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- PDB-8xl7: Structure of human 3-methylcrotonyl-CoA carboxylase in complex wi... -

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Basic information

Entry
Database: PDB / ID: 8xl7
TitleStructure of human 3-methylcrotonyl-CoA carboxylase in complex with acetyl-CoA (MCC-ACO)
Components
  • Methylcrotonoyl-CoA carboxylase beta chain, mitochondrial
  • Methylcrotonoyl-CoA carboxylase subunit alpha, mitochondrial
KeywordsLIGASE / Biotin-dependent carboxylase
Function / homology
Function and homology information


3-Methylcrotonyl-CoA carboxylase deficiency / methylcrotonoyl-CoA carboxylase / biotin metabolic process / methylcrotonoyl-CoA carboxylase complex / methylcrotonoyl-CoA carboxylase activity / Defective HLCS causes multiple carboxylase deficiency / Biotin transport and metabolism / L-leucine catabolic process / biotin carboxylase activity / branched-chain amino acid catabolic process ...3-Methylcrotonyl-CoA carboxylase deficiency / methylcrotonoyl-CoA carboxylase / biotin metabolic process / methylcrotonoyl-CoA carboxylase complex / methylcrotonoyl-CoA carboxylase activity / Defective HLCS causes multiple carboxylase deficiency / Biotin transport and metabolism / L-leucine catabolic process / biotin carboxylase activity / branched-chain amino acid catabolic process / Branched-chain amino acid catabolism / coenzyme A metabolic process / biotin binding / mitochondrial matrix / mitochondrion / ATP binding / metal ion binding / cytosol
Similarity search - Function
Methylcrotonoyl-CoA carboxylase beta chain MCCB/AccD1-like / : / 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. ...Methylcrotonoyl-CoA carboxylase beta chain MCCB/AccD1-like / : / 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 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 / 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 / BIOTIN / Methylcrotonoyl-CoA carboxylase subunit alpha, mitochondrial / Methylcrotonoyl-CoA carboxylase beta chain, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.85 Å
AuthorsZhou, F.Y. / Zhang, Y.Y. / Zhou, Q. / Hu, Q.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Elife / Year: 2024
Title: Structural insights into human propionyl-CoA carboxylase (PCC) and 3-methylcrotonyl-CoA carboxylase (MCC)
Authors: Zhou, F. / Zhang, Y. / Zhu, Y. / Zhou, Q. / Shi, Y. / Hu, Q.
History
DepositionDec 25, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 30, 2024Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2024Group: Data collection / Category: em_admin / Item: _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Methylcrotonoyl-CoA carboxylase subunit alpha, mitochondrial
B: Methylcrotonoyl-CoA carboxylase beta chain, mitochondrial
C: Methylcrotonoyl-CoA carboxylase subunit alpha, mitochondrial
D: Methylcrotonoyl-CoA carboxylase beta chain, mitochondrial
E: Methylcrotonoyl-CoA carboxylase subunit alpha, mitochondrial
F: Methylcrotonoyl-CoA carboxylase beta chain, mitochondrial
G: Methylcrotonoyl-CoA carboxylase subunit alpha, mitochondrial
H: Methylcrotonoyl-CoA carboxylase beta chain, mitochondrial
I: Methylcrotonoyl-CoA carboxylase subunit alpha, mitochondrial
J: Methylcrotonoyl-CoA carboxylase beta chain, mitochondrial
K: Methylcrotonoyl-CoA carboxylase subunit alpha, mitochondrial
L: Methylcrotonoyl-CoA carboxylase beta chain, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)858,26424
Polymers851,94012
Non-polymers6,32312
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

#1: Protein
Methylcrotonoyl-CoA carboxylase subunit alpha, mitochondrial / MCCase subunit alpha / 3-methylcrotonyl-CoA carboxylase 1 / 3-methylcrotonyl-CoA carboxylase biotin- ...MCCase subunit alpha / 3-methylcrotonyl-CoA carboxylase 1 / 3-methylcrotonyl-CoA carboxylase biotin-containing subunit / 3-methylcrotonyl-CoA:carbon dioxide ligase subunit alpha


Mass: 80584.016 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)
References: UniProt: Q96RQ3, methylcrotonoyl-CoA carboxylase
#2: Protein
Methylcrotonoyl-CoA carboxylase beta chain, mitochondrial / MCCase subunit beta / 3-methylcrotonyl-CoA carboxylase 2 / 3-methylcrotonyl-CoA carboxylase non- ...MCCase subunit beta / 3-methylcrotonyl-CoA carboxylase 2 / 3-methylcrotonyl-CoA carboxylase non-biotin-containing subunit / 3-methylcrotonyl-CoA:carbon dioxide ligase subunit beta


Mass: 61406.027 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)
References: UniProt: Q9HCC0, methylcrotonoyl-CoA carboxylase
#3: Chemical
ChemComp-BTN / BIOTIN


Mass: 244.311 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C10H16N2O3S / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-ACO / ACETYL COENZYME *A


Mass: 809.571 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C23H38N7O17P3S / Feature type: SUBJECT OF INVESTIGATION
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: Heterododecamer complex of human 3-methylcrotonyl-CoA carboxylase in complex with acetyl-CoA (MCC-ACO)
Type: COMPLEX / Entity ID: #1-#2 / Source: NATURAL
Source (natural)Organism: Homo sapiens (human)
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2200 nm / Nominal defocus min: 1200 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.85 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 117900 / Symmetry type: POINT

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