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- EMDB-62392: cryo-EM structure of acetyl-CoA carboxyltransferase holoenzyme di... -

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Basic information

Entry
Database: EMDB / ID: EMD-62392
Titlecryo-EM structure of acetyl-CoA carboxyltransferase holoenzyme dimer from Shewanella oneidensis, mutant E1238A, complexed with ADP
Map dataThe map corrected by spIsoNet, after homogeneous refinement in cryoSPARC
Sample
  • Complex: Acetyl-CoA carboxyltransferase holoenzyme dimer from Shewanella oneidensis, mutant E1238A, complexed with ADP
    • Protein or peptide: Acetyl-CoA carboxylase multifunctional enzyme AccADCB
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: MAGNESIUM ION
Keywordsacetyl-CoA carboxyltransferase / LIGASE
Function / homology
Function and homology information


acetyl-CoA carboxylase / carboxyl- or carbamoyltransferase activity / biotin carboxylase / acetyl-CoA carboxylase complex / biotin carboxylase activity / acetyl-CoA carboxylase activity / fatty acid biosynthetic process / ATP binding / metal ion binding
Similarity search - Function
Acetyl-CoA carboxylase, alpha subunit / Acetyl co-enzyme A carboxylase carboxyltransferase-like / : / Acetyl-coenzyme A carboxyltransferase, C-terminal / Acetyl-coenzyme A (CoA) carboxyltransferase C-terminal domain profile. / Biotin carboxylase-like, N-terminal domain / Biotin carboxylase, C-terminal / Biotin carboxylation domain / Biotin carboxylase, N-terminal domain / Biotin carboxylase C-terminal domain ...Acetyl-CoA carboxylase, alpha subunit / Acetyl co-enzyme A carboxylase carboxyltransferase-like / : / Acetyl-coenzyme A carboxyltransferase, C-terminal / Acetyl-coenzyme A (CoA) carboxyltransferase C-terminal domain profile. / 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 synthetase large subunit-like, ATP-binding domain / Carbamoyl-phosphate synthase L chain, ATP binding domain / Rudiment single hybrid motif / Single hybrid motif / 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 multifunctional enzyme AccADCB
Similarity search - Component
Biological speciesShewanella oneidensis MR-1 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.14 Å
AuthorsWang W / Han SR / Xu YY / Gao HC
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: cryo-EM structure of acetyl-CoA carboxyltransferase holoenzyme dimer from Shewanella oneidensis, mutant E1238A, complexed with ADP
Authors: Wang W / Han SR / Xu YY / Gao HC
History
DepositionNov 13, 2024-
Header (metadata) releaseNov 19, 2025-
Map releaseNov 19, 2025-
UpdateNov 19, 2025-
Current statusNov 19, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_62392.png

Downloads & links

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Map

FileDownload / File: emd_62392.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationThe map corrected by spIsoNet, after homogeneous refinement in cryoSPARC
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.31 Å/pix.
x 200 pix.
= 261.4 Å		1.31 Å/pix.
x 200 pix.
= 261.4 Å		1.31 Å/pix.
x 200 pix.
= 261.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.307 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 3.68
Minimum - Maximum-2.9934692 - 15.846524
Average (Standard dev.)-0.026168939 (±0.79729027)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions200200200
Spacing200200200
CellA=B=C: 261.4 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: The original map refined in cryoSPARC by homogeneous refinement

Fileemd_62392_additional_1.map
AnnotationThe original map refined in cryoSPARC by homogeneous refinement
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: The map corrected by SIRM RELION, after homogeneous refinement...

Fileemd_62392_additional_2.map
AnnotationThe map corrected by SIRM_RELION, after homogeneous refinement in cryoSPARC
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: The original half map A refined in cryoSPARC...

Fileemd_62392_half_map_1.map
AnnotationThe original half map A refined in cryoSPARC by homogeneous refinement
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: The original half map B refined in cryoSPARC...

Fileemd_62392_half_map_2.map
AnnotationThe original half map B refined in cryoSPARC by homogeneous refinement
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Acetyl-CoA carboxyltransferase holoenzyme dimer from Shewanella o...

EntireName: Acetyl-CoA carboxyltransferase holoenzyme dimer from Shewanella oneidensis, mutant E1238A, complexed with ADP
Components
  • Complex: Acetyl-CoA carboxyltransferase holoenzyme dimer from Shewanella oneidensis, mutant E1238A, complexed with ADP
    • Protein or peptide: Acetyl-CoA carboxylase multifunctional enzyme AccADCB
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: MAGNESIUM ION

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Supramolecule #1: Acetyl-CoA carboxyltransferase holoenzyme dimer from Shewanella o...

