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

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Basic information

Entry
Database: PDB / ID: 7yqm
Title2.9-angstrom cryo-EM structure of Ecoli malate synthase G
ComponentsMalate synthase G
KeywordsBIOSYNTHETIC PROTEIN / glyoxylate / malate / MSG / citric acid cycel / malate synthase G
Function / homology
Function and homology information


malate synthase / malate synthase activity / glyoxylate cycle / glyoxylate catabolic process / 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)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.89 Å
AuthorsWu, K.-P. / Wu, Y.-M. / Lu, Y.-C.
Funding support Taiwan, 1items
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, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 29, 2023Provider: repository / Type: Initial release
Revision 1.1Apr 12, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Apr 19, 2023Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.3Jul 3, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / em_3d_fitting_list / em_admin
Item: _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id ..._em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type / _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Malate synthase G


Theoretical massNumber of molelcules
Total (without water)80,5811
Polymers80,5811
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein Malate synthase G / MSG


Mass: 80581.344 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli DH5[alpha] (bacteria) / Strain: K12 / Gene: glcB, glc, b2976, JW2943 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P37330, malate synthase

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: 2.9-angstrom cryo-EM structure of 723-aa malate synthase G
Type: CELL / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Escherichia coli DH5[alpha] (bacteria)
Source (recombinant)Organism: Escherichia coli BL21(DE3) (bacteria)
Buffer solutionpH: 7.6
SpecimenConc.: 0.3 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in.
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1800 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 51.2 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 QUANTUM (4k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.19.2_4158: / Classification: refinement
EM software
IDNameCategory
1cryoSPARCparticle selection
4cryoSPARCCTF correction
7PHENIXmodel fitting
9cryoSPARCinitial Euler assignment
10cryoSPARCfinal Euler assignment
12cryoSPARC3D reconstruction
13Cootmodel refinement
CTF correctionType: NONE
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 2.89 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 211582 / Algorithm: FOURIER SPACE / Symmetry type: POINT
Atomic model buildingPDB-ID: 1P7T

1p7t


Pdb chain-ID: A / Accession code: 1P7T / Source name: PDB / Type: experimental model
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0035764
ELECTRON MICROSCOPYf_angle_d0.4427812
ELECTRON MICROSCOPYf_dihedral_angle_d11.7892155
ELECTRON MICROSCOPYf_chiral_restr0.039864
ELECTRON MICROSCOPYf_plane_restr0.0031034

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