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- EMDB-42431: Structure of synaptic vesicle protein 2A in complex with a nanobody -
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Open data
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Basic information
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Title | Structure of synaptic vesicle protein 2A in complex with a nanobody | |||||||||
![]() | DeepEMhancer sharpened map | |||||||||
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Function / homology | ![]() regulation of gamma-aminobutyric acid secretion / 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) / synaptic vesicle priming / presynaptic active zone / transmembrane transporter activity / GABA-ergic synapse / ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() ![]() ![]() | |||||||||
Method | ![]() ![]() | |||||||||
![]() | Mittal A / Martin MF / Levin E / Adams C / Yang M / Ledecq M / Horyani PS / Coleman JA | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Structure of synaptic vesicle protein 2A in complex with a nanobody Authors: Mittal A / Coleman JA | |||||||||
History |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 180.7 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 19.6 KB 19.6 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 12.7 KB | Display | ![]() |
Images | ![]() | 45.7 KB | ||
Masks | ![]() ![]() | 216 MB 216 MB | ![]() | |
Filedesc metadata | ![]() | 6.9 KB | ||
Others | ![]() ![]() ![]() | 106.9 MB 200.7 MB 200.7 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8uo9MC M: atomic model generated by this map C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Annotation | DeepEMhancer sharpened map | ||||||||||||||||||||
Voxel size | X=Y=Z: 0.648 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
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Density Histograms |
-Mask #2
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-Additional map: Unsharpened map
File | emd_42431_additional_1.map | ||||||||||||
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Annotation | Unsharpened map | ||||||||||||
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Density Histograms |
-Half map: half map A
File | emd_42431_half_map_1.map | ||||||||||||
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Annotation | half map A | ||||||||||||
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Density Histograms |
-Half map: half map B
File | emd_42431_half_map_2.map | ||||||||||||
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Annotation | half map B | ||||||||||||
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Density Histograms |
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Sample components
-Entire : Protein with a nanobody
Entire | Name: Protein with a nanobody |
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Components |
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-Supramolecule #1: Protein with a nanobody
Supramolecule | Name: Protein with a nanobody / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #2 |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 98.1 kDa/nm |
-Macromolecule #1: Synaptic vesicle glycoprotein 2A
Macromolecule | Name: Synaptic vesicle glycoprotein 2A / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 75.589188 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: MGYYRGEGTQ DEEEGGASSD ATEGHDEDDE IYEGEYQGIP RAESGGKGER MADGAPLAGV RGGLSDGEGP PGGRGEAQRR KEREELAQQ YEAILRECGH GRFQWTLYFV LGLALMADGV EVFVVGFVLP SAEKDMCLSD SNKGMLGLIV YLGMMVGAFL W GGLADRLG ...String: MGYYRGEGTQ DEEEGGASSD ATEGHDEDDE IYEGEYQGIP RAESGGKGER MADGAPLAGV RGGLSDGEGP PGGRGEAQRR KEREELAQQ YEAILRECGH GRFQWTLYFV LGLALMADGV EVFVVGFVLP SAEKDMCLSD SNKGMLGLIV YLGMMVGAFL W GGLADRLG RRQCLLISLS VNSVFAFFSS FVQGYGTFLF CRLLSGVGIG GSIPIVFSYF SEFLAQEKRG EHLSWLCMFW MI GGVYAAA MAWAIIPHYG WSFQMGSAYQ FHSWRVFVLV CAFPSVFAIG ALTTQPESPR FFLENGKHDE AWMVLKQVHD TNM RAKGHP ERVFSVTHIK TIHQEDELIE IQSDTGTWYQ RWGVRALSLG GQVWGNFLSC FGPEYRRITL MMMGVWFTMS FSYY GLTVW FPDMIRHLQA VDYASRTKVF PGERVEHVTF NFTLENQIHR GGQYFNDKFI GLRLKSVSFE DSLFEECYFE DVTSS NTFF RNCTFINTVF YNTDLFEYKF VNSRLINSTF LHNKEGCPLD VTGTGEGAYM VYFVSFLGTL AVLPGNIVSA LLMDKI GRL RMLAGSSVMS CVSCFFLSFG NSESAMIALL CLFGGVSIAS WNALDVLTVE LYPSDKRTTA FGFLNALCKL AAVLGIS IF TSFVGITKAA PILFASAALA LGSSLALKLP ETRGQVLQ UniProtKB: Synaptic vesicle glycoprotein 2A |
-Macromolecule #2: Nanobody
Macromolecule | Name: Nanobody / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() ![]() |
Molecular weight | Theoretical: 15.469103 KDa |
Recombinant expression | Organism: ![]() ![]() ![]() |
Sequence | String: QVQLVESGGG LVQPGGSLRL SCAASGSIFN MRVMGWYRQA PGEQRESVAS MASGDKTTYA DSVKGRFTIS RDNAKNTVAL QMNSLKPED TAVYYCHAVD LTRNGPRVYW GQGTQVTVSS AAAENLYFQG GSGHHHHHHH HHH |
-Macromolecule #5: (4R)-1-{[(4S)-2-(methoxymethyl)-6-(trifluoromethyl)imidazo[2,1-b]...
Macromolecule | Name: (4R)-1-{[(4S)-2-(methoxymethyl)-6-(trifluoromethyl)imidazo[2,1-b][1,3,4]thiadiazol-5-yl]methyl}-4-(4,4,4-trifluorobutyl)pyrrolidin-2-one type: ligand / ID: 5 / Number of copies: 1 / Formula: X49 |
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Molecular weight | Theoretical: 444.395 Da |
-Macromolecule #6: CHOLESTEROL HEMISUCCINATE
Macromolecule | Name: CHOLESTEROL HEMISUCCINATE / type: ligand / ID: 6 / Number of copies: 1 / Formula: Y01 |
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Molecular weight | Theoretical: 486.726 Da |
Chemical component information | ![]() ChemComp-Y01: |
-Macromolecule #7: 1,2-DIDECANOYL-SN-GLYCERO-3-[PHOSPHO-L-SERINE]
Macromolecule | Name: 1,2-DIDECANOYL-SN-GLYCERO-3-[PHOSPHO-L-SERINE] / type: ligand / ID: 7 / Number of copies: 1 / Formula: PS1 |
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Molecular weight | Theoretical: 566.642 Da |
Chemical component information | ![]() ChemComp-PS1: |
-Experimental details
-Structure determination
Method | ![]() |
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Aggregation state | particle |
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Sample preparation
Concentration | 4.38 mg/mL |
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Buffer | pH: 8 Details: 150 mM NaCl, 20 mM Tris pH 8.0, 0.02 mM LMNG, 0.020 mM CHS, 0.050mM GDN, and 1 micromolar of UCB-2500 |
Grid | Model: Quantifoil R2/1 / Material: GOLD / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. |
Vitrification | Cryogen name: ETHANE-PROPANE / Chamber humidity: 100 % / Chamber temperature: 298 K / Instrument: FEI VITROBOT MARK IV |
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Electron microscopy
Microscope | TFS KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD![]() |
Specialist optics | Energy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV |
Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 60.0 e/Å2 |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |