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Yorodumi- EMDB-45956: Cryo-EM structure of the Carboxyltransferase Domain of Trichoplus... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-45956 | |||||||||
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Title | Cryo-EM structure of the Carboxyltransferase Domain of Trichoplusia ni Acetyl-Coenzyme A Carboxylase | |||||||||
Map data | cryo-EM map of the Carboxyltransferase Domain of Trichoplusia ni Acetyl-Coenzyme A Carboxylase | |||||||||
Sample |
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Keywords | Trichoplusia ni / Carboxyltransferase Domain / Acetyl-Coenzyme A Carboxylase / Cryo-EM / Pest Control / TRANSFERASE | |||||||||
Function / homology | Function and homology information malonyl-CoA biosynthetic process / acetyl-CoA carboxylase activity / fatty acid biosynthetic process / mitochondrion / ATP binding / metal ion binding Similarity search - Function | |||||||||
Biological species | Trichoplusia ni (cabbage looper) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.12 Å | |||||||||
Authors | Liu B / Wang D / Bu F / Yang G | |||||||||
Funding support | 1 items
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Citation | Journal: J Biol Chem / Year: 2024 Title: Structure of the endogenous insect acetyl-coA carboxylase carboxyltransferase domain. Authors: Dong Wang / Fan Bu / Ge Yang / Hannah Brenke / Bin Liu / Abstract: Acetyl-coenzyme A carboxylases (ACCs) are pivotal in fatty acid metabolism, converting acetyl-CoA to malonyl-CoA. While ACCs in humans, plants, and microbes have been extensively studied, insect ...Acetyl-coenzyme A carboxylases (ACCs) are pivotal in fatty acid metabolism, converting acetyl-CoA to malonyl-CoA. While ACCs in humans, plants, and microbes have been extensively studied, insect ACCs, crucial for lipid biosynthesis and physiological processes, remain relatively unexplored. Unlike mammals, which have ACC1 and ACC2 in different tissues, insects possess a single ACC gene, underscoring its unique role in their metabolism. Noctuid moths, such as Trichoplusia ni, are major agricultural pests causing significant crop damage and economic loss. Their resistance to both biological and synthetic insecticides complicates pest control. Recent research has introduced cyclic ketoenols as novel insecticides targeting ACCs, yet structural information to guide their design is limited. Here, we present a 3.12 Å cryo-EM structure of the carboxyltransferase (CT) domain of T. ni ACC, offering the first detailed structural insights into insect ACCs. Our structural comparisons with ACC CT domains from other species and analyses of drug binding sites can guide future drug modification and design. Notably, unique interactions between the CT and the central domain in T. ni ACC provide new directions for studying the ACC holoenzyme. These findings contribute valuable information for pest control and basic biological understanding of lipid biosynthesis. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_45956.map.gz | 108.2 MB | EMDB map data format | |
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Header (meta data) | emd-45956-v30.xml emd-45956.xml | 19.1 KB 19.1 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_45956_fsc.xml | 12.7 KB | Display | FSC data file |
Images | emd_45956.png | 72.6 KB | ||
Filedesc metadata | emd-45956.cif.gz | 6 KB | ||
Others | emd_45956_additional_1.map.gz emd_45956_half_map_1.map.gz emd_45956_half_map_2.map.gz | 188.9 MB 200.2 MB 200.2 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-45956 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-45956 | HTTPS FTP |
-Validation report
Summary document | emd_45956_validation.pdf.gz | 861.4 KB | Display | EMDB validaton report |
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Full document | emd_45956_full_validation.pdf.gz | 861 KB | Display | |
Data in XML | emd_45956_validation.xml.gz | 20.9 KB | Display | |
Data in CIF | emd_45956_validation.cif.gz | 26.8 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-45956 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-45956 | HTTPS FTP |
-Related structure data
Related structure data | 9cv6M M: atomic model generated by this map |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_45956.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Annotation | cryo-EM map of the Carboxyltransferase Domain of Trichoplusia ni Acetyl-Coenzyme A Carboxylase | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.88533 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Additional map: cryo-EM sharpened map of the Carboxyltransferase Domain of...
