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- EMDB-36024: Methylcrotonoyl-CoA carboxylase core-Dimer -

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Basic information

Entry
Database: EMDB / ID: EMD-36024
TitleMethylcrotonoyl-CoA carboxylase core-Dimer
Map data
Sample
  • Complex: Methylcrotonoyl-CoA carboxylase core-Dimer
    • Protein or peptide: Methylcrotonoyl-CoA carboxylase beta chain, mitochondrial
KeywordsMCC / Mitochondria / CYTOSOLIC PROTEIN
Function / homology
Function and homology information


3-Methylcrotonyl-CoA carboxylase deficiency / methylcrotonoyl-CoA carboxylase / methylcrotonoyl-CoA carboxylase complex / methylcrotonoyl-CoA carboxylase activity / Defective HLCS causes multiple carboxylase deficiency / Biotin transport and metabolism / L-leucine catabolic process / branched-chain amino acid catabolic process / Branched-chain amino acid catabolism / coenzyme A metabolic process ...3-Methylcrotonyl-CoA carboxylase deficiency / methylcrotonoyl-CoA carboxylase / methylcrotonoyl-CoA carboxylase complex / methylcrotonoyl-CoA carboxylase activity / Defective HLCS causes multiple carboxylase deficiency / Biotin transport and metabolism / L-leucine catabolic process / branched-chain amino acid catabolic process / Branched-chain amino acid catabolism / coenzyme A metabolic process / mitochondrial matrix / mitochondrion / ATP 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 / ClpP/crotonase-like domain superfamily
Similarity search - Domain/homology
Methylcrotonoyl-CoA carboxylase beta chain, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.16 Å
AuthorsLiu DS / Su JY
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32071192 China
CitationJournal: Nat Struct Mol Biol / Year: 2025
Title: Structural insight into synergistic activation of human 3-methylcrotonyl-CoA carboxylase.
Authors: Jiayue Su / Xuyang Tian / Hang Cheng / Desheng Liu / Ziyi Wang / Shan Sun / Hong-Wei Wang / Sen-Fang Sui /
Abstract: The enzymes 3-methylcrotonyl-coenzyme A (CoA) carboxylase (MCC), pyruvate carboxylase and propionyl-CoA carboxylase belong to the biotin-dependent carboxylase family located in mitochondria. They ...The enzymes 3-methylcrotonyl-coenzyme A (CoA) carboxylase (MCC), pyruvate carboxylase and propionyl-CoA carboxylase belong to the biotin-dependent carboxylase family located in mitochondria. They participate in various metabolic pathways in human such as amino acid metabolism and tricarboxylic acid cycle. Many human diseases are caused by mutations in those enzymes but their structures have not been fully resolved so far. Here we report an optimized purification strategy to obtain high-resolution structures of intact human endogenous MCC, propionyl-CoA carboxylase and pyruvate carboxylase in different conformational states. We also determine the structures of MCC bound to different substrates. Analysis of MCC structures in different states reveals the mechanism of the substrate-induced, multi-element synergistic activation of MCC. These results provide important insights into the catalytic mechanism of the biotin-dependent carboxylase family and are of great value for the development of new drugs for the treatment of related diseases.
History
DepositionApr 27, 2023-
Header (metadata) releaseMay 1, 2024-
Map releaseMay 1, 2024-
UpdateMay 21, 2025-
Current statusMay 21, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_36024.png

Downloads & links

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Map

FileDownload / File: emd_36024.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
1.1 Å/pix.
x 320 pix.
= 351.328 Å		1.1 Å/pix.
x 320 pix.
= 351.328 Å		1.1 Å/pix.
x 320 pix.
= 351.328 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.0979 Å
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Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.27
Minimum - Maximum-0.5369298 - 1.0255684
Average (Standard dev.)0.0011114107 (±0.058666628)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 351.328 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_36024_half_map_1.map
Projections & Slices
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Half map: #1

Fileemd_36024_half_map_2.map
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Sample components

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Entire : Methylcrotonoyl-CoA carboxylase core-Dimer

EntireName: Methylcrotonoyl-CoA carboxylase core-Dimer
Components
  • Complex: Methylcrotonoyl-CoA carboxylase core-Dimer
    • Protein or peptide: Methylcrotonoyl-CoA carboxylase beta chain, mitochondrial

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Supramolecule #1: Methylcrotonoyl-CoA carboxylase core-Dimer

SupramoleculeName: Methylcrotonoyl-CoA carboxylase core-Dimer / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Methylcrotonoyl-CoA carboxylase beta chain, mitochondrial

MacromoleculeName: Methylcrotonoyl-CoA carboxylase beta chain, mitochondrial
type: protein_or_peptide / ID: 1 / Number of copies: 12 / Enantiomer: LEVO / EC number: methylcrotonoyl-CoA carboxylase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 61.406027 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MWAVLRLALR PCARASPAGP RAYHGDSVAS LGTQPDLGSA LYQENYKQMK ALVNQLHERV EHIKLGGGEK ARALHISRGK LLPRERIDN LIDPGSPFLE LSQFAGYQLY DNEEVPGGGI ITGIGRVSGV ECMIIANDAT VKGGAYYPVT VKKQLRAQEI A MQNRLPCI ...String:
MWAVLRLALR PCARASPAGP RAYHGDSVAS LGTQPDLGSA LYQENYKQMK ALVNQLHERV EHIKLGGGEK ARALHISRGK LLPRERIDN LIDPGSPFLE LSQFAGYQLY DNEEVPGGGI ITGIGRVSGV ECMIIANDAT VKGGAYYPVT VKKQLRAQEI A MQNRLPCI YLVDSGGAYL PRQADVFPDR DHFGRTFYNQ AIMSSKNIAQ IAVVMGSCTA GGAYVPAMAD ENIIVRKQGT IF LAGPPLV KAATGEEVSA EDLGGADLHC RKSGVSDHWA LDDHHALHLT RKVVRNLNYQ KKLDVTIEPS EEPLFPADEL YGI VGANLK RSFDVREVIA RIVDGSRFTE FKAFYGDTLV TGFARIFGYP VGIVGNNGVL FSESAKKGTH FVQLCCQRNI PLLF LQNIT GFMVGREYEA EGIAKDGAKM VAAVACAQVP KITLIIGGSY GAGNYGMCGR AYSPRFLYIW PNARISVMGG EQAAN VLAT ITKDQRAREG KQFSSADEAA LKEPIIKKFE EEGNPYYSSA RVWDDGIIDP ADTRLVLGLS FSAALNAPIE KTDFGI FRM

UniProtKB: Methylcrotonoyl-CoA carboxylase beta chain, mitochondrial

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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

BufferpH: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.8 µm / Nominal defocus min: 1.3 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING ONLY
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.16 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 1474
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: ANGULAR RECONSTITUTION

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