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Yorodumi- EMDB-42432: Structure of the synaptic vesicle protein 2A Luminal domain in co... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-42432 | |||||||||
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Title | Structure of the synaptic vesicle protein 2A Luminal domain in complex with a nanobody | |||||||||
Map data | Deepemhancer sharpened map | |||||||||
Sample |
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Keywords | Synaptic vesicle / SLC22 / Inhibitor / Nanobody / TRANSPORT PROTEIN | |||||||||
Function / homology | Function and homology information 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 / neuromuscular junction ...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 / neuromuscular junction / synaptic vesicle membrane / intracellular calcium ion homeostasis / cell-cell junction / synaptic vesicle / neuron projection / neuronal cell body / glutamatergic synapse / dendrite / protein kinase binding / endoplasmic reticulum / plasma membrane Similarity search - Function | |||||||||
Biological species | Lama glama (llama) / Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.8 Å | |||||||||
Authors | Mittal A / Martin MF / Levin E / Adams C / Yang M / Ledecq M / Horyani PS / Coleman JA | |||||||||
Funding support | United States, 1 items
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Citation | Journal: To Be Published Title: Structure of the synaptic vesicle protein 2A Luminal domain 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 | emd_42432.map.gz | 182.1 MB | EMDB map data format | |
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Header (meta data) | emd-42432-v30.xml emd-42432.xml | 18.6 KB 18.6 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_42432_fsc.xml | 12.8 KB | Display | FSC data file |
Images | emd_42432.png | 40 KB | ||
Masks | emd_42432_msk_1.map emd_42432_msk_2.map | 216 MB 216 MB | Mask map | |
Filedesc metadata | emd-42432.cif.gz | 6.7 KB | ||
Others | emd_42432_additional_1.map.gz emd_42432_half_map_1.map.gz emd_42432_half_map_2.map.gz | 103.8 MB 200.6 MB 200.6 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-42432 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-42432 | HTTPS FTP |
-Related structure data
Related structure data | 8uoaMC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_42432.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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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
File | emd_42432_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Mask #2
File | emd_42432_msk_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Additional map: Unsharpened map
File | emd_42432_additional_1.map | ||||||||||||
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Annotation | Unsharpened map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half map A
File | emd_42432_half_map_1.map | ||||||||||||
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Annotation | Half map A | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half map B
File | emd_42432_half_map_2.map | ||||||||||||
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Annotation | Half map B | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Luminal domain with nanobody
Entire | Name: Luminal domain with nanobody |
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Components |
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-Supramolecule #1: Luminal domain with nanobody
Supramolecule | Name: Luminal domain with nanobody / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Lama glama (llama) |
Molecular weight | Theoretical: 27 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: Homo sapiens (human) |
Molecular weight | Theoretical: 75.589188 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
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: Lama glama (llama) |
Molecular weight | Theoretical: 15.469103 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: QVQLVESGGG LVQPGGSLRL SCAASGSIFN MRVMGWYRQA PGEQRESVAS MASGDKTTYA DSVKGRFTIS RDNAKNTVAL QMNSLKPED TAVYYCHAVD LTRNGPRVYW GQGTQVTVSS AAAENLYFQG GSGHHHHHHH HHH |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-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 |
-Electron microscopy
Microscope | TFS KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.8000000000000003 µm / Nominal defocus min: 0.75 µm / Nominal magnification: 77160 |
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 |