+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-21928 | ||||||||||||
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Title | Structure of VcINDY-Na-Fab84 in nanodisc | ||||||||||||
Map data | |||||||||||||
Sample |
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Function / homology | Function and homology information citrate transmembrane transporter activity / succinate transmembrane transporter activity / transmembrane transporter activity / transmembrane transport / identical protein binding / membrane / plasma membrane Similarity search - Function | ||||||||||||
Biological species | Vibrio cholerae (bacteria) / Homo sapiens (human) | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.15 Å | ||||||||||||
Authors | Sauer DB / Marden J / Song JM / Koide A / Koide S / Wang DN | ||||||||||||
Funding support | United States, 3 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_21928.map.gz | 56.7 MB | EMDB map data format | |
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Header (meta data) | emd-21928-v30.xml emd-21928.xml | 19.3 KB 19.3 KB | Display Display | EMDB header |
Images | emd_21928.png | 79.5 KB | ||
Others | emd_21928_half_map_1.map.gz emd_21928_half_map_2.map.gz | 59.2 MB 59.2 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-21928 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-21928 | HTTPS FTP |
-Validation report
Summary document | emd_21928_validation.pdf.gz | 857.8 KB | Display | EMDB validaton report |
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Full document | emd_21928_full_validation.pdf.gz | 857.4 KB | Display | |
Data in XML | emd_21928_validation.xml.gz | 12.5 KB | Display | |
Data in CIF | emd_21928_validation.cif.gz | 14.7 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-21928 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-21928 | HTTPS FTP |
-Related structure data
Related structure data | 6ww5MC 6wtwC 6wtxC 6wu1C 6wu2C 6wu3C 6wu4C 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_21928.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Voxel size | X=Y=Z: 1.142 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Half map: #1
File | emd_21928_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_21928_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Complex of VcINDY and Fab84
Entire | Name: Complex of VcINDY and Fab84 |
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Components |
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-Supramolecule #1: Complex of VcINDY and Fab84
Supramolecule | Name: Complex of VcINDY and Fab84 / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: #1-#3 |
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Source (natural) | Organism: Vibrio cholerae (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: Vibrio cholerae (bacteria) |
Molecular weight | Theoretical: 48.157359 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: REWFLHRNSL IVLADVALFL ALYHFLPFEH NVVLGISMLA FIAVLWLTEA LHVTVTAILV PVMAVFFGIF ETQAALNNFA NSIIFLFLG GFALAAAMHH QGLDKVIADK VLAMAQGKMS VAVFMLFGVT ALLSMWISNT ATAAMMLPLV LGVLSKVDAD K QRSTYVFV ...String: REWFLHRNSL IVLADVALFL ALYHFLPFEH NVVLGISMLA FIAVLWLTEA LHVTVTAILV PVMAVFFGIF ETQAALNNFA NSIIFLFLG GFALAAAMHH QGLDKVIADK VLAMAQGKMS VAVFMLFGVT ALLSMWISNT ATAAMMLPLV LGVLSKVDAD K QRSTYVFV LLGVAYSASI GGIATLVGSP PNAIAAAEVG LSFTDWMKFG LPTAMMMLPM AIAILYFLLK PTLNGMFELD RA PVNWDKG KVVTLGIFGL TVFLWIFSSP INAALGGFKS FDTLVALGAI LMLSFARVVH WKEIQKTADW GVLLLFGGGL CLS NVLKQT GTSVFLANAL SDMVSHMGIF VVILVVATFV VFLTEFASNT ASAALLIPVF ATVAEAFGMS PVLLSVLIAV AASC AFMLP VATPPNAIVF ASGHIKQSEM MRVGLYLNIA CIGLLTAIAM LFWQ |
-Macromolecule #2: Fab84 Heavy Chain
Macromolecule | Name: Fab84 Heavy Chain / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 28.009484 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MKKNIAFLLA SMFVFSIATN AYAEISEVQL VESGGGLVQP GGSLRLSCAA SGFTIYSSSI HWVRQAPGKG LEWVASIYSS SGSTSYADS VKGRFTISAD TSKNTAYLQM NSLRAEDTAV YYCARYNIHY WRWYNPAGQA MDYWGQGTLV TVFNQIKGGP S VFPLAPSS ...String: MKKNIAFLLA SMFVFSIATN AYAEISEVQL VESGGGLVQP GGSLRLSCAA SGFTIYSSSI HWVRQAPGKG LEWVASIYSS SGSTSYADS VKGRFTISAD TSKNTAYLQM NSLRAEDTAV YYCARYNIHY WRWYNPAGQA MDYWGQGTLV TVFNQIKGGP S VFPLAPSS KSTSGGTAAL GCLVKDYFPE PVTVSWNSGA LTSGVHTFPA VLQSSGLYSL SSVVTVPSSS LGTQTYICNV NH KPSNTKV DKKVEPKSCD KTHT |
-Macromolecule #3: Fab84 Light Chain
Macromolecule | Name: Fab84 Light Chain / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 25.923102 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MKKNIAFLLA SMFVFSIATN AYASDIQMTQ SPSSLSASVG DRVTITCRAS QSVSSAVAWY QQKPGKAPKL LIYSASSLYS GVPSRFSGS RSGTDFTLTI SSLQPEDFAT YYCQQRYGLL VTFGQGTKVE IKRTVAAPSV FIFPPSDSQL KSGTASVVCL L NNFYPREA ...String: MKKNIAFLLA SMFVFSIATN AYASDIQMTQ SPSSLSASVG DRVTITCRAS QSVSSAVAWY QQKPGKAPKL LIYSASSLYS GVPSRFSGS RSGTDFTLTI SSLQPEDFAT YYCQQRYGLL VTFGQGTKVE IKRTVAAPSV FIFPPSDSQL KSGTASVVCL L NNFYPREA KVQWKVDNAL QSGNSQESVT EQDSKDSTYS LSSTLTLSKA DYEKHKVYAC EVTHQGLSSP VTKSFNRGEC |
-Macromolecule #4: 1,2-DIHEXANOYL-SN-GLYCERO-3-PHOSPHOETHANOLAMINE
Macromolecule | Name: 1,2-DIHEXANOYL-SN-GLYCERO-3-PHOSPHOETHANOLAMINE / type: ligand / ID: 4 / Number of copies: 2 / Formula: 6PE |
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Molecular weight | Theoretical: 410.42 Da |
Chemical component information | ChemComp-6PE: |
-Macromolecule #5: HEXANE
Macromolecule | Name: HEXANE / type: ligand / ID: 5 / Number of copies: 2 / Formula: HEX |
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Molecular weight | Theoretical: 86.175 Da |
Chemical component information | ChemComp-HEX: |
-Macromolecule #6: N-OCTANE
Macromolecule | Name: N-OCTANE / type: ligand / ID: 6 / Number of copies: 2 / 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 TALOS ARCTICA |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Number grids imaged: 1 / Number real images: 826 / Average exposure time: 10.0 sec. / Average electron dose: 44.0 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.5 µm / Nominal defocus min: 0.1 µm / Nominal magnification: 36000 |
Experimental equipment | Model: Talos Arctica / Image courtesy: FEI Company |
-Image processing
CTF correction | Software - Name: cryoSPARC (ver. 2.12) |
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Final reconstruction | Applied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.15 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 2.12) / Number images used: 92239 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 2.12) |
Final angle assignment | Type: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 2.12) |