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- PDB-9c8s: CryoEM structure of Cryptococcus neoformans H99 Acetyl-CoA Synthe... -

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Basic information

Entry
Database: PDB / ID: 9c8s
TitleCryoEM structure of Cryptococcus neoformans H99 Acetyl-CoA Synthetase in complex with adenosine-5'-ethylphosphate
ComponentsAcetyl-coenzyme A synthetase
KeywordsLIGASE / trimer
Function / homology
Function and homology information


acetate-CoA ligase / acetate-CoA ligase activity / acetyl-CoA biosynthetic process from acetate / AMP binding / ATP binding / metal ion binding / cytosol
Similarity search - Function
Acetate-CoA ligase / Acetyl-coenzyme A synthetase, N-terminal domain / Acetyl-coenzyme A synthetase N-terminus / ANL, N-terminal domain / AMP-binding enzyme C-terminal domain / AMP-binding enzyme, C-terminal domain / AMP-binding, conserved site / Putative AMP-binding domain signature. / AMP-dependent synthetase/ligase / AMP-binding enzyme / AMP-binding enzyme, C-terminal domain superfamily
Similarity search - Domain/homology
5'-O-[(S)-ethoxy(hydroxy)phosphoryl]adenosine / Acetyl-coenzyme A synthetase
Similarity search - Component
Biological speciesCryptococcus neoformans var. grubii H99 (fungus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.37 Å
AuthorsXu, Z. / Schnicker, N.J. / Jezeski, A.J. / Krysan, D.J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)5R01AI161973 United States
CitationJournal: Not Published
Title: CryoEM structure of Cryptococcus neoformans H99 Acetyl-CoA Synthetase in complex with adenosine-5'-ethylphosphate
Authors: Xu, Z. / Schnicker, N.J. / Jezeski, A.J. / Krysan, D.J.
History
DepositionJun 12, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 3, 2024Provider: repository / Type: Initial release
Revision 1.1Jan 15, 2025Group: Data collection / Database references / Structure summary
Category: citation / em_admin / pdbx_entry_details
Item: _citation.journal_abbrev / _citation.unpublished_flag ..._citation.journal_abbrev / _citation.unpublished_flag / _em_admin.last_update / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Acetyl-coenzyme A synthetase
B: Acetyl-coenzyme A synthetase
C: Acetyl-coenzyme A synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)233,5536
Polymers232,4273
Non-polymers1,1263
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein Acetyl-coenzyme A synthetase


Mass: 77475.750 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cryptococcus neoformans var. grubii H99 (fungus)
Gene: CNAG_00797 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: J9VFT1, acetate-CoA ligase
#2: Chemical ChemComp-WTA / 5'-O-[(S)-ethoxy(hydroxy)phosphoryl]adenosine


Mass: 375.274 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C12H18N5O7P / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationN

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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: Cryptococcus neoformans H99 Acetyl-CoA Synthetase / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Molecular weightValue: 0.238 MDa / Experimental value: YES
Source (natural)Organism: Cryptococcus neoformans var. grubii H99 (fungus)
Source (recombinant)Organism: Escherichia coli BL21(DE3) (bacteria)
Buffer solutionpH: 7.5
Details: 10 mM Tris pH7.5, 150 mM NaCl, 4mM MgCl2 and 10mM DTT
Buffer component
IDConc.NameFormulaBuffer-ID
110 mMTrisTris1
2150 mMsodium chlorideNaCl1
34 mMmagnesium chlorideMgCl21
410 mMDithiothreitolDTT1
SpecimenConc.: 1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 95 % / Chamber temperature: 277 K

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Electron microscopy imaging

MicroscopyModel: TFS GLACIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 3000 nm / Nominal defocus min: 250 nm
Image recordingElectron dose: 40 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k) / Num. of grids imaged: 1

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Processing

CTF correctionType: NONE
SymmetryPoint symmetry: C3 (3 fold cyclic)
3D reconstructionResolution: 2.37 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 4519578 / Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 31.2 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.003512738
ELECTRON MICROSCOPYf_angle_d0.545917420
ELECTRON MICROSCOPYf_chiral_restr0.04681829
ELECTRON MICROSCOPYf_plane_restr0.00512259
ELECTRON MICROSCOPYf_dihedral_angle_d5.06771851

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