+Open data
-Basic information
Entry | Database: PDB / ID: 6ww5 | ||||||||||||
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Title | Structure of VcINDY-Na-Fab84 in nanodisc | ||||||||||||
Components |
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Keywords | MEMBRANE PROTEIN / Transporter | ||||||||||||
Function / homology | Function and homology information transmembrane transporter activity / transmembrane transport / identical protein binding / membrane / plasma membrane Similarity search - Function | ||||||||||||
Biological species | Vibrio cholerae (bacteria) Homo sapiens (human) | ||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.15 Å | ||||||||||||
Authors | Sauer, D.B. / Marden, J. / Song, J.M. / Koide, A. / Koide, S. / Wang, D.N. | ||||||||||||
Funding support | United States, 3items
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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 | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 6ww5.cif.gz | 615.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6ww5.ent.gz | 519.1 KB | Display | PDB format |
PDBx/mmJSON format | 6ww5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6ww5_validation.pdf.gz | 1.3 MB | Display | wwPDB validaton report |
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Full document | 6ww5_full_validation.pdf.gz | 1.4 MB | Display | |
Data in XML | 6ww5_validation.xml.gz | 61.2 KB | Display | |
Data in CIF | 6ww5_validation.cif.gz | 87.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ww/6ww5 ftp://data.pdbj.org/pub/pdb/validation_reports/ww/6ww5 | HTTPS FTP |
-Related structure data
Related structure data | 21928MC 6wtwC 6wtxC 6wu1C 6wu2C 6wu3C 6wu4C 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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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS ensembles :
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 48157.359 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Vibrio cholerae (bacteria) / Gene: VC0395_0108, GG844_00510 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0H3AG83, UniProt: Q9KNE0*PLUS |
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-Antibody , 2 types, 4 molecules CEFD
#2: Antibody | Mass: 28009.484 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) #3: Antibody | Mass: 25923.102 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) |
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-Non-polymers , 3 types, 6 molecules
#4: Chemical | #5: Chemical | #6: Chemical | |
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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: Complex of VcINDY and Fab84 / Type: ORGANELLE OR CELLULAR COMPONENT / Entity ID: #1-#3 / Source: MULTIPLE SOURCES |
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Source (natural) | Organism: Vibrio cholerae (bacteria) |
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
Experimental equipment | Model: Talos Arctica / Image courtesy: FEI Company |
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Microscopy | Model: FEI TALOS ARCTICA |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 36000 X / Nominal defocus max: 1500 nm / Nominal defocus min: 100 nm / Cs: 2.7 mm |
Image recording | Average exposure time: 10 sec. / Electron dose: 44 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 826 |
-Processing
Software |
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EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C2 (2 fold cyclic) | ||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.15 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 92239 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||
Atomic model building | PDB-ID: 5UL9 | ||||||||||||||||||||||||||||||||||||
Refinement | Cross valid method: NONE Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 57.58 Å2 | ||||||||||||||||||||||||||||||||||||
Refine LS restraints |
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Refine LS restraints NCS |
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