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Yorodumi- PDB-6iww: Cryo-EM structure of the S. typhimurium oxaloacetate decarboxylas... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6iww | ||||||
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Title | Cryo-EM structure of the S. typhimurium oxaloacetate decarboxylase beta-gamma sub-complex | ||||||
Components |
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Keywords | MEMBRANE PROTEIN / sodium pump / decarboxylase sodium pump / biotin-dependent decarboxylase | ||||||
Function / homology | Function and homology information oxaloacetate decarboxylase (Na+ extruding) / decarboxylation-driven active transmembrane transporter activity / sodium ion transmembrane transporter activity / oxaloacetate decarboxylase activity / sodium ion export across plasma membrane / sodium ion transport / lyase activity / plasma membrane Similarity search - Function | ||||||
Biological species | Salmonella enterica subsp. enterica serovar Typhimurium (bacteria) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.9 Å | ||||||
Authors | Xu, X. / Shi, H. / Zhang, X. / Xiang, S. | ||||||
Funding support | China, 1items
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Citation | Journal: Elife / Year: 2020 Title: Structural insights into sodium transport by the oxaloacetate decarboxylase sodium pump. Authors: Xin Xu / Huigang Shi / Xiaowen Gong / Pu Chen / Ying Gao / Xinzheng Zhang / Song Xiang / Abstract: The oxaloacetate decarboxylase sodium pump (OAD) is a unique primary-active transporter that utilizes the free energy derived from oxaloacetate decarboxylation for sodium transport across the cell ...The oxaloacetate decarboxylase sodium pump (OAD) is a unique primary-active transporter that utilizes the free energy derived from oxaloacetate decarboxylation for sodium transport across the cell membrane. It is composed of 3 subunits: the α subunit catalyzes carboxyl-transfer from oxaloacetate to biotin, the membrane integrated β subunit catalyzes the subsequent carboxyl-biotin decarboxylation and the coupled sodium transport, the γ subunit interacts with the α and β subunits and stabilizes the OAD complex. We present here structure of the OAD βγ sub-complex. The structure revealed that the β and γ subunits form a βγ hetero-hexamer with extensive interactions between the subunits and shed light on the OAD holo-enzyme assembly. Structure-guided functional studies provided insights into the sodium binding sites in the β subunit and the coupling between carboxyl-biotin decarboxylation and sodium transport by the OAD β subunit. | ||||||
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 | 6iww.cif.gz | 231.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6iww.ent.gz | 186.3 KB | Display | PDB format |
PDBx/mmJSON format | 6iww.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6iww_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 6iww_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 6iww_validation.xml.gz | 40.4 KB | Display | |
Data in CIF | 6iww_validation.cif.gz | 61.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/iw/6iww ftp://data.pdbj.org/pub/pdb/validation_reports/iw/6iww | HTTPS FTP |
-Related structure data
Related structure data | 9743MC 6ivaC 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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-Components
#1: Protein | Mass: 44928.801 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Salmonella enterica subsp. enterica serovar Typhimurium (bacteria) Strain: enterica serovar Typhimurium / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) References: UniProt: A0A0F7JAV8, UniProt: Q8ZRY4*PLUS, oxaloacetate decarboxylase (Na+ extruding) #2: Protein | Mass: 11137.029 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Salmonella enterica subsp. enterica serovar Typhimurium (bacteria) Strain: enterica serovar Typhimurium / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) References: UniProt: A0A0F7JC72, UniProt: Q03032*PLUS, oxaloacetate decarboxylase (Na+ extruding) #3: Sugar | Sequence details | Authors state that this conflict may be a natural occurring mutation that happen to exist in the ...Authors state that this conflict may be a natural occurring mutation that happen to exist in the genomic DNA they used. | |
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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: The oxaloacetate decarboxylase beta-gamma sub-complex / Type: COMPLEX / Entity ID: #2 / Source: RECOMBINANT |
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Molecular weight | Experimental value: NO |
Source (natural) | Organism: Salmonella enterica subsp. enterica serovar Typhimurium (bacteria) Strain: enterica serovar Typhimurium |
Source (recombinant) | Organism: Escherichia coli (E. coli) / Strain: BL21(DE3) |
Buffer solution | pH: 7.5 |
Specimen | Conc.: 8 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: This sample was monodisperse |
Specimen support | Grid material: COPPER / Grid type: Quantifoil R1.2/1.3 |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Calibrated defocus min: 1500 nm / Calibrated defocus max: 3500 nm |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Electron dose: 50 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 821 |
Image scans | Movie frames/image: 32 / Used frames/image: 1-50 |
-Processing
Software | Name: PHENIX / Version: 1.13_2998: / Classification: refinement | ||||||||||||||||||||||||||||||||
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EM software |
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CTF correction | Type: PHASE FLIPPING ONLY | ||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C3 (3 fold cyclic) | ||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 75699 / Algorithm: FOURIER SPACE / Num. of class averages: 1 / Symmetry type: POINT |