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Yorodumi- EMDB-23602: Cryo-EM structure of unliganded octameric prenyltransferase domai... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-23602 | |||||||||
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Title | Cryo-EM structure of unliganded octameric prenyltransferase domain of Phomopsis amygdali fusicoccadiene synthase, reconstruction in C1 | |||||||||
Map data | Unfiltered, sharpened, asymmetric reconstruction of PaFS prenyltransferase domain | |||||||||
Sample |
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Function / homology | Function and homology information fusicocca-2,10(14)-diene synthase / alcohol biosynthetic process / mycotoxin biosynthetic process / ketone biosynthetic process / geranylgeranyl diphosphate synthase / farnesyltranstransferase activity / isoprenoid biosynthetic process / lyase activity / metal ion binding Similarity search - Function | |||||||||
Biological species | Phomopsis amygdali (fungus) / Diaporthe amygdali (fungus) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.18 Å | |||||||||
Authors | Faylo JL / van Eeuwen T | |||||||||
Funding support | United States, 1 items
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Citation | Journal: Nat Commun / Year: 2021 Title: Structural insight on assembly-line catalysis in terpene biosynthesis. Authors: Jacque L Faylo / Trevor van Eeuwen / Hee Jong Kim / Jose J Gorbea Colón / Benjamin A Garcia / Kenji Murakami / David W Christianson / Abstract: Fusicoccadiene synthase from Phomopsis amygdali (PaFS) is a unique bifunctional terpenoid synthase that catalyzes the first two steps in the biosynthesis of the diterpene glycoside Fusicoccin A, a ...Fusicoccadiene synthase from Phomopsis amygdali (PaFS) is a unique bifunctional terpenoid synthase that catalyzes the first two steps in the biosynthesis of the diterpene glycoside Fusicoccin A, a mediator of 14-3-3 protein interactions. The prenyltransferase domain of PaFS generates geranylgeranyl diphosphate, which the cyclase domain then utilizes to generate fusicoccadiene, the tricyclic hydrocarbon skeleton of Fusicoccin A. Here, we use cryo-electron microscopy to show that the structure of full-length PaFS consists of a central octameric core of prenyltransferase domains, with the eight cyclase domains radiating outward via flexible linker segments in variable splayed-out positions. Cryo-electron microscopy and chemical crosslinking experiments additionally show that compact conformations can be achieved in which cyclase domains are more closely associated with the prenyltransferase core. This structural analysis provides a framework for understanding substrate channeling, since most of the geranylgeranyl diphosphate generated by the prenyltransferase domains remains on the enzyme for cyclization to form fusicoccadiene. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_23602.map.gz | 191.6 MB | EMDB map data format | |
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Header (meta data) | emd-23602-v30.xml emd-23602.xml | 20.8 KB 20.8 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_23602_fsc.xml | 13.7 KB | Display | FSC data file |
Images | emd_23602.png | 130 KB | ||
Masks | emd_23602_msk_1.map | 216 MB | Mask map | |
Others | emd_23602_additional_1.map.gz emd_23602_half_map_1.map.gz emd_23602_half_map_2.map.gz | 108.5 MB 200.2 MB 200.2 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-23602 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-23602 | HTTPS FTP |
-Validation report
Summary document | emd_23602_validation.pdf.gz | 575.6 KB | Display | EMDB validaton report |
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Full document | emd_23602_full_validation.pdf.gz | 575.2 KB | Display | |
Data in XML | emd_23602_validation.xml.gz | 21.6 KB | Display | |
Data in CIF | emd_23602_validation.cif.gz | 27.8 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-23602 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-23602 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_23602.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Unfiltered, sharpened, asymmetric reconstruction of PaFS prenyltransferase domain | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.142 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Mask #1
File | emd_23602_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Additional map: Unsharpened, unfiltered, asymmetric reconstruction of PaFS prenyltransferase domain...
