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- EMDB-16631: The ACP crosslinked to the KS of the cercosporin fungal non-reduc... -

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Basic information

Entry
Database: EMDB / ID: EMD-16631
TitleThe ACP crosslinked to the KS of the cercosporin fungal non-reducing polyketide synthase (NR-PKS) CTB1 (SAT-KS:ACP-MAT)
Map data
Sample
  • Complex: ACP crosslinked to the KS of the condensing region of the non-reducing polyketide synthase CTB1
    • Protein or peptide: Non-reducing polyketide synthase CTB1
    • Protein or peptide: Acyl carrier protein (ACP) of Non-reducing polyketide synthase CTB1
  • Ligand: N~3~-[(2R)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-N-[2-(propanoylamino)ethyl]-beta-alaninamide
KeywordsFungal non-reducing polyketide synthase (NR-PKS) / BIOSYNTHETIC PROTEIN
Function / homology
Function and homology information


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 / Polyketide and metazoan fatty acid synthase dehydratase (PKS/mFAS DH) domain profile. / Thioesterase / Thioesterase domain / Polyketide synthase, dehydratase domain superfamily / Malonyl-CoA ACP transacylase, ACP-binding ...Polyketide product template domain / Polyketide synthase, thioesterase domain / Thioesterase / Starter unit:ACP transacylase / Starter unit:ACP transacylase in aflatoxin biosynthesis / Polyketide and metazoan fatty acid synthase dehydratase (PKS/mFAS DH) domain profile. / Thioesterase / Thioesterase domain / Polyketide synthase, dehydratase domain superfamily / Malonyl-CoA ACP transacylase, ACP-binding / Acyl transferase domain superfamily / Acyl transferase / Acyl transferase domain / Acyl transferase domain in polyketide synthase (PKS) enzymes. / Acyl transferase/acyl hydrolase/lysophospholipase / Ketosynthase family 3 (KS3) domain profile. / Polyketide synthase, phosphopantetheine-binding domain / Phosphopantetheine attachment site / Beta-ketoacyl synthase / Beta-ketoacyl synthase, active site / Ketosynthase family 3 (KS3) active site signature. / Polyketide synthase, beta-ketoacyl synthase domain / Beta-ketoacyl synthase, N-terminal / Beta-ketoacyl synthase, C-terminal / 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
Non-reducing polyketide synthase CTB1
Similarity search - Component
Biological speciesCercospora nicotianae (fungus)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.7 Å
AuthorsMunoz-Hernandez H / Tittes YU / Maier T
Funding supportEuropean Union, Switzerland, 2 items
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, 2023-
Header (metadata) releaseFeb 21, 2024-
Map releaseFeb 21, 2024-
UpdateFeb 21, 2024-
Current statusFeb 21, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_16631.png

Downloads & links

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Map

FileDownload / File: emd_16631.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.82 Å/pix.
x 384 pix.
= 314.88 Å		0.82 Å/pix.
x 384 pix.
= 314.88 Å		0.82 Å/pix.
x 384 pix.
= 314.88 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.82 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.055
Minimum - Maximum-0.28386235 - 0.5348662
Average (Standard dev.)-0.0002398867 (±0.013880063)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 314.88 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_16631_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_16631_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 : ACP crosslinked to the KS of the condensing region of the non-red...

EntireName: ACP crosslinked to the KS of the condensing region of the non-reducing polyketide synthase CTB1
Components
  • Complex: ACP crosslinked to the KS of the condensing region of the non-reducing polyketide synthase CTB1
    • Protein or peptide: Non-reducing polyketide synthase CTB1
    • Protein or peptide: Acyl carrier protein (ACP) of Non-reducing polyketide synthase CTB1
  • Ligand: N~3~-[(2R)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-N-[2-(propanoylamino)ethyl]-beta-alaninamide

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Supramolecule #1: ACP crosslinked to the KS of the condensing region of the non-red...

SupramoleculeName: ACP crosslinked to the KS of the condensing region of the non-reducing polyketide synthase CTB1
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Cercospora nicotianae (fungus)

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Macromolecule #1: Non-reducing polyketide synthase CTB1

