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- EMDB-35059: Human Pyruvate Carboxylase -

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Basic information

Entry
Database: EMDB / ID: EMD-35059
TitleHuman Pyruvate Carboxylase
Map data
Sample
  • Complex: 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


pyruvate carboxylase / pyruvate carboxylase activity / Defective HLCS causes multiple carboxylase deficiency / Biotin transport and metabolism / viral RNA genome packaging / NADP metabolic process / Pyruvate metabolism / positive regulation by host of viral process / Gluconeogenesis / NADH metabolic process ...pyruvate carboxylase / pyruvate carboxylase activity / Defective HLCS causes multiple carboxylase deficiency / Biotin transport and metabolism / viral RNA genome packaging / NADP metabolic process / Pyruvate metabolism / positive regulation by host of viral process / Gluconeogenesis / NADH metabolic process / pyruvate 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: 5.63 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
DepositionDec 30, 2022-
Header (metadata) releaseJan 31, 2024-
Map releaseJan 31, 2024-
UpdateJan 31, 2024-
Current statusJan 31, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_35059.png

Downloads & links

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Map

FileDownload / File: emd_35059.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
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AxesZ (Sec.)Y (Row.)X (Col.)
1.1 Å/pix.
x 320 pix.
= 351.328 Å		1.1 Å/pix.
x 320 pix.
= 351.328 Å		1.1 Å/pix.
x 320 pix.
= 351.328 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.0979 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.043
Minimum - Maximum-0.16642268 - 0.65033126
Average (Standard dev.)-0.0008528653 (±0.027029239)
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_35059_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_35059_half_map_2.map
Projections & Slices
AxesZYX

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Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Pyruvate carboxylase

EntireName: Pyruvate carboxylase
Components
  • Complex: 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: Pyruvate carboxylase

SupramoleculeName: 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
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: 5.63 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 21450
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: RANDOM ASSIGNMENT

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