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- EMDB-36044: Human pyruvate carboxylase in BCCP-CTS state without BC -

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Basic information

Entry
Database: EMDB / ID: EMD-36044
TitleHuman pyruvate carboxylase in BCCP-CTS state without BC
Map data
Sample
  • Complex: Tetramer complex of human pyruvate carboxylase
    • Protein or peptide: Pyruvate carboxylase, mitochondrial
  • Ligand: 5-(HEXAHYDRO-2-OXO-1H-THIENO[3,4-D]IMIDAZOL-6-YL)PENTANAL
KeywordsPC / Mitochondrial / CYTOSOLIC PROTEIN
Function / homology
Function and homology information


Defective HLCS causes multiple carboxylase deficiency / Biotin transport and metabolism / pyruvate carboxylase / pyruvate carboxylase activity / viral RNA genome packaging / NADP metabolic process / positive regulation by host of viral process / pyruvate metabolic process / Gluconeogenesis / NADH metabolic process ...Defective HLCS causes multiple carboxylase deficiency / Biotin transport and metabolism / pyruvate carboxylase / pyruvate carboxylase activity / viral RNA genome packaging / NADP metabolic process / positive regulation by host of viral process / pyruvate metabolic process / Gluconeogenesis / NADH metabolic process / biotin binding / viral release from host cell / gluconeogenesis / lipid metabolic process / mitochondrial matrix / negative regulation of gene expression / mitochondrion / ATP binding / identical protein binding / metal ion binding / cytosol / cytoplasm
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 / Biotin carboxylase, C-terminal ...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: 3.83 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 pyruvate carboxylase
Authors: Liu DS / Su JY
History
DepositionApr 27, 2023-
Header (metadata) releaseMay 8, 2024-
Map releaseMay 8, 2024-
UpdateMay 8, 2024-
Current statusMay 8, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_36044.png

Downloads & links

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Map

FileDownload / File: emd_36044.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.0979 Å
Density
Contour LevelBy AUTHOR: 0.138
Minimum - Maximum-0.3144675 - 0.80964243
Average (Standard dev.)-0.0016422679 (±0.034656737)
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_36044_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_36044_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 : Tetramer complex of human pyruvate carboxylase

EntireName: Tetramer complex of human pyruvate carboxylase
Components
  • Complex: Tetramer complex of human pyruvate carboxylase
    • Protein or peptide: Pyruvate carboxylase, mitochondrial
  • Ligand: 5-(HEXAHYDRO-2-OXO-1H-THIENO[3,4-D]IMIDAZOL-6-YL)PENTANAL

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Supramolecule #1: Tetramer complex of human pyruvate carboxylase

SupramoleculeName: Tetramer 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
Recombinant expressionOrganism: Homo sapiens (human)
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: 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: 2 / Number of copies: 4 / 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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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
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 1.8 µm / Nominal defocus min: 1.3 µm
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: INSILICO MODEL
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: ANGULAR RECONSTITUTION
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.83 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 21326

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