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- PDB-9h5i: Haemophilus influenzae serotype b capsule polymerase bcs3 in comp... -

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Basic information

Entry
Database: PDB / ID: 9h5i
TitleHaemophilus influenzae serotype b capsule polymerase bcs3 in complex with acceptor polymer
ComponentsBcs3
KeywordsBIOSYNTHETIC PROTEIN / Capsule polymerase / Haemophilus influenzae serotype b / Pathogens
Function / homology
Function and homology information


CDP-glycerol glycerophosphotransferase activity / teichoic acid biosynthetic process / metal ion binding / plasma membrane
Similarity search - Function
Domain of unknown function DUF5776 / Domain of unknown function (DUF5776) / CDP-glycerol glycerophosphotransferase / CDP-glycerol glycerophosphotransferase, C-terminal domain / CDP-glycerol glycerophosphotransferase, N-terminal domain / : / CDP-Glycerol:Poly(glycerophosphate) glycerophosphotransferase / HAD superfamily / HAD-like superfamily
Similarity search - Domain/homology
beta-D-ribosyl-(1->1)-D-ribitol-5-phosphate / Bcs3
Similarity search - Component
Biological speciesHaemophilus influenzae (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.65 Å
AuthorsDi Domenico, V. / Mast, T. / Cifuente, J.O. / Schulze, J. / Litschko, C. / Alcaide, A. / Villegas, J.C. / Fiebig, T. / Guerin, M.E.
Funding support Spain, United States, Germany, 3items
OrganizationGrant numberCountry
Ministry of Economy and Competitiveness (MINECO) Spain
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
German Research Foundation (DFG) Germany
CitationJournal: To Be Published
Title: Haemophilus influenzae serotype b capsule polymerase bcs3 in complex with acceptor polymer
Authors: Di Domenico, V. / Mast, T. / Cifuente, J.O. / Schulze, J. / Litschko, C. / Alcaide, A. / Villegas, J.C. / Fiebig, T. / Guerin, M.E.
History
DepositionOct 22, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 6, 2026Provider: repository / Type: Initial release
Revision 1.0May 6, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0May 6, 2026Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0May 6, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0May 6, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0May 6, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0May 6, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0May 6, 2026Data 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: Bcs3
B: Bcs3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)279,18216
Polymers274,7622
Non-polymers4,41914
Water1,29772
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area5040 Å2
ΔGint-38 kcal/mol
Surface area97200 Å2
MethodPISA

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Components

#1: Protein Bcs3


Mass: 137381.172 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Haemophilus influenzae (bacteria) / Gene: bcs3', bcs3 / Production host: Escherichia coli (E. coli) / References: UniProt: Q2ERG0
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-KOF / beta-D-ribosyl-(1->1)-D-ribitol-5-phosphate / (2R,3S,4S)-5-(((2R,3R,4S,5R)-3,4-dihydroxy-5-(hydroxymethyl)tetrahydrofuran-2-yl)oxy)-2,3,4-trihydroxypentyl hydrogen phosphate


Mass: 364.240 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C10H21O12P / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 72 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: Physiological dimeric assembly of Bcs3 / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Haemophilus influenzae (bacteria)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.5
Buffer component
IDConc.NameFormulaBuffer-ID
150 mMTrisTris1
2150 mMSodium ChlorideNaCl1
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 90 % / Chamber temperature: 277.15 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 51.85 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of real images: 27103

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Processing

EM software
IDNameVersionCategory
1cryoSPARC4.1particle selection
2EPU3.8.1.7603image acquisition
4cryoSPARC4.1CTF correction
7UCSF Chimeramodel fitting
12cryoSPARC4.23D reconstruction
13PHENIXmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 1578386
3D reconstructionResolution: 2.65 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 388941 / Symmetry type: POINT
Atomic model buildingProtocol: OTHER
Atomic model buildingPDB-ID: 8A0M

8a0m


Accession code: 8A0M / Source name: PDB / Type: experimental model
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00318050
ELECTRON MICROSCOPYf_angle_d0.42224553
ELECTRON MICROSCOPYf_dihedral_angle_d9.0716441
ELECTRON MICROSCOPYf_chiral_restr0.0392730
ELECTRON MICROSCOPYf_plane_restr0.0033135

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