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- EMDB-42430: Structure of synaptic vesicle protein 2B with padsevonil -

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Basic information

Entry
Database: EMDB / ID: EMD-42430
TitleStructure of synaptic vesicle protein 2B with padsevonil
Map dataMain map sharpened
Sample
  • Complex: SV2B complexed with padsevonil
    • Protein or peptide: Synaptic vesicle glycoprotein 2B
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: (4R)-4-(2-chloro-2,2-difluoroethyl)-1-{[(4R)-2-(methoxymethyl)-6-(trifluoromethyl)imidazo[2,1-b][1,3,4]thiadiazol-5-yl]methyl}pyrrolidin-2-one
  • Ligand: 1,2-DIDECANOYL-SN-GLYCERO-3-[PHOSPHO-L-SERINE]
  • Ligand: (3beta,14beta,17beta,25R)-3-[4-methoxy-3-(methoxymethyl)butoxy]spirost-5-en
  • Ligand: [(2R)-3-[oxidanyl-[2-(trimethyl-$l^{4}-azanyl)ethoxy]phosphoryl]oxy-2-propanoyloxy-propyl] propanoate
  • Ligand: CHOLESTEROL HEMISUCCINATE
  • Ligand: water
KeywordsSynaptic vesicle / SLC22 / Inhibitor / Antiepileptic / TRANSPORT PROTEIN
Function / homology
Function and homology information


Toxicity of botulinum toxin type F (botF) / Toxicity of botulinum toxin type D (botD) / Toxicity of botulinum toxin type E (botE) / Toxicity of botulinum toxin type A (botA) / regulation of presynaptic cytosolic calcium ion concentration / neurotransmitter transport / regulation of synaptic vesicle exocytosis / transmembrane transporter activity / acrosomal vesicle / synaptic vesicle membrane ...Toxicity of botulinum toxin type F (botF) / Toxicity of botulinum toxin type D (botD) / Toxicity of botulinum toxin type E (botE) / Toxicity of botulinum toxin type A (botA) / regulation of presynaptic cytosolic calcium ion concentration / neurotransmitter transport / regulation of synaptic vesicle exocytosis / transmembrane transporter activity / acrosomal vesicle / synaptic vesicle membrane / synaptic vesicle / chemical synaptic transmission / membrane / plasma membrane
Similarity search - Function
Synaptic vesicle protein SV2 / Pentapeptide repeats (9 copies) / Pentapeptide repeat / Major facilitator, sugar transporter-like / Sugar (and other) transporter / Sugar transporter, conserved site / Major facilitator superfamily / Major Facilitator Superfamily / Major facilitator superfamily domain / Major facilitator superfamily (MFS) profile. / MFS transporter superfamily
Similarity search - Domain/homology
Synaptic vesicle glycoprotein 2B
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsMartin MF / Mittal A / Levin E / Adams C / Yang M / Ledecq M / Horyani PS / Coleman JA
Funding support United States, 1 items
OrganizationGrant numberCountry
Brain & Behavior Research Foundation30153 United States
CitationJournal: To Be Published
Title: Structure of synaptic vesicle protein 2B with padsevonil
Authors: Martin MF / Coleman JA
History
DepositionOct 19, 2023-
Header (metadata) releaseMay 22, 2024-
Map releaseMay 22, 2024-
UpdateMay 22, 2024-
Current statusMay 22, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_42430.png

Downloads & links

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Map

FileDownload / File: emd_42430.map.gz / Format: CCP4 / Size: 144.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMain map sharpened
Voxel sizeX=Y=Z: 0.72 Å
Density
Contour LevelBy AUTHOR: 0.406
Minimum - Maximum-2.9103923 - 4.459402
Average (Standard dev.)0.001747748 (±0.07713039)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions336336336
Spacing336336336
CellA=B=C: 241.92001 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_42430_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Mask #2

Fileemd_42430_msk_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Unsharpened map

Fileemd_42430_additional_1.map
AnnotationUnsharpened map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map B

Fileemd_42430_half_map_1.map
AnnotationHalf map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map A

Fileemd_42430_half_map_2.map
AnnotationHalf map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : SV2B complexed with padsevonil

EntireName: SV2B complexed with padsevonil
Components
  • Complex: SV2B complexed with padsevonil
    • Protein or peptide: Synaptic vesicle glycoprotein 2B
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: (4R)-4-(2-chloro-2,2-difluoroethyl)-1-{[(4R)-2-(methoxymethyl)-6-(trifluoromethyl)imidazo[2,1-b][1,3,4]thiadiazol-5-yl]methyl}pyrrolidin-2-one
  • Ligand: 1,2-DIDECANOYL-SN-GLYCERO-3-[PHOSPHO-L-SERINE]
  • Ligand: (3beta,14beta,17beta,25R)-3-[4-methoxy-3-(methoxymethyl)butoxy]spirost-5-en
  • Ligand: [(2R)-3-[oxidanyl-[2-(trimethyl-$l^{4}-azanyl)ethoxy]phosphoryl]oxy-2-propanoyloxy-propyl] propanoate
  • Ligand: CHOLESTEROL HEMISUCCINATE
  • Ligand: water

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Supramolecule #1: SV2B complexed with padsevonil

SupramoleculeName: SV2B complexed with padsevonil / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 77.4 kDa/nm

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Macromolecule #1: Synaptic vesicle glycoprotein 2B

