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- EMDB-64089: Cryo-EM structure of CT-BCCP domain of Pyruvate carboxylase from ... -

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Basic information

Entry
Database: EMDB / ID: EMD-64089
TitleCryo-EM structure of CT-BCCP domain of Pyruvate carboxylase from Mycobacterium tuberculosis
Map data
Sample
  • Complex: Pyruvate carboxylase CT and BCCP domain
    • Protein or peptide: Pyruvate carboxylase
  • Ligand: ZINC ION
  • Ligand: BIOTIN
  • Ligand: OXALATE ION
  • Ligand: water
KeywordsPyruvate Carboxylase / BCCP / CT / Mycobacterium tuberculosis / LIGASE
Function / homology
Function and homology information


pyruvate carboxylase / pyruvate carboxylase activity / biotin carboxylase activity / pyruvate metabolic process / gluconeogenesis / ATP binding / metal ion binding / 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 ...: / 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. / Carbamoyl-phosphate synthase subdomain signature 2. / Aldolase-type TIM barrel
Similarity search - Domain/homology
Pyruvate carboxylase
Similarity search - Component
Biological speciesMycobacterium tuberculosis H37Rv (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsSingh A / Sharma D / 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 in complex with Acetyl-CoA and ADP
Authors: Singh A / Sharma D / Raza M / Singh S / Das U
History
DepositionApr 9, 2025-
Header (metadata) releaseMay 14, 2025-
Map releaseMay 14, 2025-
UpdateMay 14, 2025-
Current statusMay 14, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_64089.png

Downloads & links

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Map

FileDownload / File: emd_64089.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.86 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: 0.0392
Minimum - Maximum-0.21908224 - 0.5021735
Average (Standard dev.)0.00018455439 (±0.010840025)
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_64089_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: DeepEMhancer sharpened map

Fileemd_64089_additional_1.map
AnnotationDeepEMhancer sharpened map
Projections & Slices
AxesZYX

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Density Histograms

Histogram

Histogram (log scale)

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Half map: half Map A

Fileemd_64089_half_map_1.map
Annotationhalf Map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half Map B

Fileemd_64089_half_map_2.map
Annotationhalf Map B
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Pyruvate carboxylase CT and BCCP domain

EntireName: Pyruvate carboxylase CT and BCCP domain
Components
  • Complex: Pyruvate carboxylase CT and BCCP domain
    • Protein or peptide: Pyruvate carboxylase
  • Ligand: ZINC ION
  • Ligand: BIOTIN
  • Ligand: OXALATE ION
  • Ligand: water

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Supramolecule #1: Pyruvate carboxylase CT and BCCP domain

SupramoleculeName: Pyruvate carboxylase CT and BCCP domain / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
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: 2 / Enantiomer: LEVO / EC number: pyruvate carboxylase
Source (natural)Organism: Mycobacterium tuberculosis H37Rv (bacteria)
Molecular weightTheoretical: 72.465047 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: ADRGTKILNF LADVTVNNPY GSRPSTIYPD DKLPDLDLRA APPAGSKQRL VKLGPEGFAR WLRESAAVGV TDTTFRDAHQ SLLATRVRT SGLSRVAPYL ARTMPQLLSV ECWGGATYDV ALRFLKEDPW ERLATLRAAM PNICLQMLLR GRNTVGYTPY P EIVTSAFV ...String:
ADRGTKILNF LADVTVNNPY GSRPSTIYPD DKLPDLDLRA APPAGSKQRL VKLGPEGFAR WLRESAAVGV TDTTFRDAHQ SLLATRVRT SGLSRVAPYL ARTMPQLLSV ECWGGATYDV ALRFLKEDPW ERLATLRAAM PNICLQMLLR GRNTVGYTPY P EIVTSAFV QEATATGIDI FRIFDALNNI ESMRPAIDAV RETGSAIAEV AMCYTGDLTD PGEQLYTLDY YLKLAEQIVD AG AHVLAIK DMAGLLRPPA AQRLVSALRS RFDLPVHLHT HDTPGGQLAS YVAAWHAGAD AVDGAAAPLA GTTSQPALSS IVA AAAHTE YDTGLSLSAV CALEPYWEAL RKVYAPFESG LPGPTGRVYH HEIPGGQLSN LRQQAIALGL GDRFEEIEEA YAGA DRVLG RLVKVTPTSK VVGDLALALV GAGVSADEFA SDPARFGIPE SVLGFLRGEL GDPPGGWPEP LRTAALAGRG AARPT AQLA ADDEIALSSV GAKRQATLNR LLFPSPTKEF NEHREAYGDT SQLSANQFFY GLRQGEEHRV KLERGVELLI GLEAIS EPD ERGMRTVMCI LNGQLRPVLV RDRSIASAVP AAEKADRGNP GHIAAPFAGV VTVGVCVGER VGAGQTIATI EAMKMEA PI TAPVAGTVER VAVSDTAQVE GGDLLVVVSG HHHHHHG

UniProtKB: Pyruvate carboxylase

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Macromolecule #2: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 2 / Number of copies: 1 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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Macromolecule #3: BIOTIN

MacromoleculeName: BIOTIN / type: ligand / ID: 3 / Number of copies: 1 / Formula: BTN
Molecular weightTheoretical: 244.311 Da
Chemical component information

ChemComp-BTN:
BIOTIN

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Macromolecule #4: OXALATE ION

MacromoleculeName: OXALATE ION / type: ligand / ID: 4 / Number of copies: 1 / Formula: OXL
Molecular weightTheoretical: 88.019 Da
Chemical component information

ChemComp-OXL:
OXALATE ION

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Macromolecule #5: water

MacromoleculeName: water / type: ligand / ID: 5 / Number of copies: 3 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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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 R2/1 / Material: COPPER / Mesh: 300 / 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: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.6.2) / Number images used: 110575
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

9ubg


Chain - Source name: PDB / Chain - Initial model type: experimental model
SoftwareName: UCSF ChimeraX
RefinementProtocol: AB INITIO MODEL
Output model

PDB-9ueq:
Cryo-EM structure of CT-BCCP domain of Pyruvate carboxylase from Mycobacterium tuberculosis

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