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- EMDB-45076: Structure of Sialyl transferase from Pasturella Multocida -

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Basic information

Entry
Database: EMDB / ID: EMD-45076
TitleStructure of Sialyl transferase from Pasturella Multocida
Map data
Sample
  • Organelle or cellular component: Tetramer of Pasturella multocida sialyl transferase.
    • Protein or peptide: CMP-Neu5Ac--lipooligosaccharide alpha 2-3 sialyltransferase
KeywordsGlycosyl Transferase / TRANSFERASE
Function / homologyAlpha-2,3-sialyltransferase / Alpha-2,3-sialyltransferase superfamily / Alpha-2,3-sialyltransferase (CST-I) / CMP-Neu5Ac--lipooligosaccharide alpha 2-3 sialyltransferase
Function and homology information
Biological speciesPasteurella (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.96 Å
AuthorsSubramanian R / Dhanabalan K
Funding support India, 1 items
OrganizationGrant numberCountry
Department of Biotechnology (DBT, India)DBT/PR12422/MED/31/287/2014 India
CitationJournal: To Be Published
Title: Ambient Ionization Mass Spectrometry and Cryo-Electron Microscopy for Label-Free Enzyme Characterization
Authors: Morato Gutierrez NM / Dhanabalan K
History
DepositionMay 24, 2024-
Header (metadata) releaseJun 11, 2025-
Map releaseJun 11, 2025-
UpdateJun 11, 2025-
Current statusJun 11, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_45076.png

Downloads & links

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Map

FileDownload / File: emd_45076.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.1 Å/pix.
x 256 pix.
= 281.6 Å		1.1 Å/pix.
x 256 pix.
= 281.6 Å		1.1 Å/pix.
x 256 pix.
= 281.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.1 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.27
Minimum - Maximum-2.6711264 - 3.8865662
Average (Standard dev.)-0.0010200922 (±0.07041967)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 281.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_45076_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_45076_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 of Pasturella multocida sialyl transferase.

EntireName: Tetramer of Pasturella multocida sialyl transferase.
Components
  • Organelle or cellular component: Tetramer of Pasturella multocida sialyl transferase.
    • Protein or peptide: CMP-Neu5Ac--lipooligosaccharide alpha 2-3 sialyltransferase

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Supramolecule #1: Tetramer of Pasturella multocida sialyl transferase.

SupramoleculeName: Tetramer of Pasturella multocida sialyl transferase. / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: all
Details: The C-terminal 32 aminoacids that are in the membrane are deleted for recombinant expression.
Source (natural)Organism: Pasteurella (bacteria)
Molecular weightTheoretical: 128 KDa

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Macromolecule #1: CMP-Neu5Ac--lipooligosaccharide alpha 2-3 sialyltransferase

MacromoleculeName: CMP-Neu5Ac--lipooligosaccharide alpha 2-3 sialyltransferase
type: protein_or_peptide / ID: 1
Details: The construct used for expression did not contain the C-terminal 32 amino acids.
Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Pasteurella (bacteria)
Molecular weightTheoretical: 35.696895 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MDKFAEHEIP KAVIVAGNGE SLSQIDYRLL PKNYDVFRCN QFYFEERYFL GNKIKAVFFT PGVFLEQYYT LYHLKRNNEY FVDNVILSS FNHPTVDLEK SQKIQALFID VINGYEKHLS KLTAFDVYLR YKELYENQRI TSGVYMCAVA IAMGYTDIYL T GIDFYQAS ...String:
MDKFAEHEIP KAVIVAGNGE SLSQIDYRLL PKNYDVFRCN QFYFEERYFL GNKIKAVFFT PGVFLEQYYT LYHLKRNNEY FVDNVILSS FNHPTVDLEK SQKIQALFID VINGYEKHLS KLTAFDVYLR YKELYENQRI TSGVYMCAVA IAMGYTDIYL T GIDFYQAS EENYAFDNKK PNIIRLLPDF RKEKTLFSYH SKDIDLEALS FLQQHYHVNF YSISPMSPLS KHFPIPTVED DC ETTFVAP LKENYINDIL LPPHFVYEKL GTIVSKKSRF HSNLIVRLIR DLLKLPSALK HYLKEK

UniProtKB: CMP-Neu5Ac--lipooligosaccharide alpha 2-3 sialyltransferase

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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

Concentration0.8 mg/mL
BufferpH: 7.8 / Component - Concentration: 50.0 mM / Component - Formula: PO4 / Component - Name: PBS
Details: 50 mM HEPES pH 8, 250 mM NaCl, 2% glycerol, and 3 mM DTT
GridModel: Quantifoil R0.6/1 / Material: GOLD / Mesh: 300 / Support film - Material: GOLD / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 150 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 293 K / Instrument: FEI VITROBOT MARK IV
DetailsThe sample is monodisperse

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Average electron dose: 53.5 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated defocus max: 5.0 µm / Calibrated defocus min: 1.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 4.0 µm / Nominal defocus min: 2.5 µm / Nominal magnification: 81000
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

Particle selectionNumber selected: 1205487
CTF correctionSoftware - Name: cryoSPARC (ver. 4.1) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL / In silico model: Alphafold-2 predicted model
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C4 (4 fold cyclic) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 2.96 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.1) / Number images used: 265055
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE
Final 3D classificationNumber classes: 50 / Avg.num./class: 3000 / Software - Name: cryoSPARC
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelChain - Source name: AlphaFold / Chain - Initial model type: in silico model
RefinementSpace: REAL / Protocol: FLEXIBLE FIT / Overall B value: 51.24
Output model

PDB-9c08:
Structure of Sialyl transferase from Pasturella Multocida

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