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- EMDB-35980: Human 3-methylcrotonyl-CoA carboxylase in BCCP-CTS state with sub... -

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Basic information

Entry
Database: EMDB / ID: EMD-35980
TitleHuman 3-methylcrotonyl-CoA carboxylase in BCCP-CTS state with substrate
Map data
Sample
  • Complex: Heterododecamer of human MCC
    • Protein or peptide: Methylcrotonoyl-CoA carboxylase beta chain, mitochondrial
    • Protein or peptide: Methylcrotonoyl-CoA carboxylase subunit alpha, mitochondrial
  • Ligand: 5-(HEXAHYDRO-2-OXO-1H-THIENO[3,4-D]IMIDAZOL-6-YL)PENTANAL
  • Ligand: ~{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
KeywordsMCC / Mitochondria / 3-methylcrotonyl-CoA / CYTOSOLIC PROTEIN
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
Methylcrotonoyl-CoA carboxylase subunit alpha, mitochondrial / Methylcrotonoyl-CoA carboxylase beta chain, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.73 Å
AuthorsLiu DS / Su JY
Funding support China, 1 items
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 DS / Su JY
History
DepositionApr 21, 2023-
Header (metadata) releaseApr 24, 2024-
Map releaseApr 24, 2024-
UpdateApr 24, 2024-
Current statusApr 24, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_35980.png

Downloads & links

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Map

FileDownload / File: emd_35980.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.97 Å/pix.
x 360 pix.
= 349.2 Å		0.97 Å/pix.
x 360 pix.
= 349.2 Å		0.97 Å/pix.
x 360 pix.
= 349.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.97 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.092
Minimum - Maximum-0.3164897 - 0.91457176
Average (Standard dev.)-0.00071104744 (±0.03279736)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 349.2 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_35980_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_35980_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Heterododecamer of human MCC

EntireName: Heterododecamer of human MCC
Components
  • Complex: Heterododecamer of human MCC
    • Protein or peptide: Methylcrotonoyl-CoA carboxylase beta chain, mitochondrial
    • Protein or peptide: Methylcrotonoyl-CoA carboxylase subunit alpha, mitochondrial
  • Ligand: 5-(HEXAHYDRO-2-OXO-1H-THIENO[3,4-D]IMIDAZOL-6-YL)PENTANAL
  • Ligand: ~{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

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Supramolecule #1: Heterododecamer of human MCC

SupramoleculeName: Heterododecamer of human MCC / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
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: 6 / 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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Macromolecule #2: Methylcrotonoyl-CoA carboxylase subunit alpha, mitochondrial

MacromoleculeName: Methylcrotonoyl-CoA carboxylase subunit alpha, mitochondrial
type: protein_or_peptide / ID: 2 / Number of copies: 6 / Enantiomer: LEVO / EC number: methylcrotonoyl-CoA carboxylase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 80.584016 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MAAASAVSVL LVAAERNRWH RLPSLLLPPR TWVWRQRTMK YTTATGRNIT KVLIANRGEI ACRVMRTAKK LGVQTVAVYS EADRNSMHV DMADEAYSIG PAPSQQSYLS MEKIIQVAKT SAAQAIHPGC GFLSENMEFA ELCKQEGIIF IGPPPSAIRD M GIKSTSKS ...String:
MAAASAVSVL LVAAERNRWH RLPSLLLPPR TWVWRQRTMK YTTATGRNIT KVLIANRGEI ACRVMRTAKK LGVQTVAVYS EADRNSMHV DMADEAYSIG PAPSQQSYLS MEKIIQVAKT SAAQAIHPGC GFLSENMEFA ELCKQEGIIF IGPPPSAIRD M GIKSTSKS IMAAAGVPVV EGYHGEDQSD QCLKEHARRI GYPVMIKAVR GGGGKGMRIV RSEQEFQEQL ESARREAKKS FN DDAMLIE KFVDTPRHVE VQVFGDHHGN AVYLFERDCS VQRRHQKIIE EAPAPGIKSE VRKKLGEAAV RAAKAVNYVG AGT VEFIMD SKHNFCFMEM NTRLQVEHPV TEMITGTDLV EWQLRIAAGE KIPLSQEEIT LQGHAFEARI YAEDPSNNFM PVAG PLVHL STPRADPSTR IETGVRQGDE VSVHYDPMIA KLVVWAADRQ AALTKLRYSL RQYNIVGLHT NIDFLLNLSG HPEFE AGNV HTDFIPQHHK QLLLSRKAAA KESLCQAALG LILKEKAMTD TFTLQAHDQF SPFSSSSGRR LNISYTRNMT LKDGKN NVA IAVTYNHDGS YSMQIEDKTF QVLGNLYSEG DCTYLKCSVN GVASKAKLII LENTIYLFSK EGSIEIDIPV PKYLSSV SS QETQGGPLAP MTGTIEKVFV KAGDKVKAGD SLMVMIAMKM EHTIKSPKDG TVKKVFYREG AQANRHTPLV EFEEEESD K RESE

UniProtKB: Methylcrotonoyl-CoA carboxylase subunit alpha, mitochondrial

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Macromolecule #3: 5-(HEXAHYDRO-2-OXO-1H-THIENO[3,4-D]IMIDAZOL-6-YL)PENTANAL

MacromoleculeName: 5-(HEXAHYDRO-2-OXO-1H-THIENO[3,4-D]IMIDAZOL-6-YL)PENTANAL
type: ligand / ID: 3 / Number of copies: 6 / Formula: BTI
Molecular weightTheoretical: 228.311 Da
Chemical component information

ChemComp-BTI:
5-(HEXAHYDRO-2-OXO-1H-THIENO[3,4-D]IMIDAZOL-6-YL)PENTANAL

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Macromolecule #4: ~{S}-[2-[3-[[(2~{R})-4-[[[(2~{S},3~{S},4~{S},5~{S})-5-(6-aminopur...

MacromoleculeName: ~{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- ...Name: ~{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
type: ligand / ID: 4 / Number of copies: 6 / Formula: TW3
Molecular weightTheoretical: 849.635 Da

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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

Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.73 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 273383
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: ANGULAR RECONSTITUTION

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