeleton organization / SNARE binding / positive regulation of release of sequestered calcium ion into cytosol / adult locomotory behavior / negative regulation of protein kinase activity / excitatory postsynaptic potential / fatty acid metabolic process / regulation of actin cytoskeleton organization / phosphoprotein binding / protein tetramerization / microglial cell activation / regulation of long-term neuronal synaptic plasticity / synapse organization / ferrous iron binding / protein destabilization / PKR-mediated signaling / phospholipid binding / receptor internalization / tau protein binding / long-term synaptic potentiation / synaptic vesicle membrane / positive regulation of inflammatory response / actin cytoskeleton / actin binding / growth cone / cell cortex / cellular response to oxidative stress / neuron apoptotic process / chemical synaptic transmission / molecular adaptor activity / negative regulation of neuron apoptotic process / response to lipopolysaccharide / histone binding
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
COENZYME A / Alpha-synuclein / N-alpha-acetyltransferase 20 / N-alpha-acetyltransferase 25, NatB auxiliary subunit
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.14 Å
AuthorsDeng, S. / Marmorstein, R.
Funding support United States, 1items
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, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 22, 2021Provider: repository / Type: Initial release
Revision 1.1Jul 5, 2023Group: Database references / Category: citation / Item: _citation.journal_abbrev / _citation.unpublished_flag
Revision 2.0Dec 25, 2024Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Polymer sequence / Source and taxonomy / Structure summary
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / em_admin / em_entity_assembly / entity / entity_poly / entity_poly_seq / entity_src_gen / pdbx_entity_nonpoly / pdbx_entry_details / pdbx_modification_feature / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_struct_assembly_gen / pdbx_validate_close_contact / pdbx_validate_rmsd_angle / pdbx_validate_rmsd_bond / struct_asym / struct_conn / struct_ref_seq / struct_ref_seq_dif
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.group_PDB / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.label_seq_id / _atom_site.type_symbol / _em_admin.last_update / _em_entity_assembly.entity_id_list / _entity_poly.nstd_monomer / _entity_poly.pdbx_seq_one_letter_code / _entity_poly.pdbx_seq_one_letter_code_can / _entity_src_gen.gene_src_common_name / _entity_src_gen.pdbx_end_seq_num / _pdbx_entry_details.has_protein_modification / _pdbx_struct_assembly_gen.asym_id_list / _struct_ref_seq.seq_align_beg / _struct_ref_seq.seq_align_end

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Structure visualization

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  • Deposited structure unit
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  • EMDB-25438
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Structure viewerMolecule:
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Assembly

Deposited unit
A: N-alpha-acetyltransferase 20
B: N-alpha-acetyltransferase 25, NatB auxiliary subunit
C: Alpha-synuclein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)131,4684
Polymers130,7003
Non-polymers7681
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein N-alpha-acetyltransferase 20 / Methionine N-acetyltransferase / N-acetyltransferase 5 / N-terminal acetyltransferase B complex ...Methionine N-acetyltransferase / N-acetyltransferase 5 / N-terminal acetyltransferase B complex catalytic subunit NAA20 / N-terminal acetyltransferase B complex catalytic subunit NAT5 / NatB complex subunit NAT5 / NatB catalytic subunit


Mass: 20390.133 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NAA20, NAT5 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: P61599, N-terminal methionine Nalpha-acetyltransferase NatB
#2: Protein N-alpha-acetyltransferase 25, NatB auxiliary subunit / Mitochondrial distribution and morphology protein 20 / N-terminal acetyltransferase B complex ...Mitochondrial distribution and morphology protein 20 / N-terminal acetyltransferase B complex subunit MDM20 / NatB complex subunit MDM20 / N-terminal acetyltransferase B complex subunit NAA25 / p120


Mass: 109642.250 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NAA25, C12orf30, MDM20, NAP1 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q14CX7
#3: Protein/peptide Alpha-synuclein / Non-A beta component of AD amyloid / Non-A4 component of amyloid precursor / NACP


Mass: 667.837 Da / Num. of mol.: 1 / Fragment: UNP residues 1-5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SNCA, NACP, PARK1 / Production host: Escherichia coli (E. coli) / References: UniProt: P37840
#4: Chemical ChemComp-COA / COENZYME A


Mass: 767.534 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H36N7O16P3S / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

Component
IDNameTypeEntity IDParent-IDSource
1human NatB complexCOMPLEX#1-#20MULTIPLE SOURCES
2N-alpha-acetyltransferase 20, N-alpha-acetyltransferase 25, NatB auxiliary subunitCOMPLEX#1-#21RECOMBINANT
3MDVFM peptideCOMPLEX#31RECOMBINANT
Molecular weightUnits: MEGADALTONS / Experimental value: NO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
12Homo sapiens (human)9606
23Homo sapiens (human)9606
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-ID
12Spodoptera frugiperda (fall armyworm)7108
23Escherichia coli (E. coli)562
Buffer solutionpH: 7
Buffer component
IDConc.NameFormulaBuffer-ID
1200 mMsodium chlorideNaCl1
225 mM4-(2-hydroxyethyl)-1-piperazineethanesulfonic acidHEPES1
31 mMDithiothreitolDTT1
SpecimenConc.: 1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK II / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 289 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD
Image recording
IDImaging-IDElectron dose (e/Å2)Film or detector model
111.6GATAN K3 (6k x 4k)
211.3GATAN K3 (6k x 4k)

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Processing

EM software
IDNameVersionCategory
4CTFFINDCTF correction
7Coot0.8.9.2model fitting
9PHENIX1.17.1-3660model refinement
10RELION3initial Euler assignment
11RELION3final Euler assignment
12RELION3classification
13RELION33D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.14 Å / Resolution method: OTHER / Num. of particles: 726923 / Details: not sure exactly how many particles were used / Symmetry type: POINT
Atomic model buildingProtocol: AB INITIO MODEL / Space: REAL

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