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- PDB-8j4z: Human 3-methylcrotonyl-CoA carboxylase in BCCP-CTS state with sub... -

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Basic information

Entry
Database: PDB / ID: 8j4z
TitleHuman 3-methylcrotonyl-CoA carboxylase in BCCP-CTS state with substrate
Components
  • Methylcrotonoyl-CoA carboxylase beta chain, mitochondrial
  • Methylcrotonoyl-CoA carboxylase subunit alpha, mitochondrial
KeywordsCYTOSOLIC PROTEIN / MCC / Mitochondria / 3-methylcrotonyl-CoA
Function / homology
Function and homology information


: / methylcrotonoyl-CoA carboxylase / biotin metabolic process / methylcrotonoyl-CoA carboxylase complex / methylcrotonoyl-CoA carboxylase activity / Defective HLCS causes multiple carboxylase deficiency / L-leucine catabolic process / Biotin transport and metabolism / biotin carboxylase activity / branched-chain amino acid catabolic process ...: / methylcrotonoyl-CoA carboxylase / biotin metabolic process / methylcrotonoyl-CoA carboxylase complex / methylcrotonoyl-CoA carboxylase activity / Defective HLCS causes multiple carboxylase deficiency / L-leucine catabolic process / Biotin transport and metabolism / 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
Chem-BTI / : / 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: 2.73 Å
AuthorsLiu, D.S. / Su, J.Y.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32071192 China
CitationJournal: To Be Published
Title: Human 3-methylcrotonyl-CoA carboxylase in BCCP-CTS state with substrate
Authors: Liu, D.S. / Su, J.Y.
History
DepositionApr 21, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 24, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)858,40824
Polymers851,94012
Non-polymers6,46812
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: 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 genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MCCC2, MCCB / Production host: Homo sapiens (human)
References: UniProt: Q9HCC0, methylcrotonoyl-CoA carboxylase
#2: 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 genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MCCC1, MCCA / Production host: Homo sapiens (human)
References: UniProt: Q96RQ3, methylcrotonoyl-CoA carboxylase
#3: Chemical
ChemComp-BTI / 5-(HEXAHYDRO-2-OXO-1H-THIENO[3,4-D]IMIDAZOL-6-YL)PENTANAL


Mass: 228.311 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C10H16N2O2S
#4: Chemical
ChemComp-TW3 / ~{S}-[2-[3-[[(2~{R})-4-[[[(2~{S},3~{S},4~{S},5~{S})-5-(6-aminopurin-9-yl)-4-oxidanyl-3-phosphonooxy-oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxy-3,3-dimethyl-2-oxidanyl-butanoyl]amino]propanoylamino]ethyl] 3-methylbut-2-enethioate


Mass: 849.635 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C26H42N7O17P3S
Has ligand of interestN

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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 of human MCC / Type: COMPLEX / Entity ID: #1-#2 / Source: NATURAL
Source (natural)Organism: Homo sapiens (human)
Buffer solutionpH: 8
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: 1800 nm / Nominal defocus min: 1300 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 ONLY
3D reconstructionResolution: 2.73 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 273383 / Symmetry type: POINT

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