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- EMDB-38438: Structure of human propionyl-CoA carboxylase in complex with prop... -

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Basic information

Entry
Database: EMDB / ID: EMD-38438
TitleStructure of human propionyl-CoA carboxylase in complex with propionyl-CoA (PCC-PCO)
Map data
Sample
  • Complex: Heterododecamer complex of human propionyl-CoA carboxylase in complex with propionyl-CoA (PCC-PCO)
    • Protein or peptide: Propionyl-CoA carboxylase alpha chain, mitochondrial
    • Protein or peptide: Propionyl-CoA carboxylase beta chain, mitochondrial
  • Ligand: BIOTIN
  • Ligand: propionyl Coenzyme A
KeywordsBiotin-dependent carboxylase / LIGASE
Function / homology
Function and homology information


short-chain fatty acid catabolic process / branched-chain amino acid metabolic process / Propionyl-CoA catabolism / propionyl-CoA carboxylase / propionyl-CoA carboxylase activity / Defective HLCS causes multiple carboxylase deficiency / Biotin transport and metabolism / biotin binding / catalytic complex / Mitochondrial protein degradation ...short-chain fatty acid catabolic process / branched-chain amino acid metabolic process / Propionyl-CoA catabolism / propionyl-CoA carboxylase / propionyl-CoA carboxylase activity / Defective HLCS causes multiple carboxylase deficiency / Biotin transport and metabolism / biotin binding / catalytic complex / Mitochondrial protein degradation / fatty acid metabolic process / mitochondrial matrix / enzyme binding / mitochondrion / ATP binding / metal ion binding / cytosol
Similarity search - Function
Propionyl-coenzyme A carboxylase, BT domain / Propionyl-coenzyme A carboxylase BT domain / : / : / 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 ...Propionyl-coenzyme A carboxylase, BT domain / Propionyl-coenzyme A carboxylase BT domain / : / : / 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 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 / ATP-grasp fold / ATP-grasp fold profile. / ClpP/crotonase-like domain superfamily / Carbamoyl-phosphate synthase subdomain signature 2.
Similarity search - Domain/homology
Propionyl-CoA carboxylase alpha chain, mitochondrial / Propionyl-CoA carboxylase beta chain, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.8 Å
AuthorsZhou FY / Zhang YY / Zhou Q / Hu Q
Funding support1 items
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, 2023-
Header (metadata) releaseOct 30, 2024-
Map releaseOct 30, 2024-
UpdateNov 20, 2024-
Current statusNov 20, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_38438.png

Downloads & links

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Map

FileDownload / File: emd_38438.map.gz / Format: CCP4 / Size: 443.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.08 Å/pix.
x 488 pix.
= 525.722 Å		1.08 Å/pix.
x 488 pix.
= 525.722 Å		1.08 Å/pix.
x 488 pix.
= 525.722 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.0773 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.5
Minimum - Maximum-2.3707364 - 4.708598
Average (Standard dev.)0.00021871549 (±0.110602885)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions488488488
Spacing488488488
CellA=B=C: 525.72235 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_38438_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_38438_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 complex of human propionyl-CoA carboxylase in com...

EntireName: Heterododecamer complex of human propionyl-CoA carboxylase in complex with propionyl-CoA (PCC-PCO)
Components
  • Complex: Heterododecamer complex of human propionyl-CoA carboxylase in complex with propionyl-CoA (PCC-PCO)
    • Protein or peptide: Propionyl-CoA carboxylase alpha chain, mitochondrial
    • Protein or peptide: Propionyl-CoA carboxylase beta chain, mitochondrial
  • Ligand: BIOTIN
  • Ligand: propionyl Coenzyme A

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Supramolecule #1: Heterododecamer complex of human propionyl-CoA carboxylase in com...

SupramoleculeName: Heterododecamer complex of human propionyl-CoA carboxylase in complex with propionyl-CoA (PCC-PCO)
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Propionyl-CoA carboxylase alpha chain, mitochondrial

