+Open data
-Basic information
Entry | Database: PDB / ID: 7vfi | |||||||||||||||
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Title | Cryo-EM structure of the mouse TAPL (9mer-peptide bound) | |||||||||||||||
Components |
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Keywords | MEMBRANE PROTEIN / TAPL / Peptide transporter / Lipid floppase | |||||||||||||||
Function / homology | Function and homology information ABC-type oligopeptide transporter / ABC-type oligopeptide transporter activity / ABC-type peptide transporter activity / peptide metabolic process / ABC-family proteins mediated transport / peptide transport / ATPase-coupled transmembrane transporter activity / transmembrane transport / protein transport / lysosome ...ABC-type oligopeptide transporter / ABC-type oligopeptide transporter activity / ABC-type peptide transporter activity / peptide metabolic process / ABC-family proteins mediated transport / peptide transport / ATPase-coupled transmembrane transporter activity / transmembrane transport / protein transport / lysosome / lysosomal membrane / endoplasmic reticulum membrane / protein homodimerization activity / ATP hydrolysis activity / ATP binding / membrane Similarity search - Function | |||||||||||||||
Biological species | Mus musculus (house mouse) | |||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.98 Å | |||||||||||||||
Authors | Park, J.G. / Kim, S. / Jang, E. / Choi, S.H. / Han, H. / Kim, J.W. / Ju, S. / Min, D.S. / Jin, M.S. | |||||||||||||||
Funding support | Korea, Republic Of, 4items
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Citation | Journal: Nat Commun / Year: 2022 Title: The lysosomal transporter TAPL has a dual role as peptide translocator and phosphatidylserine floppase. Authors: Jun Gyou Park / Songwon Kim / Eunhong Jang / Seung Hun Choi / Hyunsu Han / Seulgi Ju / Ji Won Kim / Da Sol Min / Mi Sun Jin / Abstract: TAPL is a lysosomal ATP-binding cassette transporter that translocates a broad spectrum of polypeptides from the cytoplasm into the lysosomal lumen. Here we report that, in addition to its well-known ...TAPL is a lysosomal ATP-binding cassette transporter that translocates a broad spectrum of polypeptides from the cytoplasm into the lysosomal lumen. Here we report that, in addition to its well-known role as a peptide translocator, TAPL exhibits an ATP-dependent phosphatidylserine floppase activity that is the possible cause of its high basal ATPase activity and of the lack of coupling between ATP hydrolysis and peptide efflux. We also present the cryo-EM structures of mouse TAPL complexed with (i) phospholipid, (ii) cholesteryl hemisuccinate (CHS) and 9-mer peptide, and (iii) ADP·BeF. The inward-facing structure reveals that F449 protrudes into the cylindrical transport pathway and divides it into a large hydrophilic central cavity and a sizable hydrophobic upper cavity. In the structure, the peptide binds to TAPL in horizontally-stretched fashion within the central cavity, while lipid molecules plug vertically into the upper cavity. Together, our results suggest that TAPL uses different mechanisms to function as a peptide translocase and a phosphatidylserine floppase. | |||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7vfi.cif.gz | 210.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7vfi.ent.gz | 165.3 KB | Display | PDB format |
PDBx/mmJSON format | 7vfi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7vfi_validation.pdf.gz | 983.1 KB | Display | wwPDB validaton report |
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Full document | 7vfi_full_validation.pdf.gz | 1005.6 KB | Display | |
Data in XML | 7vfi_validation.xml.gz | 38.5 KB | Display | |
Data in CIF | 7vfi_validation.cif.gz | 56.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vf/7vfi ftp://data.pdbj.org/pub/pdb/validation_reports/vf/7vfi | HTTPS FTP |
-Related structure data
Related structure data | 31955MC 7v5cC 7v5dC 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: 84046.805 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Abcb9 / Production host: Trichoplusia ni (cabbage looper) References: UniProt: Q9JJ59, ABC-type oligopeptide transporter #2: Protein/peptide | | Mass: 1183.338 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Production host: Trichoplusia ni (cabbage looper) #3: Chemical | Has ligand of interest | Y | |
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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: Mouse TAPL (9mer-peptide bound) / Type: COMPLEX / Details: Mouse TAPL (9mer-peptide bound) / Entity ID: #1-#2 / Source: RECOMBINANT |
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Source (natural) | Organism: Mus musculus (house mouse) |
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: Talos Arctica / Image courtesy: FEI Company |
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Microscopy | Model: FEI TALOS ARCTICA |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 2200 nm / Nominal defocus min: 800 nm |
Image recording | Electron dose: 40 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) |
-Processing
Software | Name: PHENIX / Version: 1.16_3549: / Classification: refinement | ||||||||||||||||||||||||
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CTF correction | Type: NONE | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.98 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 102428 / Symmetry type: POINT | ||||||||||||||||||||||||
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