MacromoleculeName: Synaptic vesicle glycoprotein 2B / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 77.515016 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MDDYKYQDNY GGYAPSDGYY RGNESNPEED AQSDVTEGHD EEDEIYEGEY QGIPHPDDVK AKQAKMAPSR MDSLRGQTDL MAERLEDEE QLAHQYETIM DECGHGRFQW ILFFVLGLAL MADGVEVFVV SFALPSAEKD MCLSSSKKGM LGMIVYLGMM A GAFILGGL ...String:
MDDYKYQDNY GGYAPSDGYY RGNESNPEED AQSDVTEGHD EEDEIYEGEY QGIPHPDDVK AKQAKMAPSR MDSLRGQTDL MAERLEDEE QLAHQYETIM DECGHGRFQW ILFFVLGLAL MADGVEVFVV SFALPSAEKD MCLSSSKKGM LGMIVYLGMM A GAFILGGL ADKLGRKRVL SMSLAVNASF ASLSSFVQGY GAFLFCRLIS GIGIGGALPI VFAYFSEFLS REKRGEHLSW LG IFWMTGG LYASAMAWSI IPHYGWGFSM GTNYHFHSWR VFVIVCALPC TVSMVALKFM PESPRFLLEM GKHDEAWMIL KQV HDTNMR AKGTPEKVFT VSNIKTPKQM DEFIEIQSST GTWYQRWLVR FKTIFKQVWD NALYCVMGPY RMNTLILAVV WFAM AFSYY GLTVWFPDMI RYFQDEEYKS KMKVFFGEHV YGATINFTME NQIHQHGKLV NDKFTRMYFK HVLFEDTFFD ECYFE DVTS TDTYFKNCTI ESTIFYNTDL YEHKFINCRF INSTFLEQKE GCHMDLEQDN DFLIYLVSFL GSLSVLPGNI ISALLM DRI GRLKMIGGSM LISAVCCFFL FFGNSESAMI GWQCLFCGTS IAAWNALDVI TVELYPTNQR ATAFGILNGL CKFGAIL GN TIFASFVGIT KVVPILLAAA SLVGGGLIAL RLPETREQVL M

UniProtKB: Synaptic vesicle glycoprotein 2B

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Macromolecule #2: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 2 / Number of copies: 3 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine

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Macromolecule #3: (4R)-4-(2-chloro-2,2-difluoroethyl)-1-{[(4R)-2-(methoxymethyl)-6-...

MacromoleculeName: (4R)-4-(2-chloro-2,2-difluoroethyl)-1-{[(4R)-2-(methoxymethyl)-6-(trifluoromethyl)imidazo[2,1-b][1,3,4]thiadiazol-5-yl]methyl}pyrrolidin-2-one
type: ligand / ID: 3 / Number of copies: 1 / Formula: X3U
Molecular weightTheoretical: 432.797 Da

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Macromolecule #4: 1,2-DIDECANOYL-SN-GLYCERO-3-[PHOSPHO-L-SERINE]

MacromoleculeName: 1,2-DIDECANOYL-SN-GLYCERO-3-[PHOSPHO-L-SERINE] / type: ligand / ID: 4 / Number of copies: 1 / Formula: PS1
Molecular weightTheoretical: 566.642 Da
Chemical component information

ChemComp-PS1:
1,2-DIDECANOYL-SN-GLYCERO-3-[PHOSPHO-L-SERINE]

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Macromolecule #5: (3beta,14beta,17beta,25R)-3-[4-methoxy-3-(methoxymethyl)butoxy]sp...

MacromoleculeName: (3beta,14beta,17beta,25R)-3-[4-methoxy-3-(methoxymethyl)butoxy]spirost-5-en
type: ligand / ID: 5 / Number of copies: 2 / Formula: 9Z9
Molecular weightTheoretical: 544.805 Da
Chemical component information

ChemComp-9Z9:
(3beta,14beta,17beta,25R)-3-[4-methoxy-3-(methoxymethyl)butoxy]spirost-5-en / detergent*YM

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Macromolecule #6: [(2R)-3-[oxidanyl-[2-(trimethyl-$l^{4}-azanyl)ethoxy]phosphoryl]o...

MacromoleculeName: [(2R)-3-[oxidanyl-[2-(trimethyl-$l^{4}-azanyl)ethoxy]phosphoryl]oxy-2-propanoyloxy-propyl] propanoate
type: ligand / ID: 6 / Number of copies: 1 / Formula: 43Y
Molecular weightTheoretical: 370.356 Da
Chemical component information

ChemComp-43Y:
[(2R)-3-[oxidanyl-[2-(trimethyl-$l^{4}-azanyl)ethoxy]phosphoryl]oxy-2-propanoyloxy-propyl] propanoate

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Macromolecule #7: CHOLESTEROL HEMISUCCINATE

MacromoleculeName: CHOLESTEROL HEMISUCCINATE / type: ligand / ID: 7 / Number of copies: 1 / Formula: Y01
Molecular weightTheoretical: 486.726 Da
Chemical component information

ChemComp-Y01:
CHOLESTEROL HEMISUCCINATE

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Macromolecule #8: water

MacromoleculeName: water / type: ligand / ID: 8 / Number of copies: 5 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER / Water

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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

Concentration4 mg/mL
BufferpH: 8
Details: 150 mM NaCl, 20 mM Tris pH 8.0, .4 mM glyco-diosgenin, 1 uM padsevonil
GridModel: Quantifoil R2/1 / Material: GOLD / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE-PROPANE / Chamber humidity: 100 % / Chamber temperature: 298 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 1.5 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 194000
Specialist opticsEnergy filter - Name: TFS Selectris / Energy filter - Slit width: 10 eV
Image recordingFilm or detector model: TFS FALCON 4i (4k x 4k) / Average electron dose: 60.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER / Details: Ab-initio reconstruction
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 62528
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

2-f1


Chain - Source name: AlphaFold / Chain - Initial model type: in silico model
Output model

PDB-8uo8:
Structure of synaptic vesicle protein 2B with padsevonil

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