[English] 日本語
Yorodumi
- EMDB-17456: Single particle cryo-EM structure of the complex between Coryneba... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-17456
TitleSingle particle cryo-EM structure of the complex between Corynebacterium glutamicum homohexameric 2-oxoglutarate dehydrogenase OdhA and the FHA-protein inhibitor OdhI
Map dataOdhA_OdhI dens_mod_primary_map
Sample
  • Complex: Complex of homohexameric 2-oxoglutarate dehydrogenase OdhA and the FHA-domain inhibitor OdhI
    • Protein or peptide: 2-oxoglutarate dehydrogenase E1/E2 component
    • Protein or peptide: Oxoglutarate dehydrogenase inhibitor
  • Ligand: THIAMINE DIPHOSPHATE
  • Ligand: MAGNESIUM ION
Keywords2-oxoglutarate dehydrogenase / ODH / OXIDOREDUCTASE
Function / homology
Function and homology information


oxoglutarate dehydrogenase (succinyl-transferring) / oxoglutarate dehydrogenase (succinyl-transferring) activity / dihydrolipoyllysine-residue succinyltransferase / dihydrolipoyllysine-residue succinyltransferase activity / thiamine pyrophosphate binding / tricarboxylic acid cycle / magnesium ion binding / cytoplasm
Similarity search - Function
: / 2-oxoglutarate dehydrogenase E1 component, N-terminal domain / 2-oxoglutarate dehydrogenase N-terminus / Multifunctional 2-oxoglutarate metabolism enzyme, C-terminal / Multifunctional 2-oxoglutarate metabolism enzyme, C-terminal domain superfamily / 2-oxoglutarate dehydrogenase C-terminal / 2-oxoglutarate dehydrogenase E1 component / : / Dehydrogenase, E1 component / Dehydrogenase E1 component ...: / 2-oxoglutarate dehydrogenase E1 component, N-terminal domain / 2-oxoglutarate dehydrogenase N-terminus / Multifunctional 2-oxoglutarate metabolism enzyme, C-terminal / Multifunctional 2-oxoglutarate metabolism enzyme, C-terminal domain superfamily / 2-oxoglutarate dehydrogenase C-terminal / 2-oxoglutarate dehydrogenase E1 component / : / Dehydrogenase, E1 component / Dehydrogenase E1 component / 2-oxoacid dehydrogenase acyltransferase, catalytic domain / 2-oxoacid dehydrogenases acyltransferase (catalytic domain) / Transketolase-like, pyrimidine-binding domain / Transketolase, pyrimidine binding domain / Transketolase, pyrimidine binding domain / Forkhead associated domain / Forkhead-associated (FHA) domain profile. / FHA domain / Forkhead-associated (FHA) domain / Chloramphenicol acetyltransferase-like domain superfamily / SMAD/FHA domain superfamily / Thiamin diphosphate-binding fold
Similarity search - Domain/homology
Oxoglutarate dehydrogenase inhibitor / 2-oxoglutarate dehydrogenase E1/E2 component
Similarity search - Component
Biological speciesCorynebacterium glutamicum ATCC 13032 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.29 Å
AuthorsYang L / Mechaly AM / Bellinzoni M
Funding support France, 2 items
OrganizationGrant numberCountry
Agence Nationale de la Recherche (ANR)ANR-13-JSV8-0003 France
Agence Nationale de la Recherche (ANR)ANR-18-CE92-0003 France
Citation
Journal: Nat Commun / Year: 2023
Title: High resolution cryo-EM and crystallographic snapshots of the actinobacterial two-in-one 2-oxoglutarate dehydrogenase.
Authors: Lu Yang / Tristan Wagner / Ariel Mechaly / Alexandra Boyko / Eduardo M Bruch / Daniela Megrian / Francesca Gubellini / Pedro M Alzari / Marco Bellinzoni /
Abstract: Actinobacteria possess unique ways to regulate the oxoglutarate metabolic node. Contrary to most organisms in which three enzymes compose the 2-oxoglutarate dehydrogenase complex (ODH), ...Actinobacteria possess unique ways to regulate the oxoglutarate metabolic node. Contrary to most organisms in which three enzymes compose the 2-oxoglutarate dehydrogenase complex (ODH), actinobacteria rely on a two-in-one protein (OdhA) in which both the oxidative decarboxylation and succinyl transferase steps are carried out by the same polypeptide. Here we describe high-resolution cryo-EM and crystallographic snapshots of representative enzymes from Mycobacterium smegmatis and Corynebacterium glutamicum, showing that OdhA is an 800-kDa homohexamer that assembles into a three-blade propeller shape. The obligate trimeric and dimeric states of the acyltransferase and dehydrogenase domains, respectively, are critical for maintaining the overall assembly, where both domains interact via subtle readjustments of their interfaces. Complexes obtained with substrate analogues, reaction products and allosteric regulators illustrate how these domains operate. Furthermore, we provide additional insights into the phosphorylation-dependent regulation of this enzymatic machinery by the signalling protein OdhI.
#1: Journal: Biorxiv / Year: 2023
Title: High resolution cryo-EM and crystallographic snapshots of the large actinobacterial 2-oxoglutarate dehydrogenase: an all-in-one fusion with unique properties
Authors: Yang L / Wagner T / Mechaly A / Boyko A / Bruch EM / Megrian D / Gubellini F / Alzari PM / Bellinzoni M
History
DepositionMay 24, 2023-
Header (metadata) releaseAug 16, 2023-
Map releaseAug 16, 2023-
UpdateAug 23, 2023-
Current statusAug 23, 2023Processing site: PDBe / Status: Released

