+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-21902 | |||||||||||||||
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Title | Structure of apo LaINDY | |||||||||||||||
Map data | apo LaINDY | |||||||||||||||
Sample |
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Keywords | Transporter / Structural Genomics / PSI-Biology / New York Consortium on Membrane Protein Structure / NYCOMPS / MEMBRANE PROTEIN | |||||||||||||||
Function / homology | Citrate carrier CitT-related / Sodium:sulfate symporter transmembrane region / Solute carrier family 13 / transmembrane transporter activity / membrane => GO:0016020 / plasma membrane / DASS family sodium-coupled anion symporter / 2-oxoglutarate-malate translocator Function and homology information | |||||||||||||||
Biological species | Lactobacillus acidophilus (bacteria) | |||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.09 Å | |||||||||||||||
Authors | Sauer DB / Marden JJ | |||||||||||||||
Funding support | United States, 4 items
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Citation | Journal: Elife / Year: 2020 Title: Structural basis for the reaction cycle of DASS dicarboxylate transporters. Authors: David B Sauer / Noah Trebesch / Jennifer J Marden / Nicolette Cocco / Jinmei Song / Akiko Koide / Shohei Koide / Emad Tajkhorshid / Da-Neng Wang / Abstract: Citrate, α-ketoglutarate and succinate are TCA cycle intermediates that also play essential roles in metabolic signaling and cellular regulation. These di- and tricarboxylates are imported into the ...Citrate, α-ketoglutarate and succinate are TCA cycle intermediates that also play essential roles in metabolic signaling and cellular regulation. These di- and tricarboxylates are imported into the cell by the divalent anion sodium symporter (DASS) family of plasma membrane transporters, which contains both cotransporters and exchangers. While DASS proteins transport substrates via an elevator mechanism, to date structures are only available for a single DASS cotransporter protein in a substrate-bound, inward-facing state. We report multiple cryo-EM and X-ray structures in four different states, including three hitherto unseen states, along with molecular dynamics simulations, of both a cotransporter and an exchanger. Comparison of these outward- and inward-facing structures reveal how the transport domain translates and rotates within the framework of the scaffold domain through the transport cycle. Additionally, we propose that DASS transporters ensure substrate coupling by a charge-compensation mechanism, and by structural changes upon substrate release. | |||||||||||||||
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_21902.map.gz | 27.6 MB | EMDB map data format | |
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Header (meta data) | emd-21902-v30.xml emd-21902.xml | 16.8 KB 16.8 KB | Display Display | EMDB header |
Images | emd_21902.png | 48.4 KB | ||
Filedesc metadata | emd-21902.cif.gz | 5.6 KB | ||
Others | emd_21902_half_map_1.map.gz emd_21902_half_map_2.map.gz | 28.2 MB 28.2 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-21902 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-21902 | HTTPS FTP |
-Validation report
Summary document | emd_21902_validation.pdf.gz | 950.2 KB | Display | EMDB validaton report |
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Full document | emd_21902_full_validation.pdf.gz | 949.8 KB | Display | |
Data in XML | emd_21902_validation.xml.gz | 11.1 KB | Display | |
Data in CIF | emd_21902_validation.cif.gz | 12.9 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-21902 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-21902 | HTTPS FTP |
-Related structure data
Related structure data | 6wu1MC 6wtwC 6wtxC 6wu2C 6wu3C 6wu4C 6ww5C 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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-Map
File | Download / File: emd_21902.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | apo LaINDY | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.048 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Half map: apo LaINDY
File | emd_21902_half_map_1.map | ||||||||||||
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Annotation | apo LaINDY | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: apo LaINDY
File | emd_21902_half_map_2.map | ||||||||||||
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Annotation | apo LaINDY | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : LaINDY
Entire | Name: LaINDY |
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Components |
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-Supramolecule #1: LaINDY
Supramolecule | Name: LaINDY / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: Lactobacillus acidophilus (bacteria) |
-Macromolecule #1: DASS family sodium-coupled anion symporter
Macromolecule | Name: DASS family sodium-coupled anion symporter / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Lactobacillus acidophilus (bacteria) |
Molecular weight | Theoretical: 56.563758 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MHHHHHHHHH HSSGVDLGTE NLYFQSNAMK TLEKVNYKGF IWPLAVGIVL WLITPWRPGG LSVQAWEMFA IFVATIVGCI TKPLPIGGT TLLGMVVTVL VGLAPVKDVV NSKGVVIQTG ILSSFGNSAA WLIAMAFIMA HGISKTGLGN RVAYVMIEKF G KRSIGIGY ...String: MHHHHHHHHH HSSGVDLGTE NLYFQSNAMK TLEKVNYKGF IWPLAVGIVL WLITPWRPGG LSVQAWEMFA IFVATIVGCI TKPLPIGGT TLLGMVVTVL VGLAPVKDVV NSKGVVIQTG ILSSFGNSAA WLIAMAFIMA HGISKTGLGN RVAYVMIEKF G KRSIGIGY AITGLELMMG ALIPSNSART GGVTWPVVES ISKSYDSKPN DPSRKKIGAY LDFMAFHANI LSTALFITGA AP NLVAQQM AAQKGYQMSW VSWFWAALVP VLVATVIIPL VIYKMYPPEV KETPNAKNWA DDKLKEMGPI SKPEKIMATV FCL AILLWV LSGFFKIPQL DSAFVAFLAV TLLLITGVLS MEDALHETGA WNILIWLSIL IFMAGKLISY GFIAWFAKFI QSEV HGINW GLVLVVLILL MFYTHYFFAS GTAHMTALYL PFLTVATAMG APLGLSAMLL AFTGVINAST THYANGPASI LATTG YVKQ SEWWKMNFIL GLIYMVIFGI VGTIWMKIIG IW UniProtKB: DASS family sodium-coupled anion symporter |
-Macromolecule #2: HEXANE
Macromolecule | Name: HEXANE / type: ligand / ID: 2 / Number of copies: 10 / Formula: HEX |
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Molecular weight | Theoretical: 86.175 Da |
Chemical component information | ChemComp-HEX: |
-Macromolecule #3: DECANE
Macromolecule | Name: DECANE / type: ligand / ID: 3 / Number of copies: 8 / Formula: D10 |
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Molecular weight | Theoretical: 142.282 Da |
Chemical component information | ChemComp-D10: |
-Macromolecule #4: N-OCTANE
Macromolecule | Name: N-OCTANE / type: ligand / ID: 4 / Number of copies: 6 / Formula: OCT |
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Molecular weight | Theoretical: 114.229 Da |
Chemical component information | ChemComp-OCT: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.4 |
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Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Number grids imaged: 1 / Number real images: 3122 / Average exposure time: 10.0 sec. / Average electron dose: 75.05 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.5 µm / Nominal magnification: 130000 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: OTHER |
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Final reconstruction | Applied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.09 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 2.12) / Number images used: 278663 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 2.12) |
Final angle assignment | Type: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 2.12) |