File | emd_45956_additional_1.map | ||||||||||||
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Annotation | cryo-EM sharpened map of the Carboxyltransferase Domain of Trichoplusia ni Acetyl-Coenzyme A Carboxylase | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: half map A of the Carboxyltransferase Domain of...
File | emd_45956_half_map_1.map | ||||||||||||
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Annotation | half map A of the Carboxyltransferase Domain of Trichoplusia ni Acetyl-Coenzyme A Carboxylase | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: half map B of the Carboxyltransferase Domain of...
File | emd_45956_half_map_2.map | ||||||||||||
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Annotation | half map B of the Carboxyltransferase Domain of Trichoplusia ni Acetyl-Coenzyme A Carboxylase | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Trichoplusia ni Acetyl-Coenzyme A Carboxylase
Entire | Name: Trichoplusia ni Acetyl-Coenzyme A Carboxylase |
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Components |
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-Supramolecule #1: Trichoplusia ni Acetyl-Coenzyme A Carboxylase
Supramolecule | Name: Trichoplusia ni Acetyl-Coenzyme A Carboxylase / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Trichoplusia ni (cabbage looper) |
-Macromolecule #1: Acetyl-CoA carboxylase
Macromolecule | Name: Acetyl-CoA carboxylase / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Trichoplusia ni (cabbage looper) |
Molecular weight | Theoretical: 87.732602 KDa |
Sequence | String: DYLQQKRFLA TSQGTTYVYD IPDMFRQMVE RRWRECIEEG SVDGPQPDNV MTLVELVVEP DGERRVVEVT RLPGQNNVGM VAWRLTLYT PECPDGRDIV LIANDLTYYM GSFGPQEDWV YFKASQYARE LKIPRIYISV NSGARIGVAE EVKSDFNVAW L DAERPERG ...String: DYLQQKRFLA TSQGTTYVYD IPDMFRQMVE RRWRECIEEG SVDGPQPDNV MTLVELVVEP DGERRVVEVT RLPGQNNVGM VAWRLTLYT PECPDGRDIV LIANDLTYYM GSFGPQEDWV YFKASQYARE LKIPRIYISV NSGARIGVAE EVKSDFNVAW L DAERPERG FKYLYLTPEV YSKLGALGSV KTELIEDEGE SRYRITDIIG KEDGLGVECL RDAGLIAGET AQAYEDIVTI SI VTCRAIG IGSYIVRLGH RVIQVESSYI ILTGYAALNK VLGRAVYASN NQLGGVQVMH HNGVSHAVAP SDLEAVRTAL RWL AFVPKD KLSTVPILRV SDPVDRPVEW KPPRAAHDPR LMLAGDAARA GFFDVGSFDE IMQPWAQTVI TGRARLGGIP VGVI AVETR TVELTQPADP ANLDSEAKTL QQAGQVWFPD SAYKTAQAIN DFSRENLPIM IFANWRGFSG GQKDMYEQIL KFGAE IVRA LRGATAPVLV YIPPGAELRG GAWAVVDPSV NSLRMEMYAD PEARGGVLEA EGIVEVKFKQ RDILKTMHRL DPELLR TGA RISELKEQIK EISKGLDRRG SVDESLIRTD AGRAAETRVR ELETELLAAE KTAKAREKEL SPIYHEIAVQ FAELHDT AE RMLEKGCIFE IIPWRDSRRL FYWRLKRLLR QNEQERRVQA AVKPADNMQQ GPAAATLRRW FTEDRGETQS HQWEHDNE A VCKWLEAQAG DDNSVLERNL RAIHQDALMQ AVNNLVLELT PSQRSEFIRK LSALEMEQ UniProtKB: Acetyl-CoA carboxylase isoform X5 |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 8 |
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Grid | Model: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Temperature | Min: 63.0 K / Max: 77.0 K |
Specialist optics | Energy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV |
Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Digitization - Dimensions - Width: 4092 pixel / Digitization - Dimensions - Height: 5760 pixel / Number grids imaged: 1 / Number real images: 6463 / Average exposure time: 1.7 sec. / Average electron dose: 53.7 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 130000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
+Image processing
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: OTHER / Overall B value: 47.91 |
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Output model | PDB-9cv6: |