-
Structure visualization

Supplemental images

emd_17456.png

Downloads & links

-
Map

FileDownload / File: emd_17456.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationOdhA_OdhI dens_mod_primary_map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesX (Sec.)Y (Row.)Z (Col.)
0.86 Å/pix.
x 384 pix.
= 330.24 Å		0.86 Å/pix.
x 384 pix.
= 330.24 Å		0.86 Å/pix.
x 384 pix.
= 330.24 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.86 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1.0
Minimum - Maximum-1.2834102 - 49.96942
Average (Standard dev.)0.020188853 (±1.2522621)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 330.24 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: OdhA OdhI half map A cryoSPARC

Fileemd_17456_half_map_1.map
AnnotationOdhA_OdhI_half_map_A_cryoSPARC
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: OdhA OdhI half map B cryoSPARC

Fileemd_17456_half_map_2.map
AnnotationOdhA_OdhI_half_map_B_cryoSPARC
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Complex of homohexameric 2-oxoglutarate dehydrogenase OdhA and th...

EntireName: Complex of homohexameric 2-oxoglutarate dehydrogenase OdhA and the FHA-domain inhibitor OdhI
Components
  • Complex: Complex of homohexameric 2-oxoglutarate dehydrogenase OdhA and the FHA-domain inhibitor OdhI
    • Protein or peptide: 2-oxoglutarate dehydrogenase E1/E2 component
    • Protein or peptide: Oxoglutarate dehydrogenase inhibitor
  • Ligand: THIAMINE DIPHOSPHATE
  • Ligand: MAGNESIUM ION

-
Supramolecule #1: Complex of homohexameric 2-oxoglutarate dehydrogenase OdhA and th...

SupramoleculeName: Complex of homohexameric 2-oxoglutarate dehydrogenase OdhA and the FHA-domain inhibitor OdhI
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2 / Details: 1:1 complex
Source (natural)Organism: Corynebacterium glutamicum ATCC 13032 (bacteria)
Molecular weightTheoretical: 808 KDa

