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- PDB-8cg4: The organise full-length structure of the fungal non-reducing pol... -

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Basic information

Entry
Database: PDB / ID: 8cg4
TitleThe organise full-length structure of the fungal non-reducing polyketide synthase (NR-PKS) PksA
ComponentsNorsolorinic acid synthase
KeywordsBIOSYNTHETIC PROTEIN / Fungal non-reducing polyketide synthase (NR-PKS)
Function / homology
Function and homology information


noranthrone synthase / aflatoxin biosynthetic process / norsolorinate anthrone synthase activity / phosphopantetheine binding / identical protein binding
Similarity search - Function
Polyketide product template domain / Starter unit:ACP transacylase / Starter unit:ACP transacylase in aflatoxin biosynthesis / CurL-like, PKS C-terminal / Thioesterase / Thioesterase domain / : / Polyketide synthase dehydratase N-terminal domain / Polyketide synthase, dehydratase domain superfamily / : ...Polyketide product template domain / Starter unit:ACP transacylase / Starter unit:ACP transacylase in aflatoxin biosynthesis / CurL-like, PKS C-terminal / Thioesterase / Thioesterase domain / : / Polyketide synthase dehydratase N-terminal domain / Polyketide synthase, dehydratase domain superfamily / : / Polyketide and metazoan fatty acid synthase dehydratase (PKS/mFAS DH) domain profile. / Malonyl-CoA ACP transacylase, ACP-binding / : / Acyl transferase / Acyl transferase domain / Acyl transferase domain in polyketide synthase (PKS) enzymes. / Acyl transferase domain superfamily / Acyl transferase/acyl hydrolase/lysophospholipase / Polyketide synthase, phosphopantetheine-binding domain / Phosphopantetheine attachment site / Beta-ketoacyl synthase / Ketosynthase family 3 (KS3) domain profile. / Beta-ketoacyl synthase, N-terminal / Beta-ketoacyl synthase, C-terminal / Polyketide synthase, beta-ketoacyl synthase domain / Beta-ketoacyl synthase, N-terminal domain / Beta-ketoacyl synthase, C-terminal domain / Thiolase-like / Phosphopantetheine attachment site / ACP-like superfamily / Carrier protein (CP) domain profile. / Phosphopantetheine binding ACP domain / Alpha/Beta hydrolase fold
Similarity search - Domain/homology
Norsolorinic acid synthase
Similarity search - Component
Biological speciesAspergillus parasiticus (mold)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.6 Å
AuthorsMunoz-Hernandez, H. / Maier, T.
Funding supportEuropean Union, Switzerland, 2items
OrganizationGrant numberCountry
European CommissionID: 845941European Union
Swiss National Science Foundation Switzerland
CitationJournal: To Be Published
Title: CryoEM structure of the Aspergilus sp. fungal non-reducing polyketide synthase (NR-PKS) PksA at 2.6 Angstroms resolution
Authors: Munoz-Hernandez, H. / Maier, T.
History
DepositionFeb 3, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 21, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Norsolorinic acid synthase
B: Norsolorinic acid synthase


Theoretical massNumber of molelcules
Total (without water)475,4832
Polymers475,4832
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, electron microscopy, microscopy, Mass photometry with Refeyn OneMP
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein Norsolorinic acid synthase / NSAS / Aflatoxin biosynthesis polyketide synthase / Aflatoxin biosynthesis protein C / Polyketide synthase A


Mass: 237741.250 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aspergillus parasiticus (mold) / Gene: aflC, pksA, pksL1, P875_00052995 / Production host: Escherichia coli (E. coli) / References: UniProt: Q12053, noranthrone 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: The full-length Non-reducing polyketide synthase PksA / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 0.45 MDa / Experimental value: YES
Source (natural)Organism: Aspergillus parasiticus (mold)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
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: SPOT SCAN
Electron lensMode: BRIGHT FIELD / Nominal magnification: 165000 X / Nominal defocus max: 3000 nm / Nominal defocus min: 600 nm / Calibrated defocus min: 900 nm / Calibrated defocus max: 3200 nm / Cs: 2.7 mm / C2 aperture diameter: 70 µm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 60 e/Å2 / Film or detector model: GATAN K2 QUANTUM (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 6479
EM imaging opticsEnergyfilter name: GIF Bioquantum / Energyfilter slit width: 20 eV
Image scansMovie frames/image: 35

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Processing

SoftwareName: PHENIX / Version: 1.20rc4_4425: / Classification: refinement
EM software
IDNameCategory
1cryoSPARCparticle selection
2SerialEMimage acquisition
4cryoSPARCCTF correction
7UCSF Chimeramodel fitting
8UCSF ChimeraXmodel fitting
9Cootmodel fitting
10PHENIXmodel fitting
12cryoSPARCinitial Euler assignment
13cryoSPARCfinal Euler assignment
14cryoSPARCclassification
15cryoSPARC3D reconstruction
CTF correctionType: NONE
Particle selectionNum. of particles selected: 468256
SymmetryPoint symmetry: C2 (2 fold cyclic)
3D reconstructionResolution: 2.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 361377 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00419768
ELECTRON MICROSCOPYf_angle_d0.58626888
ELECTRON MICROSCOPYf_dihedral_angle_d31.8372696
ELECTRON MICROSCOPYf_chiral_restr0.0453042
ELECTRON MICROSCOPYf_plane_restr0.0063502

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