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- EMDB-34029: 2.9-angstrom cryo-EM structure of Ecoli malate synthase G -

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Basic information

Entry
Database: EMDB / ID: EMD-34029
Title2.9-angstrom cryo-EM structure of Ecoli malate synthase G
Map data
Sample
  • Cell: 2.9-angstrom cryo-EM structure of 723-aa malate synthase G
    • Protein or peptide: Malate synthase G
Function / homology
Function and homology information


malate synthase / malate synthase activity / glyoxylate catabolic process / glyoxylate cycle / tricarboxylic acid cycle / magnesium ion binding / cytosol
Similarity search - Function
: / Malate synthase G, alpha-beta insertion domain / : / : / Malate synthase, N-terminal domain / Malate synthase, C-terminal / Malate synthase G / Malate synthase, N-terminal and TIM-barrel domains / Malate synthase, C-terminal superfamily / Malate synthase ...: / Malate synthase G, alpha-beta insertion domain / : / : / Malate synthase, N-terminal domain / Malate synthase, C-terminal / Malate synthase G / Malate synthase, N-terminal and TIM-barrel domains / Malate synthase, C-terminal superfamily / Malate synthase / Malate synthase superfamily / Malate synthase, TIM barrel domain
Similarity search - Domain/homology
Biological speciesEscherichia coli DH5[alpha] (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.89 Å
AuthorsWu K-P / Wu Y-M / Lu Y-C
Funding support Taiwan, 1 items
OrganizationGrant numberCountry
Academia Sinica (Taiwan) Taiwan
CitationJournal: J Struct Biol / Year: 2023
Title: Cryo-EM reveals the structure and dynamics of a 723-residue malate synthase G.
Authors: Meng-Ru Ho / Yi-Ming Wu / Yen-Chen Lu / Tzu-Ping Ko / Kuen-Phon Wu /
Abstract: Determination of sub-100 kDa (kDa) structures by cryo-electron microscopy (EM) is a longstanding but not straightforward goal. Here, we present a 2.9-Å cryo-EM structure of a 723-amino acid apo- ...Determination of sub-100 kDa (kDa) structures by cryo-electron microscopy (EM) is a longstanding but not straightforward goal. Here, we present a 2.9-Å cryo-EM structure of a 723-amino acid apo-form malate synthase G (MSG) from Escherichia coli. The cryo-EM structure of the 82-kDa MSG exhibits the same global folding as structures resolved by crystallography and nuclear magnetic resonance (NMR) spectroscopy, and the crystal and cryo-EM structures are indistinguishable. Analyses of MSG dynamics reveal consistent conformational flexibilities among the three experimental approaches, most notably that the α/β domain exhibits structural heterogeneity. We observed that sidechains of F453, L454, M629, and E630 residues involved in hosting the cofactor acetyl-CoA and substrate rotate differently between the cryo-EM apo-form and complex crystal structures. Our work demonstrates that the cryo-EM technique can be used to determine structures and conformational heterogeneity of sub-100 kDa biomolecules to a quality as high as that obtained from X-ray crystallography and NMR spectroscopy.
History
DepositionAug 8, 2022-
Header (metadata) releaseMar 29, 2023-
Map releaseMar 29, 2023-
UpdateApr 19, 2023-
Current statusApr 19, 2023Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_34029.png

Downloads & links

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Map

FileDownload / File: emd_34029.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 0.822 Å
Density
Contour LevelBy AUTHOR: 0.4
Minimum - Maximum-1.5155346 - 1.9118218
Average (Standard dev.)0.00061967183 (±0.036492355)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 263.04 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: #1

Fileemd_34029_additional_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_34029_half_map_1.map
Projections & Slices
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Histogram (log scale)

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Half map: #2

Fileemd_34029_half_map_2.map
Projections & Slices
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Sample components

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Entire : 2.9-angstrom cryo-EM structure of 723-aa malate synthase G

EntireName: 2.9-angstrom cryo-EM structure of 723-aa malate synthase G
Components
  • Cell: 2.9-angstrom cryo-EM structure of 723-aa malate synthase G
    • Protein or peptide: Malate synthase G

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Supramolecule #1: 2.9-angstrom cryo-EM structure of 723-aa malate synthase G

SupramoleculeName: 2.9-angstrom cryo-EM structure of 723-aa malate synthase G
type: cell / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Escherichia coli DH5[alpha] (bacteria)

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Macromolecule #1: Malate synthase G

MacromoleculeName: Malate synthase G / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: malate synthase
Source (natural)Organism: Escherichia coli DH5[alpha] (bacteria) / Strain: K12
Molecular weightTheoretical: 80.581344 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MSQTITQSRL RIDANFKRFV DEEVLPGTGL DAAAFWRNFD EIVHDLAPEN RQLLAERDRI QAALDEWHRS NPGPVKDKAA YKSFLRELG YLVPQPERVT VETTGIDSEI TSQAGPQLVV PAMNARYALN AANARWGSLY DALYGSDIIP QEGAMVSGYD P QRGEQVIA ...String:
MSQTITQSRL RIDANFKRFV DEEVLPGTGL DAAAFWRNFD EIVHDLAPEN RQLLAERDRI QAALDEWHRS NPGPVKDKAA YKSFLRELG YLVPQPERVT VETTGIDSEI TSQAGPQLVV PAMNARYALN AANARWGSLY DALYGSDIIP QEGAMVSGYD P QRGEQVIA WVRRFLDESL PLENGSYQDV VAFKVVDKQL RIQLKNGKET TLRTPAQFVG YRGDAAAPTC ILLKNNGLHI EL QIDANGR IGKDDPAHIN DVIVEAAIST ILDCEDSVAA VDAEDKILLY RNLLGLMQGT LQEKMEKNGR QIVRKLNDDR HYT AADGSE ISLHGRSLLF IRNVGHLMTI PVIWDSEGNE IPEGILDGVM TGAIALYDLK VQKNSRTGSV YIVKPKMHGP QEVA FANKL FTRIETMLGM APNTLKMGIM DEERRTSLNL RSCIAQARNR VAFINTGFLD RTGDEMHSVM EAGPMLRKNQ MKSTP WIKA YERNNVLSGL FCGLRGKAQI GKGMWAMPDL MADMYSQKGD QLRAGANTAW VPSPTAATLH ALHYHQTNVQ SVQANI AQT EFNAEFEPLL DDLLTIPVAE NANWSAQEIQ QELDNNVQGI LGYVVRWVEQ GIGCSKVPDI HNVALMEDRA TLRISSQ HI ANWLRHGILT KEQVQASLEN MAKVVDQQNA GDPAYRPMAG NFANSCAFKA ASDLIFLGVK QPNGYTEPLL HAWRLREK E SH

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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

Concentration0.3 mg/mL
BufferpH: 7.6
GridMaterial: COPPER / Mesh: 300
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 1.8 µm / Nominal defocus min: 1.0 µm
Image recordingFilm or detector model: GATAN K2 QUANTUM (4k x 4k) / Detector mode: COUNTING / Average electron dose: 51.2 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Initial angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: cryoSPARC
Final angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: cryoSPARC
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 2.89 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 211582
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

1p7t


Chain - Chain ID: A
Output model

PDB-7yqm:
2.9-angstrom cryo-EM structure of Ecoli malate synthase G

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