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- EMDB-45956: Cryo-EM structure of the Carboxyltransferase Domain of Trichoplus... -

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Basic information

Entry
Database: EMDB / ID: EMD-45956
TitleCryo-EM structure of the Carboxyltransferase Domain of Trichoplusia ni Acetyl-Coenzyme A Carboxylase
Map datacryo-EM map of the Carboxyltransferase Domain of Trichoplusia ni Acetyl-Coenzyme A Carboxylase
Sample
  • Complex: Trichoplusia ni Acetyl-Coenzyme A Carboxylase
    • Protein or peptide: Acetyl-CoA carboxylase
KeywordsTrichoplusia 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
Acetyl-CoA carboxylase, central domain / : / : / Acetyl-CoA carboxylase, central region / Acetyl-CoA carboxylase, BT domain / Acetyl-coenzyme A carboxyltransferase, C-terminal / Acetyl-coenzyme A (CoA) carboxyltransferase C-terminal domain profile. / Acetyl-coenzyme A carboxyltransferase, N-terminal / Acetyl-coenzyme A (CoA) carboxyltransferase N-terminal domain profile. / Acetyl-CoA carboxylase ...Acetyl-CoA carboxylase, central domain / : / : / Acetyl-CoA carboxylase, central region / Acetyl-CoA carboxylase, BT domain / Acetyl-coenzyme A carboxyltransferase, C-terminal / Acetyl-coenzyme A (CoA) carboxyltransferase C-terminal domain profile. / Acetyl-coenzyme A carboxyltransferase, N-terminal / Acetyl-coenzyme A (CoA) carboxyltransferase N-terminal domain profile. / Acetyl-CoA carboxylase / Carboxyl transferase domain / Biotin-binding site / Biotin-requiring enzymes attachment site. / Biotin carboxylase-like, N-terminal domain / Biotin carboxylase, C-terminal / Biotin carboxylation domain / Biotin carboxylase, N-terminal domain / Biotin carboxylase C-terminal domain / Biotin carboxylation domain profile. / Biotin carboxylase C-terminal domain / Carbamoyl-phosphate synthase subdomain signature 1. / Carbamoyl-phosphate synthetase large subunit-like, ATP-binding domain / Carbamoyl-phosphate synthase L chain, ATP binding domain / Biotin-requiring enzyme / Rudiment single hybrid motif / Biotinyl/lipoyl domain profile. / Biotin/lipoyl attachment / Single hybrid motif / ATP-grasp fold, subdomain 1 / Pre-ATP-grasp domain superfamily / ATP-grasp fold / ATP-grasp fold profile. / ClpP/crotonase-like domain superfamily / Carbamoyl-phosphate synthase subdomain signature 2.
Similarity search - Domain/homology
Acetyl-CoA carboxylase isoform X5
Similarity search - Component
Biological speciesTrichoplusia ni (cabbage looper)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.12 Å
AuthorsLiu B / Wang D / Bu F / Yang G
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: 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
DepositionJul 28, 2024-
Header (metadata) releaseSep 25, 2024-
Map releaseSep 25, 2024-
UpdateOct 2, 2024-
Current statusOct 2, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_45956.png

Downloads & links

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Map

FileDownload / File: emd_45956.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationcryo-EM map of the Carboxyltransferase Domain of Trichoplusia ni Acetyl-Coenzyme A Carboxylase
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.89 Å/pix.
x 384 pix.
= 339.968 Å		0.89 Å/pix.
x 384 pix.
= 339.968 Å		0.89 Å/pix.
x 384 pix.
= 339.968 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.88533 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.06
Minimum - Maximum-0.3054649 - 0.5483409
Average (Standard dev.)0.00020393838 (±0.010317599)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 339.968 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: cryo-EM sharpened map of the Carboxyltransferase Domain of...

Fileemd_45956_additional_1.map
Annotationcryo-EM sharpened map of the Carboxyltransferase Domain of Trichoplusia ni Acetyl-Coenzyme A Carboxylase
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map A of the Carboxyltransferase Domain of...

Fileemd_45956_half_map_1.map
Annotationhalf map A of the Carboxyltransferase Domain of Trichoplusia ni Acetyl-Coenzyme A Carboxylase
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map B of the Carboxyltransferase Domain of...

Fileemd_45956_half_map_2.map
Annotationhalf map B of the Carboxyltransferase Domain of Trichoplusia ni Acetyl-Coenzyme A Carboxylase
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Trichoplusia ni Acetyl-Coenzyme A Carboxylase

EntireName: Trichoplusia ni Acetyl-Coenzyme A Carboxylase
Components
  • Complex: Trichoplusia ni Acetyl-Coenzyme A Carboxylase
    • Protein or peptide: Acetyl-CoA carboxylase

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Supramolecule #1: Trichoplusia ni Acetyl-Coenzyme A Carboxylase

SupramoleculeName: Trichoplusia ni Acetyl-Coenzyme A Carboxylase / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Trichoplusia ni (cabbage looper)

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Macromolecule #1: Acetyl-CoA carboxylase

MacromoleculeName: Acetyl-CoA carboxylase / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Trichoplusia ni (cabbage looper)
Molecular weightTheoretical: 87.732602 KDa
SequenceString: 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

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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: 8
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
TemperatureMin: 63.0 K / Max: 77.0 K
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Image recordingFilm 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 beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 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 stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 3236084
Startup modelType of model: NONE
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C2 (2 fold cyclic) / Algorithm: SIMULTANEOUS ITERATIVE (SIRT) / Resolution.type: BY AUTHOR / Resolution: 3.12 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 154035
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final 3D classificationNumber classes: 4
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: OTHER / Overall B value: 47.91
Output model

PDB-9cv6:
Cryo-EM structure of the Carboxyltransferase Domain of Trichoplusia ni Acetyl-Coenzyme A Carboxylase

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