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Yorodumi- PDB-9bis: Cryo-EM structure of the mammalian peptide transporter PepT2 boun... -
+Open data
-Basic information
Entry | Database: PDB / ID: 9bis | |||||||||||||||
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Title | Cryo-EM structure of the mammalian peptide transporter PepT2 bound to amoxicillin | |||||||||||||||
Components |
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Keywords | MEMBRANE PROTEIN / protein-coupled peptide transporter / peptide transport / antibiotics | |||||||||||||||
Function / homology | Function and homology information high-affinity oligopeptide transmembrane transporter activity / Proton/oligopeptide cotransporters / tripeptide import across plasma membrane / peptidoglycan transport / tripeptide transmembrane transporter activity / dipeptide transport / metanephric proximal tubule development / dipeptide import across plasma membrane / oligopeptide transport / peptide:proton symporter activity ...high-affinity oligopeptide transmembrane transporter activity / Proton/oligopeptide cotransporters / tripeptide import across plasma membrane / peptidoglycan transport / tripeptide transmembrane transporter activity / dipeptide transport / metanephric proximal tubule development / dipeptide import across plasma membrane / oligopeptide transport / peptide:proton symporter activity / dipeptide transmembrane transporter activity / antibacterial innate immune response / regulation of nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway / xenobiotic transport / renal absorption / phagocytic vesicle membrane / protein transport / apical plasma membrane / membrane / plasma membrane Similarity search - Function | |||||||||||||||
Biological species | Rattus norvegicus (Norway rat) Lama glama (llama) | |||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.2 Å | |||||||||||||||
Authors | Parker, J.L. / Deme, J.C. / Lea, S.M. / Newstead, S. | |||||||||||||||
Funding support | United Kingdom, United States, 4items
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Citation | Journal: To Be Published Title: Structural basis for antibiotic transport and inhibition in the mammalian proton-coupled peptide transporter, PepT2 Authors: Parker, J.L. / Deme, J.C. / Lichtinger, S.M. / Kuteyi, G. / Biggin, P.C. / Lea, S.M. / Newstead, S. | |||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 9bis.cif.gz | 235.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb9bis.ent.gz | 189.6 KB | Display | PDB format |
PDBx/mmJSON format | 9bis.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 9bis_validation.pdf.gz | 1.3 MB | Display | wwPDB validaton report |
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Full document | 9bis_full_validation.pdf.gz | 1.4 MB | Display | |
Data in XML | 9bis_validation.xml.gz | 40.2 KB | Display | |
Data in CIF | 9bis_validation.cif.gz | 56.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bi/9bis ftp://data.pdbj.org/pub/pdb/validation_reports/bi/9bis | HTTPS FTP |
-Related structure data
Related structure data | 44600MC 9birC 9bitC 9biuC 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
#1: Protein | Mass: 82477.766 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Slc15a2 / Production host: Homo sapiens (human) / References: UniProt: Q63424 |
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#2: Antibody | Mass: 14494.183 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Lama glama (llama) |
#3: Chemical | ChemComp-AXL / |
Has ligand of interest | 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 |
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Molecular weight |
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Source (natural) |
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Source (recombinant) |
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Buffer solution | pH: 7.5 | ||||||||||||||||||||||||
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: TFS KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 500 nm |
Image recording | Electron dose: 55.3 e/Å2 / Film or detector model: TFS FALCON 4i (4k x 4k) |
-Processing
EM software | Name: PHENIX / Version: 1.21.1_5286 / Category: model refinement |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
3D reconstruction | Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 87246 / Symmetry type: POINT |