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

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Basic information

Entry
Database: PDB / ID: 9c08
TitleStructure of Sialyl transferase from Pasturella Multocida
ComponentsCMP-Neu5Ac--lipooligosaccharide alpha 2-3 sialyltransferase
KeywordsTRANSFERASE / Glycosyl 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)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.96 Å
AuthorsSubramanian, R. / Dhanabalan, K.
Funding support India, 1items
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, N.M. / Dhanabalan, K.
History
DepositionMay 24, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 11, 2025Provider: repository / Type: Initial release
Revision 1.0Jun 11, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jun 11, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Jun 11, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jun 11, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jun 11, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jun 11, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CMP-Neu5Ac--lipooligosaccharide alpha 2-3 sialyltransferase
B: CMP-Neu5Ac--lipooligosaccharide alpha 2-3 sialyltransferase
C: CMP-Neu5Ac--lipooligosaccharide alpha 2-3 sialyltransferase
D: CMP-Neu5Ac--lipooligosaccharide alpha 2-3 sialyltransferase


Theoretical massNumber of molelcules
Total (without water)142,7884
Polymers142,7884
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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


Mass: 35696.895 Da / Num. of mol.: 4 / Fragment: C-terminal 32 amino acids deletion
Source method: isolated from a genetically manipulated source
Details: The construct used for expression did not contain the C-terminal 32 amino acids.
Source: (gene. exp.) Pasteurella (bacteria) / Gene: PM1174 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9CLP3
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Tetramer of Pasturella multocida sialyl transferase. / Type: ORGANELLE OR CELLULAR COMPONENT
Details: The C-terminal 32 aminoacids that are in the membrane are deleted for recombinant expression.
Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 0.128 MDa / Experimental value: NO
Source (natural)Organism: Pasteurella (bacteria)
Source (recombinant)Organism: Escherichia coli (E. coli) / Plasmid: PET28
Buffer solutionpH: 7.8
Details: 50 mM HEPES pH 8, 250 mM NaCl, 2% glycerol, and 3 mM DTT
Buffer componentConc.: 50 mM / Name: PBS / Formula: PO4
SpecimenConc.: 0.8 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: The sample is monodisperse
Specimen supportGrid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R0.6/1
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 90 % / Chamber temperature: 293 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 81000 X / Nominal defocus max: 4000 nm / Nominal defocus min: 2500 nm / Calibrated defocus min: 1000 nm / Calibrated defocus max: 5000 nm / Alignment procedure: BASIC
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 53.5 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of grids imaged: 1

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Processing

EM software
IDNameVersionCategory
1cryoSPARC4.1particle selection
2EMANimage acquisition
4cryoSPARC4.1CTF correction
7PHENIXmodel fitting
11cryoSPARCclassification
12cryoSPARC4.13D reconstruction
13PHENIXmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 1205487
SymmetryPoint symmetry: C4 (4 fold cyclic)
3D reconstructionResolution: 2.96 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 265055 / Algorithm: FOURIER SPACE / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingB value: 51.24 / Protocol: FLEXIBLE FIT / Space: REAL
Atomic model buildingSource name: AlphaFold / Type: in silico model

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