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Yorodumi- PDB-6wtw: Structure of LaINDY crystallized in the presence of alpha-ketoglu... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6wtw | |||||||||||||||
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Title | Structure of LaINDY crystallized in the presence of alpha-ketoglutarate and malate | |||||||||||||||
Components | DASS family sodium-coupled anion symporter | |||||||||||||||
Keywords | TRANSPORT PROTEIN / 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 | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.86 Å | |||||||||||||||
Authors | Sauer, D.B. / Cocco, N. / Marden, J.J. / Song, J.M. / Wang, D.N. / New York Consortium on Membrane Protein Structure (NYCOMPS) | |||||||||||||||
Funding support | United States, 4items
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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
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6wtw.cif.gz | 454.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6wtw.ent.gz | 314.1 KB | Display | PDB format |
PDBx/mmJSON format | 6wtw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6wtw_validation.pdf.gz | 439 KB | Display | wwPDB validaton report |
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Full document | 6wtw_full_validation.pdf.gz | 454.6 KB | Display | |
Data in XML | 6wtw_validation.xml.gz | 34.1 KB | Display | |
Data in CIF | 6wtw_validation.cif.gz | 46.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wt/6wtw ftp://data.pdbj.org/pub/pdb/validation_reports/wt/6wtw | HTTPS FTP |
-Related structure data
Related structure data | 6wtxC 6wu1SC 6wu2C 6wu3C 6wu4C 6ww5C S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ALA / Beg label comp-ID: ALA / End auth comp-ID: ILE / End label comp-ID: ILE / Auth seq-ID: 0 - 487 / Label seq-ID: 3 - 490
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-Components
#1: Protein | Mass: 53539.527 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Lactobacillus acidophilus (bacteria) / Gene: D7H66_01865 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A3A9Y7Q2, UniProt: Q5FKK5*PLUS |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3 Å3/Da / Density % sol: 58.97 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.8 / Details: 30% Jeffamine ED-2001, 100 mM HEPES pH 6.8 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 13, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.86→50.09 Å / Num. obs: 30640 / % possible obs: 99.4 % / Redundancy: 6.3 % / Biso Wilson estimate: 71.52 Å2 / CC1/2: 0.966 / Net I/σ(I): 16 |
Reflection shell | Resolution: 2.86→2.9 Å / Num. unique obs: 1410 / CC1/2: 0.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6WU1 Resolution: 2.86→50.09 Å / SU ML: 0.4 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 31.6932
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 73.46 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.86→50.09 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: -25.6886249193 Å / Origin y: 6.20677519193 Å / Origin z: -24.3539988797 Å
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Refinement TLS group | Selection details: all |