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- PDB-8xo9: VMAT2 complex with noradrenaline in cytosol-facing state -

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Basic information

Entry
Database: PDB / ID: 8xo9
TitleVMAT2 complex with noradrenaline in cytosol-facing state
ComponentsSynaptic vesicular amine transporter,Synaptic vesicular amine transporter,transporter A
KeywordsTRANSPORT PROTEIN / transporterA
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
Noradrenaline / Synaptic vesicular amine transporter
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsJiang, D.H. / Wu, D.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31971134 China
CitationJournal: Cell Res / Year: 2024
Title: Structural snapshots of human VMAT2 reveal insights into substrate recognition and proton coupling mechanism.
Authors: Di Wu / Zhuoya Yu / Qihao Chen / Jun Zhao / Bo Huang / Yuhang Wang / Jiawei Su / Na Li / Daohua Jiang / Yan Zhao /
History
DepositionDec 31, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 8, 2024Provider: repository / Type: Initial release
Revision 2.0Jul 24, 2024Group: Atomic model / Data collection / Structure summary
Category: atom_site / em_admin ...atom_site / em_admin / em_software / entity / pdbx_contact_author
Item: _atom_site.Cartn_x / _atom_site.Cartn_y ..._atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _em_admin.last_update / _entity.pdbx_description
Description: Ligand geometry
Details: The hydroxyl group of norepinephrine was oriented incorrectly and we switched the hydroxyl group to the side of the hydrophilic residue.
Provider: author / Type: Coordinate replacement
Revision 2.1Nov 20, 2024Group: Data collection / Database references / Structure summary
Category: citation / citation_author ...citation / citation_author / em_admin / pdbx_entry_details
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _em_admin.last_update / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Synaptic vesicular amine transporter,Synaptic vesicular amine transporter,transporter A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,1232
Polymers61,9531
Non-polymers1701
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Antibody Synaptic vesicular amine transporter,Synaptic vesicular amine transporter,transporter A / Monoamine transporter / Solute carrier family 18 member 2 / Vesicular amine transporter 2 / VAT2


Mass: 61953.148 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SLC18A2, SVMT, VMAT2 / Production host: Homo sapiens (human) / References: UniProt: Q05940
#2: Chemical ChemComp-E5E / Noradrenaline


Mass: 170.186 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H12NO3 / Feature type: SUBJECT OF INVESTIGATION / Comment: neurotransmitter, hormone*YM
Has ligand of interestY
Has protein modificationN

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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

ComponentName: complex with NE / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 6.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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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 / Nominal defocus max: 2000 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 60 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 176326 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0032989
ELECTRON MICROSCOPYf_angle_d0.6714069
ELECTRON MICROSCOPYf_dihedral_angle_d4.502411
ELECTRON MICROSCOPYf_chiral_restr0.04489
ELECTRON MICROSCOPYf_plane_restr0.006498

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