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Yorodumi- PDB-7s8u: Cryo-EM structure of a mammalian peptide transporter (PepT1/slc15... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7s8u | |||||||||||||||||||||
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Title | Cryo-EM structure of a mammalian peptide transporter (PepT1/slc15a1) in nanodisc | |||||||||||||||||||||
Components | Solute carrier family 15 member 1 | |||||||||||||||||||||
Keywords | TRANSPORT PROTEIN / PepT1 / SLC15 / ECD / transporter / nanodisc | |||||||||||||||||||||
Function / homology | Function and homology information proton-dependent oligopeptide secondary active transmembrane transporter activity / dipeptide import across plasma membrane / peptide:proton symporter activity / dipeptide transmembrane transporter activity / plasma membrane => GO:0005886 / brush border Similarity search - Function | |||||||||||||||||||||
Biological species | Equus caballus (horse) | |||||||||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.7 Å | |||||||||||||||||||||
Authors | Shen, J. / Zhou, M. | |||||||||||||||||||||
Funding support | United States, 6items
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Citation | Journal: Structure / Year: 2022 Title: Extracellular domain of PepT1 interacts with TM1 to facilitate substrate transport. Authors: Jiemin Shen / Miaohui Hu / Xiao Fan / Zhenning Ren / Corinne Portioli / Xiuwen Yan / Mingqiang Rong / Ming Zhou / Abstract: Mammalian peptide transporters, PepT1 and PepT2, mediate uptake of small peptides and are essential for their absorption. PepT also mediates absorption of many drugs and prodrugs to enhance their ...Mammalian peptide transporters, PepT1 and PepT2, mediate uptake of small peptides and are essential for their absorption. PepT also mediates absorption of many drugs and prodrugs to enhance their bioavailability. PepT has twelve transmembrane (TM) helices that fold into an N-terminal domain (NTD, TM1-6) and a C-terminal domain (CTD, TM7-12) and has a large extracellular domain (ECD) between TM9-10. It is well recognized that peptide transport requires movements of the NTD and CTD, but the role of the ECD in PepT1 remains unclear. Here we report the structure of horse PepT1 encircled in lipid nanodiscs and captured in the inward-open apo conformation. The structure shows that the ECD bridges the NTD and CTD by interacting with TM1. Deletion of ECD or mutations to the ECD-TM1 interface impairs the transport activity. These results demonstrate an important role of ECD in PepT1 and enhance our understanding of the transport mechanism in PepT1. | |||||||||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7s8u.cif.gz | 122.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7s8u.ent.gz | 96.9 KB | Display | PDB format |
PDBx/mmJSON format | 7s8u.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/s8/7s8u ftp://data.pdbj.org/pub/pdb/validation_reports/s8/7s8u | HTTPS FTP |
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-Related structure data
Related structure data | 24922MC 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: 78723.992 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Equus caballus (horse) / Gene: SLC15A1 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: F6SG69 |
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-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: PepT1 in MSP1D1 nanodisc / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT |
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Molecular weight | Experimental value: NO |
Source (natural) | Organism: Equus caballus (horse) |
Source (recombinant) | Organism: Trichoplusia ni (cabbage looper) |
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: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2100 nm / Nominal defocus min: 1900 nm |
Image recording | Electron dose: 50 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
-Processing
Software | Name: PHENIX / Version: 1.19.2_4158: / Classification: refinement | ||||||||||||||||||||||||
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 315767 / Symmetry type: POINT | ||||||||||||||||||||||||
Refine LS restraints |
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