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- EMDB-34030: Cryo-EM map of a dimeric form of Ecoli Malate Synthase G (MSG) -

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Basic information

Entry
Database: EMDB / ID: EMD-34030
TitleCryo-EM map of a dimeric form of Ecoli Malate Synthase G (MSG)
Map data
Sample
  • Cell: 2.9-angstrom cryo-EM structure of 723-aa malate synthase G
Keywordsglyoxylate / malate / MSG / citric acid cycel / malate synthase G / BIOSYNTHETIC PROTEIN
Biological speciesEscherichia coli DH5[alpha] (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.14 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) releaseJun 21, 2023-
Map releaseJun 21, 2023-
UpdateJun 21, 2023-
Current statusJun 21, 2023Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_34030.png

Downloads & links

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Map

FileDownload / File: emd_34030.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: 0.05
Minimum - Maximum-0.14517538 - 0.36493236
Average (Standard dev.)0.00020508848 (±0.011412177)
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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Half map: #1

Fileemd_34030_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_34030_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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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

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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: #1
Source (natural)Organism: Escherichia coli DH5[alpha] (bacteria)

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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
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

Startup modelType of model: INSILICO MODEL
Initial angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: cryoSPARC
Final angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: cryoSPARC
Final reconstructionAlgorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 4.14 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 15832
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

1p7t


Chain - Chain ID: A

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