[English] 日本語
Yorodumi
- EMDB-9743: Cryo-EM structure of the S. typhimurium oxaloacetate decarboxylas... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-9743
TitleCryo-EM structure of the S. typhimurium oxaloacetate decarboxylase beta-gamma sub-complex
Map data
Sample
  • Complex: The oxaloacetate decarboxylase beta-gamma sub-complex
    • Protein or peptide: Probable oxaloacetate decarboxylase gamma chain
  • Protein or peptide: Oxaloacetate decarboxylase beta chain
  • Ligand: DODECYL-BETA-D-MALTOSIDE
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)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.9 Å
AuthorsXu X / Shi H
Funding support China, 1 items
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, 2018-
Header (metadata) releaseJun 17, 2020-
Map releaseJun 17, 2020-
UpdateMar 27, 2024-
Current statusMar 27, 2024Processing site: PDBj / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.11
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.11
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-6iww
  • Surface level: 0.11
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_9743.png

Downloads & links

-
Map

FileDownload / File: emd_9743.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)X (Row.)Y (Col.)
1.32 Å/pix.
x 200 pix.
= 264.06 Å		1.32 Å/pix.
x 200 pix.
= 264.06 Å		1.32 Å/pix.
x 200 pix.
= 264.06 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.3203 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0641 / Movie #1: 0.11
Minimum - Maximum-0.2787711 - 0.5004934
Average (Standard dev.)-0.0002599823 (±0.02164941)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderYXZ
Origin000
Dimensions200200200
Spacing200200200
CellA=B=C: 264.06 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.32031.32031.3203
M x/y/z200200200
origin x/y/z0.0000.0000.000
length x/y/z264.060264.060264.060
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ200200200
MAP C/R/S213
start NC/NR/NS000
NC/NR/NS200200200
D min/max/mean-0.2790.500-0.000

-
Supplemental data

-
Sample components

-
Entire : The oxaloacetate decarboxylase beta-gamma sub-complex

EntireName: The oxaloacetate decarboxylase beta-gamma sub-complex
Components
  • Complex: The oxaloacetate decarboxylase beta-gamma sub-complex
    • Protein or peptide: Probable oxaloacetate decarboxylase gamma chain
  • Protein or peptide: Oxaloacetate decarboxylase beta chain
  • Ligand: DODECYL-BETA-D-MALTOSIDE

-
Supramolecule #1: The oxaloacetate decarboxylase beta-gamma sub-complex

SupramoleculeName: The oxaloacetate decarboxylase beta-gamma sub-complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #2
Source (natural)Organism: Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)
Strain: enterica serovar Typhimurium

-
Macromolecule #1: Oxaloacetate decarboxylase beta chain

MacromoleculeName: Oxaloacetate decarboxylase beta chain / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO / EC number: oxaloacetate decarboxylase (Na+ extruding)
Source (natural)Organism: Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)
Strain: enterica serovar Typhimurium
Molecular weightTheoretical: 44.928801 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MESLNALLQG MGLMHLGAGQ AIMLLVSLLL LWLAIAKKFE PLLLLPIGFG GLLSNIPEAG MALTALESLL AHHDAGQLAV IAAKLNCAP DVHAIKEALA LALPSVQGQM ENLAVDMGYT PGVLALFYKV AIGSGVAPLV IFMGVGAMTD FGPLLANPRT L LLGAAAQF ...String:
MESLNALLQG MGLMHLGAGQ AIMLLVSLLL LWLAIAKKFE PLLLLPIGFG GLLSNIPEAG MALTALESLL AHHDAGQLAV IAAKLNCAP DVHAIKEALA LALPSVQGQM ENLAVDMGYT PGVLALFYKV AIGSGVAPLV IFMGVGAMTD FGPLLANPRT L LLGAAAQF GIFATVLGAL TLNYFGLISF TLPQAAAIGI IGGADGPTAI YLSGKLAPEL LGAIAVAAYS YMALVPLIQP PI MRALTSE KERKIRMVQL RTVSKREKIL FPVVLLLLVA LLLPDAAPLL GMFCFGNLMR ESGVVERLSD TVQNGLINIV TIF LGLSVG AKLVADKFLQ PQTLGILLLG VIAFGIGTAA GVLMAKLLNL CSKNKINPLI GSAGVSAVPM AARVSNKVGL ESDA QNFLL MHAMGPNVAG VIGSAIAAGV MLKYVLAM

UniProtKB: Oxaloacetate decarboxylase beta chain

-
Macromolecule #2: Probable oxaloacetate decarboxylase gamma chain

MacromoleculeName: Probable oxaloacetate decarboxylase gamma chain / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO / EC number: oxaloacetate decarboxylase (Na+ extruding)
Source (natural)Organism: Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)
Strain: enterica serovar Typhimurium
Molecular weightTheoretical: 11.137029 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
MGSSHHHHHH SSGLVPRGSH MTNAALLLGE GFTLMFLGMG FVLAFLFLLI FAIRGMSAAV NRFFPEPAPA PKAAPAAAAP VVDDFTRLK PVIAAAIHHH HRLNA

UniProtKB: Probable oxaloacetate decarboxylase gamma chain

-
Macromolecule #3: DODECYL-BETA-D-MALTOSIDE

MacromoleculeName: DODECYL-BETA-D-MALTOSIDE / type: ligand / ID: 3 / Number of copies: 3 / Formula: LMT
Molecular weightTheoretical: 510.615 Da
Chemical component information

ChemComp-LMT:
DODECYL-BETA-D-MALTOSIDE / detergent*YM

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration8 mg/mL
BufferpH: 7.5
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec.
VitrificationCryogen name: ETHANE
DetailsThis sample was monodisperse

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Digitization - Frames/image: 1-50 / Number grids imaged: 1 / Number real images: 821 / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated defocus max: 3.5 µm / Calibrated defocus min: 1.5 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Startup modelType of model: OTHER / Details: From startcsym in EMAN
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C3 (3 fold cyclic) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 2.1.0) / Number images used: 75699
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 2.1.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 2.1.0)
Final 3D classificationNumber classes: 5 / Avg.num./class: 24000 / Software - Name: RELION (ver. 2.1.0)

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more