File | emd_23602_additional_1.map | ||||||||||||
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Annotation | Unsharpened, unfiltered, asymmetric reconstruction of PaFS prenyltransferase domain | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: half-map of PaFS prenyltransferase domain
File | emd_23602_half_map_1.map | ||||||||||||
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Annotation | half-map of PaFS prenyltransferase domain | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: half-map of PaFS prenyltransferase domain
File | emd_23602_half_map_2.map | ||||||||||||
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Annotation | half-map of PaFS prenyltransferase domain | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Unliganded Phomopsis amygdali fusicoccadiene synthase octamer
Entire | Name: Unliganded Phomopsis amygdali fusicoccadiene synthase octamer |
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Components |
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-Supramolecule #1: Unliganded Phomopsis amygdali fusicoccadiene synthase octamer
Supramolecule | Name: Unliganded Phomopsis amygdali fusicoccadiene synthase octamer type: complex / ID: 1 / Parent: 0 / Macromolecule list: all / Details: Octamer of C-terminal prenyltransferase domain |
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Source (natural) | Organism: Phomopsis amygdali (fungus) |
Recombinant expression | Organism: Escherichia coli BL21(DE3) (bacteria) / Recombinant strain: BL21-CodonPlus (DE3)-RIL / Recombinant plasmid: pET28a(+) |
Molecular weight | Theoretical: 392 KDa |
-Macromolecule #1: Fusicoccadiene synthase
Macromolecule | Name: Fusicoccadiene synthase / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO / EC number: fusicocca-2,10(14)-diene synthase |
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Source (natural) | Organism: Diaporthe amygdali (fungus) |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MEFKYSEVVE PSTYYTEGLC EGIDVRKSKF TTLEDRGAIR AHEDWNKHIG PCGEYRGTLG PRFSFISVA VPECIPERLE VISYANEFAF LHDDVTDHVG HDTGEVENDE MMTVFLEAAH T GAIDTSNK VDIRRAGKKR IQSQLFLEML AIDPECAKTT MKSWARFVEV ...String: MEFKYSEVVE PSTYYTEGLC EGIDVRKSKF TTLEDRGAIR AHEDWNKHIG PCGEYRGTLG PRFSFISVA VPECIPERLE VISYANEFAF LHDDVTDHVG HDTGEVENDE MMTVFLEAAH T GAIDTSNK VDIRRAGKKR IQSQLFLEML AIDPECAKTT MKSWARFVEV GSSRQHETRF VE LAKYIPY RIMDVGEMFW FGLVTFGLGL HIPDHELELC RELMANAWIA VGLQNDIWSW PKE RDAATL HGKDHVVNAI WVLMQEHQTD VDGAMQICRK LIVEYVAKYL EVIEATKNDE SISL DLRKY LDAMLYSISG NVVWSLECPR YNPDVSFNKT QLEWMRQGLP SLESCPVLAR SPEID SDES AVSPTADESD STEDSLGSGS RQDSSLSTGL SLSPVHSNEG KDLQRVDTDH IFFEKA VLE APYDYIASMP SKGVRDQFID ALNDWLRVPD VKVGKIKDAV RVLHNSSLLL DDFQDNS PL RRGKPSTHNI FGSAQTVNTA TYSIIKAIGQ IMEFSAGESV QEVMNSIMIL FQGQAMDL F WTYNGHVPSE EEYYRMIDQK TGQLFSIATS LLLNAADNEI PRTKIQSCLH RLTRLLGRC FQIRDDYQNL VSADYTKQKG FCEDLDEGKW SLALIHMIHK QRSHMALLNV LSTGRKHGGM TLEQKQFVL DIIEEEKSLD YTRSVMMDLH VQLRAEIGRI EILLDSPNPA MRLLLELLRV |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 2 mg/mL | ||||||||||||
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Buffer | pH: 7.5 Component:
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Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 298 K / Instrument: FEI VITROBOT MARK IV / Details: Blot for 4.5 seconds before plunging.. | ||||||||||||
Details | This sample was monodisperse |
-Electron microscopy
Microscope | FEI TALOS ARCTICA |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Number grids imaged: 1 / Number real images: 1500 / Average electron dose: 43.0 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm |
Sample stage | Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Talos Arctica / Image courtesy: FEI Company |
+Image processing
-Atomic model buiding 1
Initial model | PDB ID: |
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