SupramoleculeName: Acetyl-CoA carboxyltransferase holoenzyme dimer from Shewanella oneidensis, mutant E1238A, complexed with ADP
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Details: The complex lacks BCCP domain due to the flexibility of it.
Source (natural)Organism: Shewanella oneidensis MR-1 (bacteria)

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Macromolecule #1: Acetyl-CoA carboxylase multifunctional enzyme AccADCB

MacromoleculeName: Acetyl-CoA carboxylase multifunctional enzyme AccADCB / type: protein_or_peptide / ID: 1
Details: E1238 has been mutated to A, 1-17aa, 427-441aa and 1394-1517aa have no density in the map
Number of copies: 2 / Enantiomer: LEVO / EC number: biotin carboxylase
Source (natural)Organism: Shewanella oneidensis MR-1 (bacteria)
Molecular weightTheoretical: 167.752078 KDa
Recombinant expressionOrganism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
SequenceString: MTSNNQPKHM TQAQTPDPLF LQAEHLAKDF SLFPKHSKQS LSEEIKGLLN DDAIQANLKD LASLDVDGYV AKVIQPTQDK GRPGAKRII ADLKGRLITE THLGSFYSAE VELNFGSRTR RIGFIAQERT TANGAWMPEH HYAACKAIRH FAELSMPIVY L IDTPGADA ...String:
MTSNNQPKHM TQAQTPDPLF LQAEHLAKDF SLFPKHSKQS LSEEIKGLLN DDAIQANLKD LASLDVDGYV AKVIQPTQDK GRPGAKRII ADLKGRLITE THLGSFYSAE VELNFGSRTR RIGFIAQERT TANGAWMPEH HYAACKAIRH FAELSMPIVY L IDTPGADA GEVANSQNQA HSISKAIAES ANVDVPTVGI VIGAGYSGGA IPLAAANILL SLRDGIFNTI QPQGLQSIAR KY NLSWQEC AKSVGVSPEE LYTSGCIDGI IDFSPGDRDE RQHNLRRAII SSIEAVERAA VNFVRESKDL REHYDRSLAR FLN PSKNLM ALELNAELAV ATSPTNHHNL FGSAYRYLRY LTLRSRIHSI SQEQYGRLSR VSVPEGDLLA RIQQEQDRVF QAWL ASPDK LVYDEDLNKL WANFIAKRDE ISTERNMLTR FILGEPKENY KKARKALLFN ISWSLYHRWK SNAANNFKGL IQHLE NLPK SVTQAKWPEL NQLTVLDVVV NDELREDFIW QCHNILIFNS LYDNVVGSLA SIAKEAMMSK SLSRNSVNNL LHKSID HAL STQDTANDKA KFYKWLKYFM GQSNRADLLV RVEQWKSVGF PQLNDSLFVI LTYFFERLLP EYFDSESDHS KYTGAIN PV RIGRRKDFWN RLTMGYQDLL IQKVLRDEKR TGKMTWENVI KQFFTHFDEI NGDKMSANLL NFPGFRLSIE DALDKGIR P CGLITGIADF KEKGQKVRVG LAVSNTAFQA GAFDMASAEK FSALLIECAK RKLPVVCFIS SGGMQTKEGA AALFSMAVV NDRITRFIRD NELPVLMFGF GDCTGGAQAS FVTHPLVQTY YLSGTNMPFA GQMVVPAYLP STSTLSNYLS KVPGAMAGLV HNPFSENLD NQLASIDPLM PMPTAKINEV IINALSTLVV EAPAEEEEIV QNDPRKLMKP INKVLVHARG CTAVKLIRKA H DNNINVVL VASDPDMTAV PADMLKESDK LVCLGGNTSD ESYLNAYSVL KVAEYEQVDA LHPGIGFLSE SPQFAALCVN NG VNFVGPS VHSMTTMGNK SNAIKTSQAQ NVPVVPGSHG ILTNAEQAVN VASEIGYPVL LKAVQGGGGK GIQVVKRPED MIG LFQKTA TEAAAAFGNG DLYLEKYVTS LRHIEVQLLR DKFGHAKVLG LRDCSVQRNN QKVVEESGST MLPDELKKQV LAYT RALGD ATDYMGAGTV EFIYNLDANE VYFMEMNTRL QVAHPVTEAT SGIDIVSAQF DIAAGRSIEH LEPKEIGYAM EVRVT AEKA ALDSHGVLQL IPNPGKITEC VFPDHPDVEI ISIAAPGKEV SPYYDSLIAQ VIMRGENRED VIAKLHAYLD SVVLKG IAT NIPLLKLILS DGTFKEGVYD TNYLPRFMAE LDIPALIAEM EAAAETVGVD TESLRVGESN ELKVLAQGAG IFYTSPA PG EPDFVKEGDI VTAEQTLALT EAMKMFSQVN LAGFNRQGAV LYPEDKKYRI ERILNSNGQQ VSQGDLLFVV SPVED

UniProtKB: Acetyl-CoA carboxylase multifunctional enzyme AccADCB

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Macromolecule #2: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 2 / Number of copies: 2 / Formula: ADP
Molecular weightTheoretical: 427.201 Da
Chemical component information

ChemComp-ADP:
ADENOSINE-5'-DIPHOSPHATE / ADP, energy-carrying molecule*YM

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Macromolecule #3: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 3 / Number of copies: 2 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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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

Concentration0.3 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormulaName
50.0 mMNaClSodium chloride
20.0 mMHEPESN-2-Hydroxyethylpiperazine-N-2-Ethane Sulfonic Acid
GridModel: Quantifoil R2/2 / Material: GOLD / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY / Support film - Film thickness: 10 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 180 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 289 K / Instrument: FEI VITROBOT MARK IV
DetailsAdd 1 mM acetyl-CoA and 2 mM Mg-ADP into the specimen before freezing

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 51.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.8 µm / Nominal defocus min: 1.2 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: NONE
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

9iih
PDB Unreleased entry

Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 4.14 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 146508
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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