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- EMDB-65383: Cryo-EM structure of Pyruvate carboxylase from Mycobacterium tube... -

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Basic information

Entry
Database: EMDB / ID: EMD-65383
TitleCryo-EM structure of Pyruvate carboxylase from Mycobacterium tuberculosis
Map dataMain map by cryosparc non uniform refinement
Sample
  • Complex: Pyruvate carboxylase
    • Protein or peptide: Pyruvate carboxylase
KeywordsPyruvate Carboxylase / Mycobacterium tuberculosis / LIGASE
Function / homology
Function and homology information


pyruvate carboxylase / pyruvate carboxylase activity / biotin carboxylase activity / gluconeogenesis / ATP binding / metal ion binding
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 / Carbamoyl-phosphate synthase subdomain signature 2.
Similarity search - Domain/homology
Pyruvate carboxylase
Similarity search - Component
Biological speciesMycobacterium tuberculosis H37Rv (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.85 Å
AuthorsSingh A / Raza M / Singh S / Das U
Funding support India, 1 items
OrganizationGrant numberCountry
Not funded India
CitationJournal: To Be Published
Title: Cryo-EM structure of Pyruvate carboxylase from Mycobacterium tuberculosis
Authors: Singh A / Sharma D / Raza M / Singh S / Das U
History
DepositionJul 15, 2025-
Header (metadata) releaseJul 22, 2026-
Map releaseJul 22, 2026-
UpdateJul 22, 2026-
Current statusJul 22, 2026Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_65383.png

Downloads & links

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Map

FileReleased
AnnotationMain map by cryosparc non uniform refinement
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.86 Å/pix.
x 360 pix.
= 309.6 Å		0.86 Å/pix.
x 360 pix.
= 309.6 Å		0.86 Å/pix.
x 360 pix.
= 309.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.86 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0254
Minimum - Maximum-0.075435825 - 0.20505628
Average (Standard dev.)0.00072768895 (±0.009018445)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 309.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_65383_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Sharpened map by Em ready

Fileemd_65383_additional_1.map
AnnotationSharpened map by Em ready
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half MapB

Fileemd_65383_half_map_1.map
AnnotationHalf MapB
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half mapA

Fileemd_65383_half_map_2.map
AnnotationHalf mapA
Projections & Slices
AxesZYX

Projections

Slices (1/2)
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

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Supramolecule #1: Pyruvate carboxylase

SupramoleculeName: Pyruvate carboxylase / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Mycobacterium tuberculosis H37Rv (bacteria)
Molecular weightTheoretical: 482 KDa

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Macromolecule #1: Pyruvate carboxylase

MacromoleculeName: Pyruvate carboxylase / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO / EC number: pyruvate carboxylase
Source (natural)Organism: Mycobacterium tuberculosis H37Rv (bacteria)
Molecular weightTheoretical: 120.554477 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MFSKVLVANR GEIAIRAFRA AYELGVGTVA VYPYEDRNSQ HRLKADESYQ IGDIGHPVHA YLSVDEIVAT ARRAGADAIY PGYGFLSEN PDLAAACAAA GISFVGPSAE VLELAGNKSR AIAAAREAGL PVLMSSAPSA SVDELLSVAA GMPFPLFVKA V AGGGGRGM ...String:
MFSKVLVANR GEIAIRAFRA AYELGVGTVA VYPYEDRNSQ HRLKADESYQ IGDIGHPVHA YLSVDEIVAT ARRAGADAIY PGYGFLSEN PDLAAACAAA GISFVGPSAE VLELAGNKSR AIAAAREAGL PVLMSSAPSA SVDELLSVAA GMPFPLFVKA V AGGGGRGM RRVGDIAALP EAIEAASREA ESAFGDPTVY LEQAVINPRH IEVQILADNL GDVIHLYERD CSVQRRHQKV IE LAPAPHL DAELRYKMCV DAVAFARHIG YSCAGTVEFL LDERGEYVFI EMNPRVQVEH TVTEEITDVD LVASQLRIAA GET LEQLGL RQEDIAPHGA ALQCRITTED PANGFRPDTG RISALRTAGG AGVRLDGSTN LGAEISPYFD SMLVKLTCRG RDLP TAVSR ARRAIAEFRI RGVSTNIPFL QAVLDDPDFR AGRVTTSFID ERPQLLTARA SADRGTKILN FLADVTVNNP YGSRP STIY PDDKLPDLDL RAAPPAGSKQ RLVKLGPEGF ARWLRESAAV GVTDTTFRDA HQSLLATRVR TSGLSRVAPY LARTMP QLL SVECWGGATY DVALRFLKED PWERLATLRA AMPNICLQML LRGRNTVGYT PYPEIVTSAF VQEATATGID IFRIFDA LN NIESMRPAID AVRETGSAIA EVAMCYTGDL TDPGEQLYTL DYYLKLAEQI VDAGAHVLAI KDMAGLLRPP AAQRLVSA L RSRFDLPVHL HTHDTPGGQL ASYVAAWHAG ADAVDGAAAP LAGTTSQPAL SSIVAAAAHT EYDTGLSLSA VCALEPYWE ALRKVYAPFE SGLPGPTGRV YHHEIPGGQL SNLRQQAIAL GLGDRFEEIE EAYAGADRVL GRLVKVTPTS KVVGDLALAL VGAGVSADE FASDPARFGI PESVLGFLRG ELGDPPGGWP EPLRTAALAG RGAARPTAQL AADDEIALSS VGAKRQATLN R LLFPSPTK EFNEHREAYG DTSQLSANQF FYGLRQGEEH RVKLERGVEL LIGLEAISEP DERGMRTVMC ILNGQLRPVL VR DRSIASA VPAAEKADRG NPGHIAAPFA GVVTVGVCVG ERVGAGQTIA TIEAMKMEAP ITAPVAGTVE RVAVSDTAQV EGG DLLVVV S

UniProtKB: Pyruvate carboxylase

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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
GridModel: Quantifoil R2/2 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Support film - Film thickness: 2
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
SoftwareName: EPU
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number real images: 6780 / Average exposure time: 1.04 sec. / 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: 0.8 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionApplied symmetry - Point group: D2 (2x2 fold dihedral) / Resolution.type: BY AUTHOR / Resolution: 3.85 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.6.2) / Number images used: 199752
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelChain - Source name: AlphaFold / Chain - Initial model type: in silico model
SoftwareName: Coot
RefinementProtocol: FLEXIBLE FIT
Output model

PDB-9vvk:
Cryo-EM structure of Pyruvate carboxylase from Mycobacterium tuberculosis

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