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- EMDB-38525: VMAT2 protonated state -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-38525
TitleVMAT2 protonated state
Map data
Sample
  • Complex: complex with p
    • Protein or peptide: Synaptic vesicular amine transporter,transporter B
Keywordstransporter B / TRANSPORT PROTEIN
Function / homology
Function and homology information


serotonin secretion by mast cell / sequestering of neurotransmitter / somato-dendritic dopamine secretion / histamine uptake / neurotransmitter loading into synaptic vesicle / monoamine:proton antiporter activity / aminergic neurotransmitter loading into synaptic vesicle / clathrin-sculpted monoamine transport vesicle membrane / Serotonin Neurotransmitter Release Cycle / serotonin:sodium:chloride symporter activity ...serotonin secretion by mast cell / sequestering of neurotransmitter / somato-dendritic dopamine secretion / histamine uptake / neurotransmitter loading into synaptic vesicle / monoamine:proton antiporter activity / aminergic neurotransmitter loading into synaptic vesicle / clathrin-sculpted monoamine transport vesicle membrane / Serotonin Neurotransmitter Release Cycle / serotonin:sodium:chloride symporter activity / Dopamine Neurotransmitter Release Cycle / Norepinephrine Neurotransmitter Release Cycle / serotonin uptake / dopamine transport / dopaminergic synapse / monoamine transmembrane transporter activity / histamine secretion by mast cell / monoamine transport / Na+/Cl- dependent neurotransmitter transporters / neurotransmitter transport / negative regulation of reactive oxygen species biosynthetic process / response to amphetamine / post-embryonic development / secretory granule membrane / locomotory behavior / terminal bouton / response to toxic substance / synaptic vesicle membrane / synaptic vesicle / chemical synaptic transmission / axon / intracellular membrane-bounded organelle / centrosome / dendrite / membrane / plasma membrane
Similarity search - Function
: / Major facilitator superfamily / Major Facilitator Superfamily / Major facilitator superfamily domain / Major facilitator superfamily (MFS) profile. / MFS transporter superfamily
Similarity search - Domain/homology
Synaptic vesicular amine transporter
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.15 Å
AuthorsJiang DH / Wu D
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: VMAT2 protonated state
Authors: Jiang DH / Wu D
History
DepositionDec 31, 2023-
Header (metadata) releaseMay 8, 2024-
Map releaseMay 8, 2024-
UpdateMay 8, 2024-
Current statusMay 8, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_38525.png

Downloads & links

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Map

FileDownload / File: emd_38525.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.85 Å/pix.
x 320 pix.
= 272. Å		0.85 Å/pix.
x 320 pix.
= 272. Å		0.85 Å/pix.
x 320 pix.
= 272. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.85 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1.15
Minimum - Maximum-4.481301 - 6.1674085
Average (Standard dev.)-0.0016827717 (±0.09225842)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 272.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_38525_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_38525_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : complex with p

EntireName: complex with p
Components
  • Complex: complex with p
    • Protein or peptide: Synaptic vesicular amine transporter,transporter B

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Supramolecule #1: complex with p

SupramoleculeName: complex with p / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Synaptic vesicular amine transporter,transporter B

MacromoleculeName: Synaptic vesicular amine transporter,transporter B / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 61.926078 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: SRKLILFIVF LALLLDNMLL TVVVPIIPSY LYSIKHEKNA TEIQTARPVH TASISDSFQS IFSYYDNSTM VTGNATRDLT LHQTATQHM VTNASAVPSD CPSEDKDLLN ENVQVGLLFA SKATVQLITN PFIGLLTNRI GYPIPIFAGF CIMFVSTIMF A FSSSYAFL ...String:
SRKLILFIVF LALLLDNMLL TVVVPIIPSY LYSIKHEKNA TEIQTARPVH TASISDSFQS IFSYYDNSTM VTGNATRDLT LHQTATQHM VTNASAVPSD CPSEDKDLLN ENVQVGLLFA SKATVQLITN PFIGLLTNRI GYPIPIFAGF CIMFVSTIMF A FSSSYAFL LIARSLQGIG SSCSSVAGMG MLASVYTDDE ERGNVMGIAL GGLAMGVLVG PPFGSVLYEF VGKTAPFLVL AA LVLLDGA IQLFVLQPSR VQPESQKGTP LTTLLKDPYI LIAAGSICFA NMGIAMLEPA LPIWMMETMC SRKWQLGVAF LPA SISYLI GTNIFGILAH KMGRWLCALL GMIIVGVSIL CIPFAKNIYG LIAPNFGVGF AIGMVDSSMM PIMGYLVDLR HVSV YGSVY AIADVAFCMG YAIGPSAGGA IAKAIGFPWL MTIIGIIDIL FAPLCFFLRS PPQVQLVESG GALVQPGGSL RLSCA ASGF PVNRYSMRWY RQAPGKEREW VAGMSSAGDR SSYEDSVKGR FTISRDDARN TVYLQMNSLK PEDTAVYYCN VNVGFE YWG QGTQVTVSSK

UniProtKB: Synaptic vesicular amine transporter

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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

BufferpH: 6.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.15 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 232622
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: MAXIMUM LIKELIHOOD

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