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- EMDB-38442: Structure of human pyruvate carboxylase -

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ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-38442
TitleStructure of human pyruvate carboxylase
Map data
Sample
  • Complex: Homotetramer complex of human pyruvate carboxylase
    • Protein or peptide: Pyruvate carboxylase, mitochondrial
  • Ligand: BIOTIN
KeywordsBiotin-dependent carboxylase / LIGASE
Function / homology
Function and homology information


pyruvate carboxylase / pyruvate carboxylase activity / Defective HLCS causes multiple carboxylase deficiency / Biotin transport and metabolism / NADP+ metabolic process / viral RNA genome packaging / pyruvate metabolic process / host-mediated activation of viral process / Pyruvate metabolism / Gluconeogenesis ...pyruvate carboxylase / pyruvate carboxylase activity / Defective HLCS causes multiple carboxylase deficiency / Biotin transport and metabolism / NADP+ metabolic process / viral RNA genome packaging / pyruvate metabolic process / host-mediated activation of viral process / Pyruvate metabolism / Gluconeogenesis / : / biotin binding / viral release from host cell / gluconeogenesis / lipid metabolic process / mitochondrial matrix / negative regulation of gene expression / mitochondrion / ATP binding / metal ion binding / identical protein binding / cytoplasm / cytosol
Similarity search - Function
: / Pyruvate carboxylase / Carboxylase, conserved domain / Conserved carboxylase domain / Pyruvate carboxyltransferase / HMGL-like / Pyruvate carboxyltransferase domain. / Biotin-binding site / Biotin-requiring enzymes attachment site. / Biotin carboxylase-like, N-terminal domain ...: / Pyruvate carboxylase / Carboxylase, conserved domain / Conserved carboxylase domain / Pyruvate carboxyltransferase / HMGL-like / Pyruvate carboxyltransferase 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. / Aldolase-type TIM barrel
Similarity search - Domain/homology
Pyruvate carboxylase, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.61 Å
AuthorsZhou FY / Zhang YY / Zhou Q / Hu Q
Funding support China, 1 items
OrganizationGrant numberCountry
Westlake Education Foundation101256021901 China
CitationJournal: Elife / Year: 2024
Title: Structural insights into human propionyl-CoA carboxylase (PCC) and 3-methylcrotonyl-CoA carboxylase (MCC).
Authors: Zhou FY / Zhang YY / Zhu Y / Zhou Q / Shi Y / Hu Q
History
DepositionDec 25, 2023-
Header (metadata) releaseNov 13, 2024-
Map releaseNov 13, 2024-
UpdateNov 27, 2024-
Current statusNov 27, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_38442.png

Downloads & links

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Map

FileDownload / File: emd_38442.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.08 Å/pix.
x 256 pix.
= 275.789 Å		1.08 Å/pix.
x 256 pix.
= 275.789 Å		1.08 Å/pix.
x 256 pix.
= 275.789 Å

Surface

Projections

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.0773 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.3
Minimum - Maximum-4.424362 - 5.9013395
Average (Standard dev.)0.0011132052 (±0.14697737)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 275.7888 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_38442_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_38442_half_map_2.map
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

Histogram (log scale)

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Sample components

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Entire : Homotetramer complex of human pyruvate carboxylase

EntireName: Homotetramer complex of human pyruvate carboxylase
Components
  • Complex: Homotetramer complex of human pyruvate carboxylase
    • Protein or peptide: Pyruvate carboxylase, mitochondrial
  • Ligand: BIOTIN

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Supramolecule #1: Homotetramer complex of human pyruvate carboxylase

SupramoleculeName: Homotetramer complex of human pyruvate carboxylase / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Pyruvate carboxylase, mitochondrial

MacromoleculeName: Pyruvate carboxylase, mitochondrial / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO / EC number: pyruvate carboxylase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 129.799359 KDa
SequenceString: MLKFRTVHGG LRLLGIRRTS TAPAASPNVR RLEYKPIKKV MVANRGEIAI RVFRACTELG IRTVAIYSEQ DTGQMHRQKA DEAYLIGRG LAPVQAYLHI PDIIKVAKEN NVDAVHPGYG FLSERADFAQ ACQDAGVRFI GPSPEVVRKM GDKVEARAIA I AAGVPVVP ...String:
MLKFRTVHGG LRLLGIRRTS TAPAASPNVR RLEYKPIKKV MVANRGEIAI RVFRACTELG IRTVAIYSEQ DTGQMHRQKA DEAYLIGRG LAPVQAYLHI PDIIKVAKEN NVDAVHPGYG FLSERADFAQ ACQDAGVRFI GPSPEVVRKM GDKVEARAIA I AAGVPVVP GTDAPITSLH EAHEFSNTYG FPIIFKAAYG GGGRGMRVVH SYEELEENYT RAYSEALAAF GNGALFVEKF IE KPRHIEV QILGDQYGNI LHLYERDCSI QRRHQKVVEI APAAHLDPQL RTRLTSDSVK LAKQVGYENA GTVEFLVDRH GKH YFIEVN SRLQVEHTVT EEITDVDLVH AQIHVAEGRS LPDLGLRQEN IRINGCAIQC RVTTEDPARS FQPDTGRIEV FRSG EGMGI RLDNASAFQG AVISPHYDSL LVKVIAHGKD HPTAATKMSR ALAEFRVRGV KTNIAFLQNV LNNQQFLAGT VDTQF IDEN PELFQLRPAQ NRAQKLLHYL GHVMVNGPTT PIPVKASPSP TDPVVPAVPI GPPPAGFRDI LLREGPEGFA RAVRNH PGL LLMDTTFRDA HQSLLATRVR THDLKKIAPY VAHNFSKLFS MENWGGATFD VAMRFLYECP WRRLQELREL IPNIPFQ ML LRGANAVGYT NYPDNVVFKF CEVAKENGMD VFRVFDSLNY LPNMLLGMEA AGSAGGVVEA AISYTGDVAD PSRTKYSL Q YYMGLAEELV RAGTHILCIK DMAGLLKPTA CTMLVSSLRD RFPDLPLHIH THDTSGAGVA AMLACAQAGA DVVDVAADS MSGMTSQPSM GALVACTRGT PLDTEVPMER VFDYSEYWEG ARGLYAAFDC TATMKSGNSD VYENEIPGGQ YTNLHFQAHS MGLGSKFKE VKKAYVEANQ MLGDLIKVTP SSKIVGDLAQ FMVQNGLSRA EAEAQAEELS FPRSVVEFLQ GYIGVPHGGF P EPFRSKVL KDLPRVEGRP GASLPPLDLQ ALEKELVDRH GEEVTPEDVL SAAMYPDVFA HFKDFTATFG PLDSLNTRLF LQ GPKIAEE FEVELERGKT LHIKALAVSD LNRAGQRQVF FELNGQLRSI LVKDTQAMKE MHFHPKALKD VKGQIGAPMP GKV IDIKVV AGAKVAKGQP LCVLSAMKME TVVTSPMEGT VRKVHVTKDM TLEGDDLILE IE

UniProtKB: Pyruvate carboxylase, mitochondrial

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Macromolecule #2: BIOTIN

MacromoleculeName: BIOTIN / type: ligand / ID: 2 / Number of copies: 4 / Formula: BTN
Molecular weightTheoretical: 244.311 Da
Chemical component information

ChemComp-BTN:
BIOTIN

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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: PDB ENTRY
PDB model - PDB ID:

6g2d

Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.61 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 677493
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION

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