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- EMDB-65188: BC-BCCP/CT-BCCP domain of Mycobacterium tuberculosis Pyruvate car... -

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Basic information

Entry
Database: EMDB / ID: EMD-65188
TitleBC-BCCP/CT-BCCP domain of Mycobacterium tuberculosis Pyruvate carboxylase- local refinement
Map dataLocal refined map by cryosparc
Sample
  • Complex: Pyruvate carboxylase
    • Protein or peptide: Pyruvate carboxylase
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: BIOTIN
  • Ligand: ZINC ION
KeywordsPyruvate Carboxylase / Pyruvate / BCCP / 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 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.96 Å
AuthorsSingh A / 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 / Das U
History
DepositionJun 27, 2025-
Header (metadata) releaseJul 15, 2026-
Map releaseJul 15, 2026-
UpdateJul 15, 2026-
Current statusJul 15, 2026Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_65188.png

Downloads & links

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Map

FileDownload / File: emd_65188.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationLocal refined map by cryosparc
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: 0.0157
Minimum - Maximum-0.06809488 - 0.16305102
Average (Standard dev.)0.0002311779 (±0.0047083185)
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_65188_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 LocScale

Fileemd_65188_additional_1.map
AnnotationSharpened map by LocScale
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map A

Fileemd_65188_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_65188_half_map_2.map
AnnotationHalf map B
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
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: BIOTIN
  • Ligand: ZINC ION

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Supramolecule #1: Pyruvate carboxylase

SupramoleculeName: Pyruvate carboxylase / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Mycobacterium tuberculosis (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 (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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Macromolecule #2: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 2 / Number of copies: 1 / Formula: ADP
Molecular weightTheoretical: 427.201 Da
Chemical component information

ChemComp-ADP:
ADENOSINE-5'-DIPHOSPHATE / ADP, energy-carrying molecule*YM

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Macromolecule #3: BIOTIN

MacromoleculeName: BIOTIN / type: ligand / ID: 3 / Number of copies: 2 / Formula: BTN
Molecular weightTheoretical: 244.311 Da
Chemical component information

ChemComp-BTN:
BIOTIN

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Macromolecule #4: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 4 / Number of copies: 1 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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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

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number real images: 8400 / 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: PDB ENTRY
PDB model - PDB ID:

9ubg

Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.96 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 461170
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
RefinementProtocol: AB INITIO MODEL
Output model

PDB-9vmh:
BC-BCCP/CT-BCCP domain of Mycobacterium tuberculosis Pyruvate carboxylase- local refinement

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