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Yorodumi- PDB-8de3: Native serotonin transporter in complex with 15B8 Fab antibody in... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8de3 | |||||||||
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Title | Native serotonin transporter in complex with 15B8 Fab antibody in the presence of cocaine | |||||||||
Components |
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Keywords | MEMBRANE PROTEIN / native membrane protein / serotonin transporter / cocaine / pig brain | |||||||||
Function / homology | Function and homology information serotonin:sodium:chloride symporter activity / antiporter activity / presynapse / endosome membrane / neuron projection / focal adhesion / metal ion binding / plasma membrane Similarity search - Function | |||||||||
Biological species | Mus musculus (house mouse) Sus scrofa (pig) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.3 Å | |||||||||
Authors | Yang, D. / Gouaux, E. | |||||||||
Funding support | United States, 2items
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Citation | Journal: To Be Published Title: Native serotonin transporter in complex with 15B8 Fab antibody in the presence of cocaine Authors: Yang, D. / Gouaux, E. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8de3.cif.gz | 170.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8de3.ent.gz | 127.9 KB | Display | PDB format |
PDBx/mmJSON format | 8de3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8de3_validation.pdf.gz | 1.4 MB | Display | wwPDB validaton report |
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Full document | 8de3_full_validation.pdf.gz | 1.5 MB | Display | |
Data in XML | 8de3_validation.xml.gz | 39 KB | Display | |
Data in CIF | 8de3_validation.cif.gz | 53.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/de/8de3 ftp://data.pdbj.org/pub/pdb/validation_reports/de/8de3 | HTTPS FTP |
-Related structure data
Related structure data | 27383MC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 60778.879 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A4X1TV69 |
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-Antibody , 2 types, 2 molecules BC
#2: Antibody | Mass: 12980.533 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Production host: Baculovirus expression vector pFastBac1-HM |
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#3: Antibody | Mass: 11776.065 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Production host: Baculovirus expression vector pFastBac1-HM |
-Sugars , 2 types, 2 molecules
#4: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
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#9: Sugar | ChemComp-LMT / |
-Non-polymers , 4 types, 6 molecules
#5: Chemical | ChemComp-CL / | ||||
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#6: Chemical | #7: Chemical | ChemComp-COC / | #8: Chemical | |
-Details
Has ligand of interest | Y |
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Has protein modification | Y |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Native serotonin transporter in complex with 15B8 Fab antibody in the presence of cocaine Type: COMPLEX / Entity ID: #1-#3 / Source: MULTIPLE SOURCES | ||||||||||||
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Source (natural) |
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Source (recombinant) | Organism: Baculovirus expression vector pFastBac1-HM | ||||||||||||
Buffer solution | pH: 8 | ||||||||||||
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 1000 nm |
Image recording | Electron dose: 60 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
-Processing
Software | Name: PHENIX / Version: 1.20.1_4487: / Classification: refinement | ||||||||||||||||||||||||
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CTF correction | Type: PHASE FLIPPING ONLY | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 243207 / Symmetry type: POINT | ||||||||||||||||||||||||
Refine LS restraints |
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