+Open data
-Basic information
Entry | Database: PDB / ID: 7nf6 | |||||||||
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Title | Ovine b0,+AT-rBAT heterodimer | |||||||||
Components |
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Keywords | TRANSLOCASE / Transporter / Cystinuria / Complex | |||||||||
Function / homology | Function and homology information glucan 1,4-alpha-maltotriohydrolase activity / oligo-1,6-glucosidase activity / maltose catabolic process / : / sucrose alpha-glucosidase activity / sucrose catabolic process / alpha-amylase activity / amino acid transport / transmembrane transporter activity / membrane Similarity search - Function | |||||||||
Biological species | Ovis aries (sheep) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.05 Å | |||||||||
Authors | Lee, Y. / Kuehlbrandt, W. | |||||||||
Funding support | Germany, 2items
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Citation | Journal: Nat Commun / Year: 2022 Title: Ca-mediated higher-order assembly of heterodimers in amino acid transport system b biogenesis and cystinuria. Authors: Yongchan Lee / Pattama Wiriyasermkul / Pornparn Kongpracha / Satomi Moriyama / Deryck J Mills / Werner Kühlbrandt / Shushi Nagamori / Abstract: Cystinuria is a genetic disorder characterized by overexcretion of dibasic amino acids and cystine, causing recurrent kidney stones and kidney failure. Mutations of the regulatory glycoprotein rBAT ...Cystinuria is a genetic disorder characterized by overexcretion of dibasic amino acids and cystine, causing recurrent kidney stones and kidney failure. Mutations of the regulatory glycoprotein rBAT and the amino acid transporter bAT, which constitute system b, are linked to type I and non-type I cystinuria respectively and they exhibit distinct phenotypes due to protein trafficking defects or catalytic inactivation. Here, using electron cryo-microscopy and biochemistry, we discover that Ca mediates higher-order assembly of system b. Ca stabilizes the interface between two rBAT molecules, leading to super-dimerization of bAT-rBAT, which in turn facilitates N-glycan maturation and protein trafficking. A cystinuria mutant T216M and mutations of the Ca site of rBAT cause the loss of higher-order assemblies, resulting in protein trapping at the ER and the loss of function. These results provide the molecular basis of system b biogenesis and type I cystinuria and serve as a guide to develop new therapeutic strategies against it. More broadly, our findings reveal an unprecedented link between transporter oligomeric assembly and protein-trafficking diseases. #1: Journal: Biorxiv / Year: 2021 Title: Ca 2+ -mediated higher-order assembly of b 0,+ AT-rBAT is a key step for system b 0,+ biogenesis and cystinuria Authors: Lee, Y. / Wiriyasermkul, P. / Moriyama, S. / Mills, D.J. / Kuhlbrandt, W. / Nagamori, S. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 7nf6.cif.gz | 204 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7nf6.ent.gz | 166.6 KB | Display | PDB format |
PDBx/mmJSON format | 7nf6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7nf6_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 7nf6_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 7nf6_validation.xml.gz | 47.3 KB | Display | |
Data in CIF | 7nf6_validation.cif.gz | 69.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nf/7nf6 ftp://data.pdbj.org/pub/pdb/validation_reports/nf/7nf6 | HTTPS FTP |
-Related structure data
Related structure data | 12296MC 7nf7C 7nf8C M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-Protein , 2 types, 2 molecules BA
#1: Protein | Mass: 56318.047 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Ovis aries (sheep) / Gene: SLC7A9 / Production host: Homo sapiens (human) / References: UniProt: A0A6P3EL78 |
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#2: Protein | Mass: 78754.281 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Ovis aries (sheep) / Gene: SLC3A1 / Production host: Homo sapiens (human) / References: UniProt: A0A6P7DVK7 |
-Sugars , 2 types, 6 molecules
#3: Polysaccharide | #7: Sugar | ChemComp-NAG / |
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-Non-polymers , 3 types, 4 molecules
#4: Chemical | #5: Chemical | ChemComp-LBN / | #6: Chemical | ChemComp-CA / | |
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-Details
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: b0,+AT-rBAT heterodimer / Type: COMPLEX / Entity ID: #1-#2 / Source: RECOMBINANT |
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Molecular weight | Value: 135 kDa/nm / Experimental value: NO |
Source (natural) | Organism: Ovis aries (sheep) |
Source (recombinant) | Organism: Homo sapiens (human) |
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 |
Image recording | Electron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) |
-Processing
Software | Name: PHENIX / Version: dev_3689: / Classification: refinement | ||||||||||||||||||||||||
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.05 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 644250 / Symmetry type: POINT | ||||||||||||||||||||||||
Refine LS restraints |
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