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- PDB-8uz2: E. coli acetyl-CoA carboxylase, narrow helical local reconstructi... -

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Basic information

Entry
Database: PDB / ID: 8uz2
TitleE. coli acetyl-CoA carboxylase, narrow helical local reconstruction, 3.18 Angstrom
Components
  • (Acetyl-coenzyme A carboxylase carboxyl transferase subunit ...) x 2
  • Biotin carboxyl carrier protein of acetyl-CoA carboxylase
  • Biotin carboxylase
KeywordsBIOSYNTHETIC PROTEIN / complex / enzyme / biosynthesis of fatty acids
Function / homology
Function and homology information


acetate CoA-transferase complex / acetyl-CoA carboxytransferase / carboxyl- or carbamoyltransferase activity / biotin carboxylase / acetyl-CoA carboxylase complex / biotin carboxylase activity / malonyl-CoA biosynthetic process / acetyl-CoA carboxylase activity / negative regulation of fatty acid biosynthetic process / long-chain fatty acid biosynthetic process ...acetate CoA-transferase complex / acetyl-CoA carboxytransferase / carboxyl- or carbamoyltransferase activity / biotin carboxylase / acetyl-CoA carboxylase complex / biotin carboxylase activity / malonyl-CoA biosynthetic process / acetyl-CoA carboxylase activity / negative regulation of fatty acid biosynthetic process / long-chain fatty acid biosynthetic process / fatty acid biosynthetic process / molecular adaptor activity / negative regulation of translation / mRNA binding / protein homodimerization activity / DNA binding / zinc ion binding / ATP binding / metal ion binding / identical protein binding / cytoplasm / cytosol
Similarity search - Function
Acetyl-CoA carboxylase, alpha subunit / Acetyl co-enzyme A carboxylase carboxyltransferase-like / Acetyl-CoA biotin carboxyl carrier / Acetyl-coA carboxylase zinc finger domain / Acetyl-CoA carboxylase zinc finger domain / Acetyl-CoA carboxylase carboxyl transferase, beta subunit / : / Acetyl-CoA carboxylase, biotin carboxylase / : / Acetyl-coenzyme A carboxyltransferase, C-terminal ...Acetyl-CoA carboxylase, alpha subunit / Acetyl co-enzyme A carboxylase carboxyltransferase-like / Acetyl-CoA biotin carboxyl carrier / Acetyl-coA carboxylase zinc finger domain / Acetyl-CoA carboxylase zinc finger domain / Acetyl-CoA carboxylase carboxyl transferase, beta subunit / : / Acetyl-CoA carboxylase, biotin carboxylase / : / 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 COENZYME *A / ADENOSINE-5'-DIPHOSPHATE / BIOTIN / Acetyl-coenzyme A carboxylase carboxyl transferase subunit beta / Acetyl-coenzyme A carboxylase carboxyl transferase subunit alpha / Biotin carboxyl carrier protein of acetyl-CoA carboxylase / Biotin carboxylase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 3.18 Å
AuthorsXu, X. / Silva de Sousa, A. / Boram, T.J. / Jiang, W. / Lohman, R.J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM140290 United States
CitationJournal: To Be Published
Title: E. coli acetyl-CoA carboxylase, narrow helical local reconstruction, 3.18 Angstrom
Authors: Xu, X. / Silva de Sousa, A. / Boram, T.J. / Jiang, W. / Lohman, R.J.
History
DepositionNov 14, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 20, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Acetyl-coenzyme A carboxylase carboxyl transferase subunit alpha
B: Biotin carboxyl carrier protein of acetyl-CoA carboxylase
C: Biotin carboxylase
D: Acetyl-coenzyme A carboxylase carboxyl transferase subunit beta
E: Acetyl-coenzyme A carboxylase carboxyl transferase subunit alpha
F: Biotin carboxyl carrier protein of acetyl-CoA carboxylase
G: Biotin carboxylase
H: Acetyl-coenzyme A carboxylase carboxyl transferase subunit beta
I: Acetyl-coenzyme A carboxylase carboxyl transferase subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)281,49919
Polymers278,3589
Non-polymers3,14210
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Acetyl-coenzyme A carboxylase carboxyl transferase subunit ... , 2 types, 5 molecules AEDHI

#1: Protein Acetyl-coenzyme A carboxylase carboxyl transferase subunit alpha / ACCase subunit alpha / Acetyl-CoA carboxylase carboxyltransferase subunit alpha


Mass: 34956.098 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: accA, b0185, JW0180 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P0ABD5, acetyl-CoA carboxytransferase
#4: Protein Acetyl-coenzyme A carboxylase carboxyl transferase subunit beta / ACCase subunit beta / Acetyl-CoA carboxylase carboxyltransferase subunit beta


Mass: 31234.570 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: accD, dedB, usg, b2316, JW2313 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P0A9Q5, acetyl-CoA carboxytransferase

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Protein , 2 types, 4 molecules BFCG

#2: Protein Biotin carboxyl carrier protein of acetyl-CoA carboxylase / BCCP


Mass: 8370.667 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: accB, fabE, b3255, JW3223 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P0ABD8
#3: Protein Biotin carboxylase / Acetyl-coenzyme A carboxylase biotin carboxylase subunit A


Mass: 49000.230 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: accC, fabG, b3256, JW3224 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P24182, biotin carboxylase

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Non-polymers , 5 types, 10 molecules

#5: Chemical ChemComp-BTN / BIOTIN


Mass: 244.311 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N2O3S
#6: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#7: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#8: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#9: Chemical ChemComp-ACO / ACETYL COENZYME *A


Mass: 809.571 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C23H38N7O17P3S

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Details

Has ligand of interestN
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: HELICAL ARRAY / 3D reconstruction method: helical reconstruction

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Sample preparation

ComponentName: Escherichia coli acetyl-CoA carboxylase / Type: COMPLEX / Entity ID: #1-#4 / Source: RECOMBINANT
Source (natural)Organism: Escherichia coli (E. coli)
Source (recombinant)Organism: Escherichia coli BL21(DE3) (bacteria)
Buffer solutionpH: 7.5
Details: 2.5 mg/ml ACC complex in 50 mM HEPES pH 7.5, 100 mM bicarbonate, 7.5 mM ATP, 20 mM MgCl2 and 1 mM acetyl-CoA
Buffer component
IDConc.NameFormulaBuffer-ID
1150 mMsodium chlorideNaCl1
250 mMHEPES1
SpecimenConc.: 2.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277.15 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 600 nm / C2 aperture diameter: 50 µm
Image recordingAverage exposure time: 2.01 sec. / Electron dose: 54.44 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM software
IDNameVersionCategory
2EPU2image acquisition
13cryoSPARC23D reconstruction
CTF correctionType: NONE
Helical symmertyAngular rotation/subunit: 81.06 ° / Axial rise/subunit: 19.16 Å / Axial symmetry: C1
3D reconstructionResolution: 3.18 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 577289 / Symmetry type: HELICAL
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00417828
ELECTRON MICROSCOPYf_angle_d0.56124060
ELECTRON MICROSCOPYf_dihedral_angle_d11.292600
ELECTRON MICROSCOPYf_chiral_restr0.0432666
ELECTRON MICROSCOPYf_plane_restr0.0043134

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