-
Macromolecule #1: 2-oxoglutarate dehydrogenase E1/E2 component

MacromoleculeName: 2-oxoglutarate dehydrogenase E1/E2 component / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO
EC number: oxoglutarate dehydrogenase (succinyl-transferring)
Source (natural)Organism: Corynebacterium glutamicum ATCC 13032 (bacteria)
Molecular weightTheoretical: 134.972078 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: GSMSSASTFG QNAWLVDEMF QQFQKDPKSV DKEWRELFEA QGGPNTTPAT TEAQPSAPKE SAKPAPKAAP AAKAAPRVET KPADKTAPK AKESSVPQQP KLPEPGQTPI RGIFKSIAKN MDISLEIPTA TSVRDMPARL MFENRAMVND QLKRTRGGKI S FTHIIGYA ...String:
GSMSSASTFG QNAWLVDEMF QQFQKDPKSV DKEWRELFEA QGGPNTTPAT TEAQPSAPKE SAKPAPKAAP AAKAAPRVET KPADKTAPK AKESSVPQQP KLPEPGQTPI RGIFKSIAKN MDISLEIPTA TSVRDMPARL MFENRAMVND QLKRTRGGKI S FTHIIGYA MVKAVMAHPD MNNSYDVIDG KPTLIVPEHI NLGLAIDLPQ KDGSRALVVA AIKETEKMNF SEFLAAYEDI VA RSRKGKL TMDDYQGVTV SLTNPGGIGT RHSVPRLTKG QGTIIGVGSM DYPAEFQGAS EDRLAELGVG KLVTITSTYD HRV IQGAVS GEFLRTMSRL LTDDSFWDEI FDAMNVPYTP MRWAQDVPNT GVDKNTRVMQ LIEAYRSRGH LIADTNPLSW VQPG MPVPD HRDLDIETHN LTIWDLDRTF NVGGFGGKET MTLREVLSRL RAAYTLKVGS EYTHILDRDE RTWLQDRLEA GMPKP TQAE QKYILQKLNA AEAFENFLQT KYVGQKRFSL EGAEALIPLM DSAIDTAAGQ GLDEVVIGMP HRGRLNVLFN IVGKPL ASI FNEFEGQMEQ GQIGGSGDVK YHLGSEGQHL QMFGDGEIKV SLTANPSHLE AVNPVMEGIV RAKQDYLDKG VDGKTVV PL LLHGDAAFAG LGIVPETINL AKLRGYDVGG TIHIVVNNQI GFTTTPDSSR SMHYATDYAK AFGCPVFHVN GDDPEAVV W VGQLATEYRR RFGKDVFIDL VCYRLRGHNE ADDPSMTQPK MYELITGRET VRAQYTEDLL GRGDLSNEDA EAVVRDFHD QMESVFNEVK EGGKKQAEAQ TGITGSQKLP HGLETNISRE ELLELGQAFA NTPEGFNYHP RVAPVAKKRV SSVTEGGIDW AWGELLAFG SLANSGRLVR LAGEDSRRGT FTQRHAVAID PATAEEFNPL HELAQSKGNN GKFLVYNSAL TEYAGMGFEY G YSVGNEDS IVAWEAQFGD FANGAQTIID EYVSSGEAKW GQTSKLILLL PHGYEGQGPD HSSARIERFL QLCAEGSMTV AQ PSTPANH FHLLRRHALS DLKRPLVIFT PKSMLRNKAA ASAPEDFTEV TKFQSVINDP NVADAAKVKK VMLVSGKLYY ELA KRKEKD GRDDIAIVRI EMLHPIPFNR ISEALAGYPN AEEVLFVQDE PANQGPWPFY QEHLPELIPN MPKMRRVSRR AQSS TATGV AKVHQLEEKQ LIDEAFEA

UniProtKB: 2-oxoglutarate dehydrogenase E1/E2 component

-
Macromolecule #2: Oxoglutarate dehydrogenase inhibitor

MacromoleculeName: Oxoglutarate dehydrogenase inhibitor / type: protein_or_peptide / ID: 2 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Corynebacterium glutamicum ATCC 13032 (bacteria)
Molecular weightTheoretical: 15.474066 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
GMSDNNGTPE PQVETTSVFR ADLLKEMESS TGTAPASTGA ENLPAGSALL VVKRGPNAGA RFLLDQPTTT AGRHPESDIF LDDVTVSRR HAEFRINEGE FEVVDVGSLN GTYVNREPRN AQVMQTGDEI QIGKFRLVFL AGPAE

UniProtKB: Oxoglutarate dehydrogenase inhibitor

-
Macromolecule #3: THIAMINE DIPHOSPHATE

MacromoleculeName: THIAMINE DIPHOSPHATE / type: ligand / ID: 3 / Number of copies: 6 / Formula: TPP
Molecular weightTheoretical: 425.314 Da
Chemical component information

ChemComp-TPP:
THIAMINE DIPHOSPHATE

-
Macromolecule #4: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 4 / Number of copies: 6 / Formula: MG
Molecular weightTheoretical: 24.305 Da

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration11.5 mg/mL
BufferpH: 7.5 / Component:
ConcentrationName
20.0 mMHEPES-Na
500.0 mMNaCl
GridModel: EMS Lacey Carbon / Material: COPPER / Mesh: 200 / Pretreatment - Type: PLASMA CLEANING / Pretreatment - Time: 10 sec. / Pretreatment - Atmosphere: OTHER
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number grids imaged: 1 / Number real images: 19443 / Average exposure time: 2.45 sec. / Average electron dose: 40.0 e/Å2 / Details: Each image was composed by 40 frames
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.2 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 105000
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: INSILICO MODEL / In silico model: Ab initio model from cryoSPARC
Final reconstructionApplied symmetry - Point group: D3 (2x3 fold dihedral) / Resolution.type: BY AUTHOR / Resolution: 2.29 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 958690
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final 3D classificationSoftware - Name: cryoSPARC
FSC plot (resolution estimation)

-
Atomic model buiding 1

Initial model
PDB IDChain

8p5t

source_name: PDB, initial_model_type: experimental model

4qcj

source_name: PDB, initial_model_type: experimental model
RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-8p5x:
Single particle cryo-EM structure of the complex between Corynebacterium glutamicum homohexameric 2-oxoglutarate dehydrogenase OdhA and the FHA-protein inhibitor OdhI

+
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