MacromoleculeName: Non-reducing polyketide synthase CTB1 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
EC number: Transferases; Acyltransferases; Transferring groups other than aminoacyl groups
Source (natural)Organism: Cercospora nicotianae (fungus)
Molecular weightTheoretical: 140.255 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MEDGAQMRVV AFGDQTYDCS EAVSQLLRVR DDAIVVDFLE RAPAVLKAEL ARLSSEQQEE TPRFATLAEL VPRYRAGTLN PAVSQALTC IAQLGLFIRQ HSSGQEAYPT AHDSCITGVA TGALTAVAVG SASSVTALVP LALHTVAVAV RLGARAWEIG S CLADARRG ...String:
MEDGAQMRVV AFGDQTYDCS EAVSQLLRVR DDAIVVDFLE RAPAVLKAEL ARLSSEQQEE TPRFATLAEL VPRYRAGTLN PAVSQALTC IAQLGLFIRQ HSSGQEAYPT AHDSCITGVA TGALTAVAVG SASSVTALVP LALHTVAVAV RLGARAWEIG S CLADARRG ANGRYASWTS AVGGISPQDL QDRISAYTAE QALASVSVPY LSAAVGPGQS SVSAAPVILD AFLSTLLRPL TT TRLPITA PYHAPHLFTA KDVQHVTDCL PPSEAWPTVR IPIISFSRDE AVSRGASFPA AMSEAVRDCL IRPIALDRMA VSI ANHARD LGKDSVLPSP IALSFSDKLG PQVNSHLPGA KAPTPELTSK SIPSAIGAEQ QPMAKSPIAI LAASGRFPQS SSMD QFWDV LINGVDTHEL VPPTRWNAAT HVSEDPKAKN VSGTGFGCWL HEAGEFDAAY FNMSPREAPQ VDPAQRLALL TATEA LEQA GVVPNRTSST QKNRVGVWYG ATSNDWMETN SAQNVDTYFI PGGNRAFIPG RVNYFHKFSG PSYTIDTACS SSLAAL HMA CNALWRGEVD TAIVGGTNVL TNPDMTAGLD AGHFLSRSGN CKTFDDEADG YCRGEAVVTL ILKRLPDAQA DKDPIQA SI LGIATNHSAE AASITRPHAG AQQDLFQQVL TETGLTANDI SVCEMHGTGT QAGDSGETTS VVETLAPLNR SGSAVRTT P LYIGAVKSNV GHAESAAGVS SLAKILLMLK HSKIPPHVGI KTKLNHRLPD LAARNTHIAR SEVPWPRPKN GKRRVLLNN FSAAGGNTCL VLEDAPEPED SQEVDPREHH IVALSAKTPD SMVNNLTNMI TWIDKHSGDS LATLPQLSYT TTARRVHHRH RAVATGTDL LQIRSSLQEQ LDRRVSGERS IPHPPNGPSF VLAFTGQGSA FAGMGVDLYK RFASFRSDIA RYDQICEGMS L PSIKAMFE DEKVFSTASP TLQQLTHVCF QMALYRLWKS LGVQAKAVVG HALGEYAALY AAGVLSQSDT LYLVGRRAQL ME KHLSQGT HAMLAVRAKE EAIVAAIDGP PGEAYEFSCR NGEQRNVLGG TVAQIQAAKA ALEAKKIRCQ YLDTPMAFHT GQV DPILPE LLQVAAACSI QDPQIPVISP AYGKVIRSAK DFQPEYFTHH CRSSVNMVDA LQSAVEEGLL DKNVIGLEIG PGPV VTQFV KEAVGTTMQT FASINKDKDT WQLMTQALAK FYLAGASVEW SRYHEDFPGA QKVLELPAYG WALKNYWLQY VNDWS LRKG DPAVVVAASA AALEHHHHHH

UniProtKB: Non-reducing polyketide synthase CTB1

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Macromolecule #2: Acyl carrier protein (ACP) of Non-reducing polyketide synthase CTB1

MacromoleculeName: Acyl carrier protein (ACP) of Non-reducing polyketide synthase CTB1
type: protein_or_peptide / ID: 2
Details: Acyl carrier protein (ACP) of Non-reducing polyketide synthase CTB1
Number of copies: 1 / Enantiomer: LEVO
EC number: Transferases; Acyltransferases; Transferring groups other than aminoacyl groups
Source (natural)Organism: Cercospora nicotianae (fungus)
Molecular weightTheoretical: 9.892837 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
GSHMDPSPNE IGTVWRDALK ILSEESGLTD EELTDDTSFA DVGVDSLMSL VITSRLRDEL DIDFPDRALF EECQTIFDLR KRFSGSTE

UniProtKB: Non-reducing polyketide synthase CTB1

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Macromolecule #3: N~3~-[(2R)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-N-[2-...

MacromoleculeName: N~3~-[(2R)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-N-[2-(propanoylamino)ethyl]-beta-alaninamide
type: ligand / ID: 3 / Number of copies: 1 / Formula: 42X
Molecular weightTheoretical: 397.361 Da
Chemical component information

ChemComp-42X:
N~3~-[(2R)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-N-[2-(propanoylamino)ethyl]-beta-alaninamide

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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

BufferpH: 7.8
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Calibrated defocus max: 3.3000000000000003 µm / Calibrated defocus min: 0.9 µm / Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 0.6 µm / Nominal magnification: 165000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K2 QUANTUM (4k x 4k) / Average electron dose: 51.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 936235
Startup modelType of model: INSILICO MODEL
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final 3D classificationSoftware - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 2.7 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 255766

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-8cg5:
The ACP crosslinked to the KS of the cercosporin fungal non-reducing polyketide synthase (NR-PKS) CTB1 (SAT-KS:ACP-MAT)

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