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- PDB-6iww: Cryo-EM structure of the S. typhimurium oxaloacetate decarboxylas... -

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Basic information

Entry
Database: PDB / ID: 6iww
TitleCryo-EM structure of the S. typhimurium oxaloacetate decarboxylase beta-gamma sub-complex
Components
  • Oxaloacetate decarboxylase beta chain
  • Probable oxaloacetate decarboxylase gamma chain
KeywordsMEMBRANE 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
Na+-transporting methylmalonyl-CoA/oxaloacetate decarboxylase, beta subunit / Sodium ion-translocating decarboxylase / Oxaloacetate decarboxylase, gamma chain / Na+-transporting oxaloacetate decarboxylase beta subunit / Oxaloacetate decarboxylase, gamma chain
Similarity search - Domain/homology
Oxaloacetate decarboxylase beta chain / Probable oxaloacetate decarboxylase gamma chain / Oxaloacetate decarboxylase gamma chain 2 / Oxaloacetate decarboxylase beta chain 1
Similarity search - Component
Biological speciesSalmonella enterica subsp. enterica serovar Typhimurium (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.9 Å
AuthorsXu, X. / Shi, H. / Zhang, X. / Xiang, S.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China31570743 China
CitationJournal: 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
DepositionDec 8, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 17, 2020Provider: repository / Type: Initial release
Revision 1.1Aug 12, 2020Group: Source and taxonomy / Category: em_entity_assembly_naturalsource / entity_src_gen
Item: _em_entity_assembly_naturalsource.strain / _entity_src_gen.gene_src_strain ..._em_entity_assembly_naturalsource.strain / _entity_src_gen.gene_src_strain / _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain
Revision 1.2Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

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Assembly

Deposited unit
A: Oxaloacetate decarboxylase beta chain
B: Probable oxaloacetate decarboxylase gamma chain
C: Oxaloacetate decarboxylase beta chain
D: Probable oxaloacetate decarboxylase gamma chain
E: Oxaloacetate decarboxylase beta chain
F: Probable oxaloacetate decarboxylase gamma chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)169,7299
Polymers168,1976
Non-polymers1,5323
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area21770 Å2
ΔGint-244 kcal/mol
Surface area49530 Å2

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Components

#1: Protein Oxaloacetate decarboxylase beta chain


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 Probable oxaloacetate decarboxylase gamma chain


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 ChemComp-LMT / DODECYL-BETA-D-MALTOSIDE


Type: D-saccharide / Mass: 510.615 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C24H46O11 / Comment: detergent*YM
Sequence detailsAuthors 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

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: The oxaloacetate decarboxylase beta-gamma sub-complex / Type: COMPLEX / Entity ID: #2 / Source: RECOMBINANT
Molecular weightExperimental 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 solutionpH: 7.5
SpecimenConc.: 8 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: This sample was monodisperse
Specimen supportGrid material: COPPER / Grid type: Quantifoil R1.2/1.3
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Calibrated defocus min: 1500 nm / Calibrated defocus max: 3500 nm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron 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 scansMovie frames/image: 32 / Used frames/image: 1-50

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Processing

SoftwareName: PHENIX / Version: 1.13_2998: / Classification: refinement
EM software
IDNameVersionCategory
2SerialEMimage acquisition
4CTFFIND4.0.17CTF correction
9RELION2.1.0initial Euler assignment
10RELION2.1.0final Euler assignment
11RELION2.1.0classification
12RELION2.1.03D reconstruction
13PHENIX1.13-2998-000model refinement
CTF correctionType: PHASE FLIPPING ONLY
SymmetryPoint symmetry: C3 (3 fold cyclic)
3D reconstructionResolution: 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

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