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- PDB-9yx5: Structure of the long chain acyl-CoA carboxylase complex from Myc... -

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Basic information

Entry
Database: PDB / ID: 9yx5
TitleStructure of the long chain acyl-CoA carboxylase complex from Mycobacterium smegmatis with MSMEG_0435-MSMEG_0436 bound
Components
  • (Allophanate hydrolase subunit ...) x 2
  • (Propionyl-CoA carboxylase beta ...) x 2
  • Acetyl-/propionyl-coenzyme A carboxylase AccE5
  • Biotin-dependent acyl-coenzyme A carboxylase alpha3 subunit
KeywordsLIGASE / Carboxylase / transferase / lipid synthesis / mycolic acid synthesis
Function / homology
Function and homology information


propionyl-CoA carboxylase / biotin carboxylase / propionyl-CoA carboxylase activity / acetyl-CoA carboxylase complex / biotin carboxylase activity / acetyl-CoA carboxylase activity / carbon fixation / fatty acid biosynthetic process / hydrolase activity / ATP binding / metal ion binding
Similarity search - Function
: / KipI family / Carboxyltransferase domain, subdomain A and B / Carboxyltransferase domain, subdomain A and B / Allophanate hydrolase subunit 2 / Carboxyltransferase domain, subdomain C and D / Carboxyltransferase domain, subdomain C and D / Allophanate hydrolase subunit 1 / Biotin-dependent acetyl-/propionyl-coenzyme A carboxylase epsilon subunit / Acyl-CoA carboxylase epsilon subunit ...: / KipI family / Carboxyltransferase domain, subdomain A and B / Carboxyltransferase domain, subdomain A and B / Allophanate hydrolase subunit 2 / Carboxyltransferase domain, subdomain C and D / Carboxyltransferase domain, subdomain C and D / Allophanate hydrolase subunit 1 / Biotin-dependent acetyl-/propionyl-coenzyme A carboxylase epsilon subunit / Acyl-CoA carboxylase epsilon subunit / : / : / Acetyl-coenzyme A carboxyltransferase, N-terminal / Acetyl-coenzyme A (CoA) carboxyltransferase N-terminal domain profile. / Acetyl-coenzyme A carboxyltransferase, C-terminal / Acetyl-coenzyme A (CoA) carboxyltransferase C-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 / Cyclophilin-like domain superfamily / ATP-grasp fold / ATP-grasp fold profile. / ClpP/crotonase-like domain superfamily / Carbamoyl-phosphate synthase subdomain signature 2.
Similarity search - Domain/homology
propionyl Coenzyme A / : / ADENOSINE-5'-TRIPHOSPHATE / BICARBONATE ION / BIOTIN / Allophanate hydrolase subunit 2 / Allophanate hydrolase subunit 1 / Biotin-dependent acyl-coenzyme A carboxylase alpha3 subunit / Acetyl-/propionyl-coenzyme A carboxylase AccE5 / Propionyl-CoA carboxylase beta chain / Propionyl-CoA carboxylase beta chain
Similarity search - Component
Biological speciesMycolicibacterium smegmatis MC2 155 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.9 Å
AuthorsLiang, Y. / Rubinstein, J.L.
Funding support Canada, 1items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR)PJT191893 Canada
CitationJournal: To Be Published
Title: Structural basis for substrate specificity and MSMEG_0435-0436 binding by the mycobacterial long-chain acyl-CoA carboxylase complex
Authors: Liang, Y. / Rubinstein, J.L.
History
DepositionOct 26, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 26, 2025Provider: repository / Type: Initial release
Revision 1.0Nov 26, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Nov 26, 2025Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Nov 26, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Nov 26, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Nov 26, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Nov 26, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Nov 26, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Biotin-dependent acyl-coenzyme A carboxylase alpha3 subunit
E: Acetyl-/propionyl-coenzyme A carboxylase AccE5
F: Propionyl-CoA carboxylase beta chain
G: Propionyl-CoA carboxylase beta chain
H: Propionyl-CoA carboxylase beta chain
I: Biotin-dependent acyl-coenzyme A carboxylase alpha3 subunit
J: Biotin-dependent acyl-coenzyme A carboxylase alpha3 subunit
K: Biotin-dependent acyl-coenzyme A carboxylase alpha3 subunit
L: Biotin-dependent acyl-coenzyme A carboxylase alpha3 subunit
M: Propionyl-CoA carboxylase beta chain
N: Propionyl-CoA carboxylase beta chain
O: Propionyl-CoA carboxylase beta chain
P: Acetyl-/propionyl-coenzyme A carboxylase AccE5
Q: Biotin-dependent acyl-coenzyme A carboxylase alpha3 subunit
V: Allophanate hydrolase subunit 2
W: Allophanate hydrolase subunit 1
X: Biotin-dependent acyl-coenzyme A carboxylase alpha3 subunit
Y: Allophanate hydrolase subunit 2
Z: Allophanate hydrolase subunit 1
U: Biotin-dependent acyl-coenzyme A carboxylase alpha3 subunit
B: Biotin-dependent acyl-coenzyme A carboxylase alpha3 subunit
C: Biotin-dependent acyl-coenzyme A carboxylase alpha3 subunit
D: Biotin-dependent acyl-coenzyme A carboxylase alpha3 subunit
R: Biotin-dependent acyl-coenzyme A carboxylase alpha3 subunit
S: Biotin-dependent acyl-coenzyme A carboxylase alpha3 subunit
T: Biotin-dependent acyl-coenzyme A carboxylase alpha3 subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,367,84143
Polymers1,360,02826
Non-polymers7,81317
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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Protein , 2 types, 16 molecules AIJKLQXUBCDRSTEP

