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Yorodumi- EMDB-37621: Cryo-EM structure of human apo VMAT2 with nanobody in an outward-... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-37621 | |||||||||
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Title | Cryo-EM structure of human apo VMAT2 with nanobody in an outward-facing conformation | |||||||||
Map data | ||||||||||
Sample |
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Keywords | Human VMAT2 / outward-facing conformation / TRANSPORT PROTEIN / TRANSPORT PROTEIN-IMMUNE SYSTEM complex | |||||||||
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 / dopaminergic synapse / dopamine transport / monoamine transmembrane transporter activity / Na+/Cl- dependent neurotransmitter transporters / histamine secretion by mast cell / monoamine transport / neurotransmitter transport / negative regulation of reactive oxygen species biosynthetic process / response to amphetamine / secretory granule membrane / post-embryonic development / 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 | |||||||||
Biological species | Homo sapiens (human) / Vicugna pacos (alpaca) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.6 Å | |||||||||
Authors | Qu Q / Wang Y / Zhou Z | |||||||||
Funding support | China, 1 items
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Citation | Journal: To Be Published Title: Cryo-EM structure of human apo VMAT2 in an outward-facing conformation Authors: Qu Q / Wang Y / Zhou Z | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_37621.map.gz | 38.2 MB | EMDB map data format | |
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Header (meta data) | emd-37621-v30.xml emd-37621.xml | 15.6 KB 15.6 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_37621_fsc.xml | 7.3 KB | Display | FSC data file |
Images | emd_37621.png | 23.5 KB | ||
Filedesc metadata | emd-37621.cif.gz | 5.7 KB | ||
Others | emd_37621_half_map_1.map.gz emd_37621_half_map_2.map.gz | 37.7 MB 37.7 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-37621 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-37621 | HTTPS FTP |
-Validation report
Summary document | emd_37621_validation.pdf.gz | 904.1 KB | Display | EMDB validaton report |
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Full document | emd_37621_full_validation.pdf.gz | 903.7 KB | Display | |
Data in XML | emd_37621_validation.xml.gz | 14.8 KB | Display | |
Data in CIF | emd_37621_validation.cif.gz | 18.8 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-37621 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-37621 | HTTPS FTP |
-Related structure data
Related structure data | 8wljMC 8wlkC 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_37621.map.gz / Format: CCP4 / Size: 40.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Voxel size | X=Y=Z: 0.932 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #2
File | emd_37621_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_37621_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : vesicular Monoamine Transporter 2
Entire | Name: vesicular Monoamine Transporter 2 |
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Components |
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-Supramolecule #1: vesicular Monoamine Transporter 2
Supramolecule | Name: vesicular Monoamine Transporter 2 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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-Supramolecule #2: VMAT2
Supramolecule | Name: VMAT2 / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1 |
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Source (natural) | Organism: Homo sapiens (human) |
-Supramolecule #3: nanobody
Supramolecule | Name: nanobody / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2 |
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Source (natural) | Organism: Vicugna pacos (alpaca) |
-Macromolecule #1: Synaptic vesicular amine transporter
Macromolecule | Name: Synaptic vesicular amine transporter / 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: 53.823184 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: MALSELALVR WLQESRRSRK LILFIVFLAL LLDNMLLTVV VPIIPSYLYS IKHEKNATEI QTARPVHTAS ISDSFQSIFS YYDNSTMVT GNATRDLTLH QTATQHMVTN ASAVPSDCPS EDKDLLNENV QVGLLFASKA TVQLITNPFI GLLTNRIGYP I PIFAGFCI ...String: MALSELALVR WLQESRRSRK LILFIVFLAL LLDNMLLTVV VPIIPSYLYS IKHEKNATEI QTARPVHTAS ISDSFQSIFS YYDNSTMVT GNATRDLTLH QTATQHMVTN ASAVPSDCPS EDKDLLNENV QVGLLFASKA TVQLITNPFI GLLTNRIGYP I PIFAGFCI MFVSTIMFAF SSSYAFLLIA RSLQGIGSSC SSVAGMGMLA SVYTDDEERG NVMGIALGGL AMGVLVGPPF GS VLYEFVG KTAPFLVLAA LVLLDGAIQL FVLQPSRVQP ESQKGTPLTT LLKDPYILIA AGSICFANMG IAMLEPALPI WMM ETMCSR KWQLGVAFLP ASISYLIGTN IFGILAHKMG RWLCALLGMI IVGVSILCIP FAKNIYGLIA PNFGVGFAIG MVDS SMMPI MGYLVDLRHV SVYGSVYAIA DVAFCMGYAI GPSAGGAIAK AIGFPWLMTI IGIIDILFAP LCFFLRSPPS RLEEE LRRR TEGGSSDLEV LFQ UniProtKB: Synaptic vesicular amine transporter |
-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: Vicugna pacos (alpaca) |
Molecular weight | Theoretical: 13.817455 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MGSSEVQLQE SGGGLVQPGG SLRLSCTASG VTISALNAMA MGWYRQAPGE RRVMVAAVSE RGNAMYRESV QGRFTVTRDF TNKMVSLQM DNLKPEDTAV YYCHVLEDRV DSFHDYWGQG TQVTVSS |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 |
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Grid | Model: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 50 sec. / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 260.0 kPa |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.5 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
+Image processing
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: RIGID BODY FIT |
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Output model | PDB-8wlj: |