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- EMDB-21156: Cryo-EM Structure of Escherichia coli 2-oxoglutarate dehydrogenas... -

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Basic information

Entry
Database: EMDB / ID: EMD-21156
TitleCryo-EM Structure of Escherichia coli 2-oxoglutarate dehydrogenase E1 component sucA
Map dataEscherichia coli 2-oxoglutarate dehydrogenase E1 component sucA
Sample
  • Complex: Escherichia coli 2-oxoglutarate dehydrogenase E1 component sucA
    • Protein or peptide: 2-oxoglutarate dehydrogenase E1 component
  • Ligand: ADENOSINE MONOPHOSPHATE
  • Ligand: OXALOACETATE ION
KeywordsTCA cycle / 2-oxoglutarate dehydrogenase complex (OGDH) / E1 component / sucA / AMP / Oxaloacetate (OAA) / Dimer / OXIDOREDUCTASE
Function / homology
Function and homology information


oxoglutarate dehydrogenase (succinyl-transferring) / oxoglutarate dehydrogenase (succinyl-transferring) activity / oxoglutarate dehydrogenase complex / thiamine pyrophosphate binding / tricarboxylic acid cycle / nucleotide binding / magnesium ion binding / identical protein binding / cytosol / 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 / Transketolase-like, pyrimidine-binding domain / Transketolase, pyrimidine binding domain ...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 / Transketolase-like, pyrimidine-binding domain / Transketolase, pyrimidine binding domain / Transketolase, pyrimidine binding domain / Thiamin diphosphate-binding fold
Similarity search - Domain/homology
Oxoglutarate dehydrogenase (succinyl-transferring) / 2-oxoglutarate dehydrogenase E1 component
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.08 Å
AuthorsGao H
CitationJournal: To Be Published
Title: Cryo-EM Structure of Escherichia coli 2-oxoglutarate dehydrogenase E1 component sucA
Authors: Gao H
History
DepositionDec 31, 2019-
Header (metadata) releaseJan 29, 2020-
Map releaseJan 6, 2021-
UpdateMar 6, 2024-
Current statusMar 6, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.015
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.015
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6vef
  • Surface level: 0.015
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_21156.png

Downloads & links

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Map

FileDownload / File: emd_21156.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationEscherichia coli 2-oxoglutarate dehydrogenase E1 component sucA
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.88 Å/pix.
x 200 pix.
= 175.4 Å		0.88 Å/pix.
x 200 pix.
= 175.4 Å		0.88 Å/pix.
x 200 pix.
= 175.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.877 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.015 / Movie #1: 0.015
Minimum - Maximum-0.037528343 - 0.06811727
Average (Standard dev.)0.00031025332 (±0.0040752105)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions200200200
Spacing200200200
CellA=B=C: 175.4 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.8770.8770.877
M x/y/z200200200
origin x/y/z0.0000.0000.000
length x/y/z175.400175.400175.400
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS200200200
D min/max/mean-0.0380.0680.000

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Supplemental data

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Sample components

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Entire : Escherichia coli 2-oxoglutarate dehydrogenase E1 component sucA

EntireName: Escherichia coli 2-oxoglutarate dehydrogenase E1 component sucA
Components
  • Complex: Escherichia coli 2-oxoglutarate dehydrogenase E1 component sucA
    • Protein or peptide: 2-oxoglutarate dehydrogenase E1 component
  • Ligand: ADENOSINE MONOPHOSPHATE
  • Ligand: OXALOACETATE ION

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Supramolecule #1: Escherichia coli 2-oxoglutarate dehydrogenase E1 component sucA

SupramoleculeName: Escherichia coli 2-oxoglutarate dehydrogenase E1 component sucA
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Escherichia coli K-12 (bacteria)

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Macromolecule #1: 2-oxoglutarate dehydrogenase E1 component