#1: Protein
Biotin-dependent acyl-coenzyme A carboxylase alpha3 subunit


Mass: 63215.176 Da / Num. of mol.: 14 / Source method: isolated from a natural source
Source: (natural) Mycolicibacterium smegmatis MC2 155 (bacteria)
References: UniProt: A0QTE1, biotin carboxylase
#2: Protein Acetyl-/propionyl-coenzyme A carboxylase AccE5


Mass: 10357.693 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Mycolicibacterium smegmatis MC2 155 (bacteria)
References: UniProt: A0QTE6

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Propionyl-CoA carboxylase beta ... , 2 types, 6 molecules FOGHMN

#3: Protein Propionyl-CoA carboxylase beta chain


Mass: 56234.070 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Mycolicibacterium smegmatis MC2 155 (bacteria)
References: UniProt: A0R616, propionyl-CoA carboxylase
#4: Protein
Propionyl-CoA carboxylase beta chain


Mass: 58488.074 Da / Num. of mol.: 4 / Source method: isolated from a natural source
Source: (natural) Mycolicibacterium smegmatis MC2 155 (bacteria)
References: UniProt: A0QTE7, propionyl-CoA carboxylase

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Allophanate hydrolase subunit ... , 2 types, 4 molecules VYWZ

#5: Protein Allophanate hydrolase subunit 2


Mass: 31280.223 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Mycolicibacterium smegmatis MC2 155 (bacteria)
References: UniProt: A0QPL0
#6: Protein Allophanate hydrolase subunit 1


Mass: 22659.801 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Mycolicibacterium smegmatis MC2 155 (bacteria)
References: UniProt: A0QPL1

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Non-polymers , 6 types, 17 molecules

#7: Chemical ChemComp-A1CZD / S-{(3S,5S,9R)-1-[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-4-hydroxy-3-(phosphonooxy)oxolan-2-yl]-3,5,9-trihydroxy-8,8-dimethyl-3,5,10,14-tetraoxo-2,4,6-trioxa-11,15-diaza-3lambda~5~,5lambda~5~-diphosphaheptadecan-17-yl} (11E,14E,16E)-icosa-11,14,16-trienethioate (non-preferred name)


Mass: 1056.002 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C41H68N7O17P3S / Feature type: SUBJECT OF INVESTIGATION
#8: Chemical
ChemComp-1VU / propionyl Coenzyme A


Mass: 823.597 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C24H40N7O17P3S / Feature type: SUBJECT OF INVESTIGATION
#9: Chemical
ChemComp-BTN / BIOTIN


Mass: 244.311 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C10H16N2O3S / Feature type: SUBJECT OF INVESTIGATION
#10: Chemical ChemComp-BCT / BICARBONATE ION


Mass: 61.017 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CHO3 / Feature type: SUBJECT OF INVESTIGATION
#11: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: ATP, energy-carrying molecule*YM
#12: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION

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Details

Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Structure of the long chain acyl-CoA carboxylase complex from Mycobacterium smegmatis with MSMEG_0435-MSMEG_0436 bound
Type: COMPLEX / Entity ID: #1-#6 / Source: NATURAL
Molecular weightValue: 0.98 MDa / Experimental value: YES
Source (natural)Organism: Mycolicibacterium smegmatis MC2 155 (bacteria)
Buffer solutionpH: 6
SpecimenConc.: 5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER/RHODIUM / Grid mesh size: 400 divisions/in. / Grid type: Homemade
VitrificationInstrument: LEICA EM GP / Cryogen name: ETHANE / Humidity: 90 % / Chamber temperature: 277 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 magnification: 130000 X / Nominal defocus max: 20000 nm / Nominal defocus min: 1100 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: TFS FALCON 4i (4k x 4k) / Num. of real images: 8000
EM imaging opticsEnergyfilter name: TFS Selectris X / Energyfilter slit width: 10 eV

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Processing

EM software
IDNameVersionCategory
1cryoSPARC5.0.0-privatebetaparticle selection
2PHENIX1.19.2_4158model refinement
3EPUimage acquisition
5cryoSPARC5.0.0-privatebetaCTF correction
10cryoSPARC5.0.0-privatebetainitial Euler assignment
11cryoSPARC5.0.0-privatebetafinal Euler assignment
13cryoSPARC5.0.0-privatebeta3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 10016 / Symmetry type: POINT
RefinementHighest resolution: 2.9 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00468454
ELECTRON MICROSCOPYf_angle_d0.83793105
ELECTRON MICROSCOPYf_dihedral_angle_d14.44825111
ELECTRON MICROSCOPYf_chiral_restr0.05210519
ELECTRON MICROSCOPYf_plane_restr0.0112320

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