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- EMDB-64173: BCCP-BC Conformation of ATP-bound hPCC -

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Basic information

Entry
Database: EMDB / ID: EMD-64173
TitleBCCP-BC Conformation of ATP-bound hPCC
Map data
Sample
  • Complex: Propionyl-CoA carboxylase
    • Protein or peptide: Propionyl-CoA carboxylase alpha chain, mitochondrial
    • Protein or peptide: Propionyl-CoA carboxylase beta chain, mitochondrial
    • Protein or peptide: Propionyl-CoA carboxylase beta chain, mitochondrial
  • Ligand: BIOTIN
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: MAGNESIUM ION
  • Ligand: BICARBONATE ION
  • Ligand: propionyl Coenzyme A
Keywordscarboxylase / TRANSFERASE
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, N-terminal / Acetyl-coenzyme A (CoA) carboxyltransferase N-terminal domain profile. / Acetyl-coenzyme A carboxyltransferase, C-terminal / Acetyl-coenzyme A (CoA) carboxyltransferase C-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, N-terminal / Acetyl-coenzyme A (CoA) carboxyltransferase N-terminal domain profile. / Acetyl-coenzyme A carboxyltransferase, C-terminal / Acetyl-coenzyme A (CoA) carboxyltransferase C-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: 2.48 Å
AuthorsNi FY / Yan HF / Wang QH / Ma JP
Funding support China, 2 items
OrganizationGrant numberCountry
Other government2021YFF1200400 China
Other government2018SHZDZX01 China
CitationJournal: Structure / Year: 2025
Title: Nanoscale conformational dynamics of human propionyl-CoA carboxylase.
Authors: Huifang Yan / Fengyun Ni / Qinghua Wang / Jianpeng Ma /
Abstract: Propionyl-CoA carboxylase (PCC) is a biotin-dependent mitochondrial enzyme responsible for propionyl-CoA catabolism. Deficiencies in human PCC (hPCC) cause propionic acidemia, a severe metabolic ...Propionyl-CoA carboxylase (PCC) is a biotin-dependent mitochondrial enzyme responsible for propionyl-CoA catabolism. Deficiencies in human PCC (hPCC) cause propionic acidemia, a severe metabolic disorder driven by toxic metabolite accumulation. Despite its therapeutic relevance, the structural basis of hPCC's catalytic function remains unresolved. Here, we present high-resolution cryo-EM structures of hPCC in four distinct states, unliganded, ADP-, AMPPNP-, and ATP-bound/substrate-bound, capturing the full trajectory of the biotin carboxyl carrier protein (BCCP) domain as it translocates between active sites. Our results reinforce the crucial role of nucleotide-gated B-lid subdomain in synchronizing catalysis through coupling with BCCP movement. Structural and biochemical analysis of 10 disease-associated variants reveals how mutations disrupt key domain interfaces and dynamic motions required for activity. These new insights define the mechanistic principles governing hPCC functions, establish a structural framework for understanding PCC-related disorders, and lay the groundwork for future efforts to engineer functional replacements or modulators for metabolic therapy.
History
DepositionApr 14, 2025-
Header (metadata) releaseNov 19, 2025-
Map releaseNov 19, 2025-
UpdateNov 19, 2025-
Current statusNov 19, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_64173.png

Downloads & links

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Map

FileDownload / File: emd_64173.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.84 Å/pix.
x 384 pix.
= 322.56 Å		0.84 Å/pix.
x 384 pix.
= 322.56 Å		0.84 Å/pix.
x 384 pix.
= 322.56 Å

Surface

Projections

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.84 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.05
Minimum - Maximum-0.34391376 - 0.76983637
Average (Standard dev.)0.00043814408 (±0.013912748)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 322.56 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_64173_msk_1.map
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Half map: #1

Fileemd_64173_half_map_1.map
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Half map: #2

Fileemd_64173_half_map_2.map
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Sample components

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Entire : Propionyl-CoA carboxylase

EntireName: Propionyl-CoA carboxylase
Components
  • Complex: Propionyl-CoA carboxylase
    • Protein or peptide: Propionyl-CoA carboxylase alpha chain, mitochondrial
    • Protein or peptide: Propionyl-CoA carboxylase beta chain, mitochondrial
    • Protein or peptide: Propionyl-CoA carboxylase beta chain, mitochondrial
  • Ligand: BIOTIN
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: MAGNESIUM ION
  • Ligand: BICARBONATE ION
  • Ligand: propionyl Coenzyme A

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Supramolecule #1: Propionyl-CoA carboxylase

SupramoleculeName: Propionyl-CoA carboxylase / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
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: 1 / Enantiomer: LEVO / EC number: propionyl-CoA carboxylase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 80.161922 KDa
Recombinant expressionOrganism: Homo sapiens (human)
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: 1 / Enantiomer: LEVO / EC number: propionyl-CoA carboxylase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 27.095178 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: DPSDRLVPEL DTIVPLESTK AYNMVDIIHS VVDEREFFEI MPNYAKNIIV GFARMNGRTV GIVGNQPKVA SGCLDINSSV KGARFVRFC DAFNIPLITF VDVPGFLPGT AQEYGGIIRH GAKLLYAFAE ATVPKVTVIT RKAYGGAYDV MSSKHLCGDT N YAWPTAEI ...String:
DPSDRLVPEL DTIVPLESTK AYNMVDIIHS VVDEREFFEI MPNYAKNIIV GFARMNGRTV GIVGNQPKVA SGCLDINSSV KGARFVRFC DAFNIPLITF VDVPGFLPGT AQEYGGIIRH GAKLLYAFAE ATVPKVTVIT RKAYGGAYDV MSSKHLCGDT N YAWPTAEI AVMGAKGAVE IIFKGHENVE AAQAEYIEKF ANPFPAAVRG FVDDIIQPSS TRARICCDLD VLASKKVQRP WR KHANIPL

UniProtKB: Propionyl-CoA carboxylase beta chain, mitochondrial

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Macromolecule #3: Propionyl-CoA carboxylase beta chain, mitochondrial

MacromoleculeName: Propionyl-CoA carboxylase beta chain, mitochondrial / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO / EC number: propionyl-CoA carboxylase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 31.20749 KDa
Recombinant expressionOrganism: Homo sapiens (human)
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 VRECH

UniProtKB: Propionyl-CoA carboxylase beta chain, mitochondrial

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Macromolecule #4: BIOTIN

MacromoleculeName: BIOTIN / type: ligand / ID: 4 / Number of copies: 1 / Formula: BTN
Molecular weightTheoretical: 244.311 Da
Chemical component information

ChemComp-BTN:
BIOTIN

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Macromolecule #5: ADENOSINE-5'-TRIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 5 / Number of copies: 1 / Formula: ATP
Molecular weightTheoretical: 507.181 Da
Chemical component information

ChemComp-ATP:
ADENOSINE-5'-TRIPHOSPHATE / ATP, energy-carrying molecule*YM

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Macromolecule #6: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 6 / Number of copies: 1 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #7: BICARBONATE ION

MacromoleculeName: BICARBONATE ION / type: ligand / ID: 7 / Number of copies: 1 / Formula: BCT
Molecular weightTheoretical: 61.017 Da
Chemical component information

ChemComp-BCT:
BICARBONATE ION

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Macromolecule #8: propionyl Coenzyme A

MacromoleculeName: propionyl Coenzyme A / type: ligand / ID: 8 / Number of copies: 1 / 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: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.6 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: NONE
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.48 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 653775
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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