MacromoleculeName: Propionyl-CoA carboxylase alpha chain, mitochondrial / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO / EC number: propionyl-CoA carboxylase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 80.161922 KDa
SequenceString: MAGFWVGTAP LVAAGRRGRW PPQQLMLSAA LRTLKHVLYY SRQCLMVSRN LGSVGYDPNE KTFDKILVAN RGEIACRVIR TCKKMGIKT VAIHSDVDAS SVHVKMADEA VCVGPAPTSK SYLNMDAIME AIKKTRAQAV HPGYGFLSEN KEFARCLAAE D VVFIGPDT ...String:
MAGFWVGTAP LVAAGRRGRW PPQQLMLSAA LRTLKHVLYY SRQCLMVSRN LGSVGYDPNE KTFDKILVAN RGEIACRVIR TCKKMGIKT VAIHSDVDAS SVHVKMADEA VCVGPAPTSK SYLNMDAIME AIKKTRAQAV HPGYGFLSEN KEFARCLAAE D VVFIGPDT HAIQAMGDKI ESKLLAKKAE VNTIPGFDGV VKDAEEAVRI AREIGYPVMI KASAGGGGKG MRIAWDDEET RD GFRLSSQ EAASSFGDDR LLIEKFIDNP RHIEIQVLGD KHGNALWLNE RECSIQRRNQ KVVEEAPSIF LDAETRRAMG EQA VALARA VKYSSAGTVE FLVDSKKNFY FLEMNTRLQV EHPVTECITG LDLVQEMIRV AKGYPLRHKQ ADIRINGWAV ECRV YAEDP YKSFGLPSIG RLSQYQEPLH LPGVRVDSGI QPGSDISIYY DPMISKLITY GSDRTEALKR MADALDNYVI RGVTH NIAL LREVIINSRF VKGDISTKFL SDVYPDGFKG HMLTKSEKNQ LLAIASSLFV AFQLRAQHFQ ENSRMPVIKP DIANWE LSV KLHDKVHTVV ASNNGSVFSV EVDGSKLNVT STWNLASPLL SVSVDGTQRT VQCLSREAGG NMSIQFLGTV YKVNILT RL AAELNKFMLE KVTEDTSSVL RSPMPGVVVA VSVKPGDAVA EGQEICVIEA MKMQNSMTAG KTGTVKSVHC QAGDTVGE G DLLVELE

UniProtKB: Propionyl-CoA carboxylase alpha chain, mitochondrial

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Macromolecule #2: Propionyl-CoA carboxylase beta chain, mitochondrial

MacromoleculeName: Propionyl-CoA carboxylase beta chain, mitochondrial / type: protein_or_peptide / ID: 2 / Number of copies: 6 / Enantiomer: LEVO / EC number: propionyl-CoA carboxylase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 58.284488 KDa
SequenceString: MAAALRVAAV GARLSVLASG LRAAVRSLCS QATSVNERIE NKRRTALLGG GQRRIDAQHK RGKLTARERI SLLLDPGSFV ESDMFVEHR CADFGMAADK NKFPGDSVVT GRGRINGRLV YVFSQDFTVF GGSLSGAHAQ KICKIMDQAI TVGAPVIGLN D SGGARIQE ...String:
MAAALRVAAV GARLSVLASG LRAAVRSLCS QATSVNERIE NKRRTALLGG GQRRIDAQHK RGKLTARERI SLLLDPGSFV ESDMFVEHR CADFGMAADK NKFPGDSVVT GRGRINGRLV YVFSQDFTVF GGSLSGAHAQ KICKIMDQAI TVGAPVIGLN D SGGARIQE GVESLAGYAD IFLRNVTASG VIPQISLIMG PCAGGAVYSP ALTDFTFMVK DTSYLFITGP DVVKSVTNED VT QEELGGA KTHTTMSGVA HRAFENDVDA LCNLRDFFNY LPLSSQDPAP VRECHDPSDR LVPELDTIVP LESTKAYNMV DII HSVVDE REFFEIMPNY AKNIIVGFAR MNGRTVGIVG NQPKVASGCL DINSSVKGAR FVRFCDAFNI PLITFVDVPG FLPG TAQEY GGIIRHGAKL LYAFAEATVP KVTVITRKAY GGAYDVMSSK HLCGDTNYAW PTAEIAVMGA KGAVEIIFKG HENVE AAQA EYIEKFANPF PAAVRGFVDD IIQPSSTRAR ICCDLDVLAS KKVQRPWRKH ANIPL

UniProtKB: Propionyl-CoA carboxylase beta chain, mitochondrial

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Macromolecule #3: BIOTIN

MacromoleculeName: BIOTIN / type: ligand / ID: 3 / Number of copies: 6 / Formula: BTN
Molecular weightTheoretical: 244.311 Da
Chemical component information

ChemComp-BTN:
BIOTIN

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Macromolecule #4: propionyl Coenzyme A

MacromoleculeName: propionyl Coenzyme A / type: ligand / ID: 4 / Number of copies: 6 / Formula: 1VU
Molecular weightTheoretical: 823.597 Da
Chemical component information

ChemComp-191:
PROPIONYL COENZYME A

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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: 7.4
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: 2.2 µm / Nominal defocus min: 1.2 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: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 105293
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION

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