|Entry||Database: PDB / ID: 6wu3|
|Title||Structure of VcINDY-Na+ in amphipol|
|Keywords||MEMBRANE PROTEIN / Transporter|
|Function / homology|
Function and homology information
anion transmembrane transport / transporter activity / transmembrane transporter activity / integral component of membrane / identical protein binding
Similarity search - Function
Sodium:sulfate symporter family signature. / Sodium/sulphate symporter, conserved site / Solute carrier family 13 / Sodium:sulfate symporter transmembrane region
Similarity search - Domain/homology
Transporter, NadC family
Similarity search - Component
|Biological species||Vibrio cholerae (bacteria)|
|Method||ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.16 Å|
|Authors||Sauer, D.B. / Marden, J.J. / Song, J.M. / Wang, D.N.|
|Funding support|| United States, 3items |
|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.
|Structure viewer||Molecule: |
Downloads & links
Mass: 48157.359 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: Q9KNE0*PLUS
|Experiment||Method: ELECTRON MICROSCOPY|
|EM experiment||Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction|
|Component||Name: Dimeric structure of VcINDY in complex with sodium / Type: ORGANELLE OR CELLULAR COMPONENT / Entity ID: #1 / Source: RECOMBINANT|
|Source (natural)||Organism: Vibrio cholerae (bacteria)|
|Source (recombinant)||Organism: Escherichia coli (E. coli)|
|Buffer solution||pH: 7.4|
|Specimen||Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES|
|Vitrification||Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K|
-Electron microscopy imaging
Model: Talos Arctica / Image courtesy: FEI Company
|Microscopy||Model: FEI TALOS ARCTICA|
|Electron gun||Electron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM|
|Electron lens||Mode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 36000 X / Nominal defocus max: 2500 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm|
|Image recording||Average exposure time: 12 sec. / Electron dose: 40 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of real images: 1670|
|CTF correction||Type: PHASE FLIPPING AND AMPLITUDE CORRECTION|
|Symmetry||Point symmetry: C2 (2回回転対称)|
|3D reconstruction||Resolution: 3.16 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 192836 / Symmetry type: POINT|
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