MacromoleculeName: 2-oxoglutarate dehydrogenase E1 component / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
EC number: oxoglutarate dehydrogenase (succinyl-transferring)
Source (natural)Organism: Escherichia coli K-12 (bacteria) / Strain: K12
Molecular weightTheoretical: 94.942508 KDa
SequenceString: DTNVKQVKVL QLINAYRFRG HQHANLDPLG LYQQDKVADL DPSFHDLTEA DFQETFNVGS FASGKETMKL GELLEALKQT YCGPIGAEY MHITSTEEKR WIQQRIESGR ATFNSEEKKR FLSELTAAEG LERYLGAKFP GAKRFSLEGD ALIPMLKEMI R HAGNSGTR ...String:
DTNVKQVKVL QLINAYRFRG HQHANLDPLG LYQQDKVADL DPSFHDLTEA DFQETFNVGS FASGKETMKL GELLEALKQT YCGPIGAEY MHITSTEEKR WIQQRIESGR ATFNSEEKKR FLSELTAAEG LERYLGAKFP GAKRFSLEGD ALIPMLKEMI R HAGNSGTR EVVLGMAHRG RLNVLVNVLG KKPQDLFDEF AGKHKEHLGT GDVKYHMGFS SDFQTDGGLV HLALAFNPSH LE IVSPVVI GSVRARLDRL DEPSSNKVLP ITIHGDAAVT GQGVVQETLN MSKARGYEVG GTVRIVINNQ VGFTTSNPLD ARS TPYMTD IGKMVQAPIF HVNADDPEAV AFVTRLALDF RNTFKRDVFI DLVCYRRHGH NEADEPSATQ KIKKHPTPRK IYAD KLEQE KVATLEDATE MVNLYRDALD AGDCVVAEWR PMNMHSFTWS PYLNHEWDEE YPNKVEMKRL QELAKRISTV PEAVE MQSR VAKIYGDRQA MAAGEKLFDW GGAENLAYAT LVDEGIPVRL SGEDSGRGTF FHRHAVIHNQ SNGSTYTPLQ HIHNGQ GAF RVWDSVLSEE AVLAFEYGYA TAEPRTLTIW EAQFGDFANG AQVVIDQFIS SGEQKWGRMC GLVMLLPHGY EGQGPEH SS ARLERYLQLC AEQNMQVCVP STPAQVYHML RRQALRGMRR PLVVMSPKSL LRHPLAVSSL EELANGTFLP AIGEIDEL D PKGVKRVVMC SGKVYYDLLE QRRKNNQHDV AIVRIEQLYP FPHKAMQEVL QQFAHVKDFV WCQEEPLNQG AWYCSQHHF REVIPFGASL RYAGRPASAS PAVGHMSVHQ KQQQDLVNDA LNVE

UniProtKB: Oxoglutarate dehydrogenase (succinyl-transferring)

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Macromolecule #2: ADENOSINE MONOPHOSPHATE

MacromoleculeName: ADENOSINE MONOPHOSPHATE / type: ligand / ID: 2 / Number of copies: 2 / Formula: AMP
Molecular weightTheoretical: 347.221 Da
Chemical component information

ChemComp-AMP:
ADENOSINE MONOPHOSPHATE / AMP*YM

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Macromolecule #3: OXALOACETATE ION

MacromoleculeName: OXALOACETATE ION / type: ligand / ID: 3 / Number of copies: 2 / Formula: OAA
Molecular weightTheoretical: 131.064 Da
Chemical component information

ChemComp-OAA:
OXALOACETATE ION

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 80 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TECNAI ARCTICA
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Number real images: 800 / Average exposure time: 2.0 sec. / Average electron dose: 80.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

Startup modelType of model: INSILICO MODEL
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C2 (2 fold cyclic) / Algorithm: SIMULTANEOUS ITERATIVE (SIRT) / Resolution.type: BY AUTHOR / Resolution: 4.08 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 86461
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: PROJECTION MATCHING
Final 3D classificationSoftware - Name: RELION
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

2jgd


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL / Protocol: RIGID BODY FIT / Overall B value: 60
Output model

PDB-6vef:
Cryo-EM Structure of Escherichia coli 2-oxoglutarate dehydrogenase E1 component sucA

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