+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-12296 | |||||||||
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Title | Ovine b0,+AT-rBAT heterodimer | |||||||||
Map data | RELION postprocessed map | |||||||||
Sample |
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Function / homology | Function and homology information broad specificity neutral L-amino acid:basic L-amino acid antiporter activity / L-cystine transmembrane transporter activity / brush border membrane / carbohydrate metabolic process / protein heterodimerization activity / apical plasma membrane Similarity search - Function | |||||||||
Biological species | Ovis aries (sheep) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.05 Å | |||||||||
Authors | Lee Y / Kuehlbrandt W | |||||||||
Funding support | Germany, 2 items
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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 DJ / Kuhlbrandt W / Nagamori S | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_12296.map.gz | 10.1 MB | EMDB map data format | |
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Header (meta data) | emd-12296-v30.xml emd-12296.xml | 17.9 KB 17.9 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_12296_fsc.xml | 11.4 KB | Display | FSC data file |
Images | emd_12296.png | 98.8 KB | ||
Masks | emd_12296_msk_1.map | 125 MB | Mask map | |
Others | emd_12296_half_map_1.map.gz emd_12296_half_map_2.map.gz | 98.3 MB 98.3 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-12296 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-12296 | HTTPS FTP |
-Validation report
Summary document | emd_12296_validation.pdf.gz | 549.1 KB | Display | EMDB validaton report |
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Full document | emd_12296_full_validation.pdf.gz | 548.6 KB | Display | |
Data in XML | emd_12296_validation.xml.gz | 18.5 KB | Display | |
Data in CIF | emd_12296_validation.cif.gz | 24.3 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-12296 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-12296 | HTTPS FTP |
-Related structure data
Related structure data | 7nf6MC 7nf7C 7nf8C M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_12296.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | RELION postprocessed map | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.09856 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Mask #1
File | emd_12296_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: Half-map 2
File | emd_12296_half_map_1.map | ||||||||||||
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Annotation | Half-map 2 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half-map 1
File | emd_12296_half_map_2.map | ||||||||||||
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Annotation | Half-map 1 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : b0,+AT-rBAT heterodimer
Entire | Name: b0,+AT-rBAT heterodimer |
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Components |
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-Supramolecule #1: b0,+AT-rBAT heterodimer
Supramolecule | Name: b0,+AT-rBAT heterodimer / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2 |
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Source (natural) | Organism: Ovis aries (sheep) |
Recombinant expression | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 135 kDa/nm |
-Macromolecule #1: B(0,+)-type amino acid transporter 1
