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- PDB-8cg5: The ACP crosslinked to the KS of the cercosporin fungal non-reduc... -

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Basic information

Entry
Database: PDB / ID: 8cg5
TitleThe ACP crosslinked to the KS of the cercosporin fungal non-reducing polyketide synthase (NR-PKS) CTB1 (SAT-KS:ACP-MAT)
Components
  • Acyl carrier protein (ACP) of Non-reducing polyketide synthase CTB1
  • Non-reducing polyketide synthase CTB1
KeywordsBIOSYNTHETIC PROTEIN / Fungal non-reducing polyketide synthase (NR-PKS)
Function / homology
Function and homology information


secondary metabolite biosynthetic process / fatty acid synthase activity / phosphopantetheine binding / 3-oxoacyl-[acyl-carrier-protein] synthase activity / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / fatty acid biosynthetic process
Similarity search - Function
Polyketide product template domain / Polyketide synthase, thioesterase domain / Thioesterase / Starter unit:ACP transacylase / Starter unit:ACP transacylase in aflatoxin biosynthesis / CurL-like, PKS C-terminal / Thioesterase / Thioesterase domain / : / Polyketide and metazoan fatty acid synthase dehydratase (PKS/mFAS DH) domain profile. ...Polyketide product template domain / Polyketide synthase, thioesterase domain / Thioesterase / Starter unit:ACP transacylase / Starter unit:ACP transacylase in aflatoxin biosynthesis / CurL-like, PKS C-terminal / Thioesterase / Thioesterase domain / : / Polyketide and metazoan fatty acid synthase dehydratase (PKS/mFAS DH) domain profile. / Polyketide synthase, dehydratase domain superfamily / 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 / Beta-ketoacyl synthase, active site / Ketosynthase family 3 (KS3) active site signature. / 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
Chem-42X / Non-reducing polyketide synthase CTB1
Similarity search - Component
Biological speciesCercospora nicotianae (fungus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.7 Å
AuthorsMunoz-Hernandez, H. / Tittes, Y.U. / 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 ACP crosslinked to KS of the cercosporin fungal non-reducing polyketide synthase (NR-PKS) CTB1 (SAT-KS:ACP-MAT) at 2.7 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
Revision 1.1Nov 6, 2024Group: Data collection / Structure summary
Category: em_admin / pdbx_entry_details / pdbx_modification_feature
Item: _em_admin.last_update / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Non-reducing polyketide synthase CTB1
B: Non-reducing polyketide synthase CTB1
C: Acyl carrier protein (ACP) of Non-reducing polyketide synthase CTB1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)290,8004
Polymers290,4033
Non-polymers3971
Water00
1


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

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Components

#1: Protein Non-reducing polyketide synthase CTB1 / Cercosporin toxin biosynthesis cluster protein 1


Mass: 140255.000 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cercospora nicotianae (fungus) / Gene: CTB1 / Production host: Escherichia coli (E. coli)
References: UniProt: Q6DQW3, Transferases; Acyltransferases; Transferring groups other than aminoacyl groups
#2: Protein Acyl carrier protein (ACP) of Non-reducing polyketide synthase CTB1 / Cercosporin toxin biosynthesis cluster protein 1


Mass: 9892.837 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Acyl carrier protein (ACP) of Non-reducing polyketide synthase CTB1
Source: (gene. exp.) Cercospora nicotianae (fungus) / Gene: CTB1 / Production host: Escherichia coli (E. coli)
References: UniProt: Q6DQW3, Transferases; Acyltransferases; Transferring groups other than aminoacyl groups
#3: Chemical ChemComp-42X / N~3~-[(2R)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-N-[2-(propanoylamino)ethyl]-beta-alaninamide


Mass: 397.361 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H28N3O8P / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationY

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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: ACP crosslinked to the KS of the condensing region of the non-reducing polyketide synthase CTB1
Type: COMPLEX / Entity ID: #1-#2 / Source: RECOMBINANT
Source (natural)Organism: Cercospora nicotianae (fungus)
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: 3300 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: 51 e/Å2 / Film or detector model: GATAN K2 QUANTUM (4k x 4k)
Image scansMovie frames/image: 42

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Processing

SoftwareName: PHENIX / Version: 1.20.1_4487: / 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
16PHENIXmodel refinement
CTF correctionType: NONE
Particle selectionNum. of particles selected: 936235
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 2.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 255766 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00420454
ELECTRON MICROSCOPYf_angle_d0.56427866
ELECTRON MICROSCOPYf_dihedral_angle_d5.8232851
ELECTRON MICROSCOPYf_chiral_restr0.043182
ELECTRON MICROSCOPYf_plane_restr0.0063660

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