Macromolecule | Name: B(0,+)-type amino acid transporter 1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Ovis aries (sheep) |
Molecular weight | Theoretical: 56.318047 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: MEETSLRKRR GDEKSIQSSE PKTTSLQKEL GLFSGTCIIV GTIIGSGIFI SPKSVLSNME AVGPCLIIWA MCGVLATLGA LCFAELGTM ITKSGGEYPY LMEAFGPIPA YLFSWSSLFV IKPSSFAIIC LSFSEYVCAP FYSGCSPPQV VIKTLAAAAI L LISTVNAL ...String: MEETSLRKRR GDEKSIQSSE PKTTSLQKEL GLFSGTCIIV GTIIGSGIFI SPKSVLSNME AVGPCLIIWA MCGVLATLGA LCFAELGTM ITKSGGEYPY LMEAFGPIPA YLFSWSSLFV IKPSSFAIIC LSFSEYVCAP FYSGCSPPQV VIKTLAAAAI L LISTVNAL SVRLGSYVQN VFTAAKMVIV VIIIISGLVL LAQGNTRNFE NSFEGASLSV GSISLALYNG LWAYDGWNQL NY ITEELRN PFRNLPLAII IGIPLVTGCY ILMNVSYFTV MTATELLQSQ AVAVTFGDRV LYPASWIVPL FVAFSTIGAA NGS CFTAGR LVFVAGREGH MLKVLSYISV KRLTPAPAIM FHSMIAIIYI IPGDINSLVN YFSFAAWLFY GLTITGLIVM RFTR KELKR PIKVPIFIPI LVTLLSVFLV LAPIISAPAW EYLYCVLFML SGLVFYFLFV HYKFGWAQKI SKPLTMHLQM LMEVV PPEE APEWSHPQFE KGGGSGGGSG GSAWSHPQFE K |
-Macromolecule #2: neutral and basic amino acid transport protein rBAT
Macromolecule | Name: neutral and basic amino acid transport protein rBAT / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Ovis aries (sheep) |
Molecular weight | Theoretical: 78.754281 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: GSAEDKSKRD SIGLNAKEGQ TNNGFVQNED ILETDLDPSS PAAGPQHNTV DILGPGEPDV KDVRPYAGMP KEVLFQFSGQ ARYRIPREV LFWLTVASVL LLIAATIAII AISPKCLDWW QAGPMYQIYP RSFRDSNKDG DGDLKGIQDK LDYITTLNIK T VWITSFYK ...String: GSAEDKSKRD SIGLNAKEGQ TNNGFVQNED ILETDLDPSS PAAGPQHNTV DILGPGEPDV KDVRPYAGMP KEVLFQFSGQ ARYRIPREV LFWLTVASVL LLIAATIAII AISPKCLDWW QAGPMYQIYP RSFRDSNKDG DGDLKGIQDK LDYITTLNIK T VWITSFYK SSLKDFRHAV EDFQEIDPIF GTMKDFENLV AAIHDKGLKL IIDFIPNHTS DKHAWFQWSR NRTGKYTDYY IW HDCNYEN GTTIPPNNWL SVYGNSSWHF DEVRKQCYFH QFMKEQPDLN FRNPDVQEEI KEIIQFWLSK GVDGFSFNAL QYL LEAKHL RDEAQVNKTQ IPDTVTHYSQ LHHDFTTTQV GMHDIVRSFR QTMNQYSREP GRYRFMGTEA HGESITETMV YYGL PFIQE ADFPFNSYLS KLDKPSGNSV SEVITSWLEN MPEGKWPNWM TGGPDNVRLT SRLGEKYVNI MNMLVFTLPG TPITY YGEE IGMRNILAAN LNENYDTGTL FSKSPMQWDN SSNAGFSEGN HTWLPTSSDY HTVNVDVQKT QPRSALKLYQ ELSLLH ANE LLLSRGWFCY LRNDNHSIMY TRELDGINKV FLMVLNFGES SLLNLKEMIS NIPTRVRIRL STSSAYSGRE VDTHAVT LA SGEGLILEYN TGNLLHRQTA FKDRCFVSNR ACYSRVLNIL YSLC |
-Macromolecule #4: CHOLESTEROL
Macromolecule | Name: CHOLESTEROL / type: ligand / ID: 4 / Number of copies: 2 / Formula: CLR |
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Molecular weight | Theoretical: 386.654 Da |
Chemical component information | ChemComp-CLR: |
-Macromolecule #5: 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine
Macromolecule | Name: 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine / type: ligand / ID: 5 / Number of copies: 1 / Formula: LBN |
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Molecular weight | Theoretical: 760.076 Da |
Chemical component information | ChemComp-LBN: |
-Macromolecule #6: CALCIUM ION
Macromolecule | Name: CALCIUM ION / type: ligand / ID: 6 / Number of copies: 1 / Formula: CA |
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Molecular weight | Theoretical: 40.078 Da |
-Macromolecule #7: 2-acetamido-2-deoxy-beta-D-glucopyranose
Macromolecule | Name: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 7 / Number of copies: 4 / Formula: NAG |
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Molecular weight | Theoretical: 221.208 Da |
Chemical component information | ChemComp-NAG: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 8 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |