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- PDB-9rmk: Structure of the O-oligosaccharyl transferase PglL from Neisseria... -

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Basic information

Entry
Database: PDB / ID: 9rmk
TitleStructure of the O-oligosaccharyl transferase PglL from Neisseria meningitidis in complex with a nanobody
Components
  • Nanobody
  • Oligosaccharyltransferase
KeywordsMEMBRANE PROTEIN / glycosyl transferase / O-transferase
Function / homology
Function and homology information


protein O-linked glycosylation / transferase activity / membrane
Similarity search - Function
Virulence factor membrane-bound polymerase, C-terminal / Virulence factor membrane-bound polymerase, C-terminal / O-antigen ligase-related / : / O-Antigen ligase
Similarity search - Domain/homology
PHOSPHATIDYLETHANOLAMINE / Oligosaccharyltransferase
Similarity search - Component
Biological speciesNeisseria meningitidis (bacteria)
Lama glama (llama)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsHarrison, P.J. / Naismith, J.H. / Clare, D.K. / Quigley, A.
Funding support United Kingdom, 3items
OrganizationGrant numberCountry
Wellcome Trust223727/Z/21/Z United Kingdom
Wellcome Trust02892/Z/16/Z United Kingdom
Wellcome Trust100209/Z/12/Z United Kingdom
CitationJournal: To Be Published
Title: O-oligosaccharyl transferase PglL
Authors: Harrison, P.J. / Naismith, J.H. / Clare, D.K. / Quigley, A.
History
DepositionJun 18, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 8, 2026Provider: repository / Type: Initial release
Revision 1.0Jul 8, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jul 8, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Jul 8, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 8, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 8, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jul 8, 2026Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Jul 8, 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

Downloads & links

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Assembly

Deposited unit
A: Oligosaccharyltransferase
F: Nanobody
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,0313
Polymers83,2972
Non-polymers7341
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein Oligosaccharyltransferase


Mass: 68008.438 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neisseria meningitidis (bacteria) / Gene: pglL / Production host: Escherichia coli (E. coli) / References: UniProt: G1FG65
#2: Antibody Nanobody


Mass: 15288.760 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lama glama (llama) / Production host: Escherichia coli (E. coli)
#3: Chemical ChemComp-PTY / PHOSPHATIDYLETHANOLAMINE


Mass: 734.039 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C40H80NO8P / Feature type: SUBJECT OF INVESTIGATION / Comment: phospholipid*YM
Has ligand of interestY
Has protein modificationY

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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: PglL in complex with a nanobody / Type: ORGANELLE OR CELLULAR COMPONENT / Entity ID: #1-#2 / Source: RECOMBINANT
Molecular weightValue: 0.08321964 MDa / Experimental value: NO
Source (natural)Organism: Neiserria meningitis (bacteria)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.4
SpecimenConc.: 2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Details: Monodisperse complex of PglL with nanobody purified by gel filtration.
Specimen supportGrid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 256 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: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 130000 X / Nominal defocus max: 2500 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 65 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARC3.2particle selection
2REFMAC5.8.0430model refinement
5CTFFIND4CTF correction
13cryoSPARC3.23D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 59547 / Symmetry type: POINT
RefinementResolution: 3.3→3.3 Å / Cor.coef. Fo:Fc: 0.742 / SU B: 19.562 / SU ML: 0.302 / Cross valid method: NONE / ESU R: 0.568
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflection
Rwork0.48121 --
obs0.48121 59402 100 %
Solvent computationSolvent model: PARAMETERS FOR MASK CACLULATION
Displacement parametersBiso mean: 79.019 Å2
Refinement stepCycle: 1 / Total: 5680
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
ELECTRON MICROSCOPYr_bond_refined_d0.0070.0125834
ELECTRON MICROSCOPYr_bond_other_d00.0165608
ELECTRON MICROSCOPYr_angle_refined_deg1.3261.7927939
ELECTRON MICROSCOPYr_angle_other_deg0.4451.71612847
ELECTRON MICROSCOPYr_dihedral_angle_1_deg4.2765716
ELECTRON MICROSCOPYr_dihedral_angle_2_deg17.554535
ELECTRON MICROSCOPYr_dihedral_angle_3_deg15.27110922
ELECTRON MICROSCOPYr_dihedral_angle_4_deg
ELECTRON MICROSCOPYr_chiral_restr0.0590.2893
ELECTRON MICROSCOPYr_gen_planes_refined0.0050.026817
ELECTRON MICROSCOPYr_gen_planes_other0.0010.021415
ELECTRON MICROSCOPYr_nbd_refined
ELECTRON MICROSCOPYr_nbd_other
ELECTRON MICROSCOPYr_nbtor_refined
ELECTRON MICROSCOPYr_nbtor_other
ELECTRON MICROSCOPYr_xyhbond_nbd_refined
ELECTRON MICROSCOPYr_xyhbond_nbd_other
ELECTRON MICROSCOPYr_metal_ion_refined
ELECTRON MICROSCOPYr_metal_ion_other
ELECTRON MICROSCOPYr_symmetry_vdw_refined
ELECTRON MICROSCOPYr_symmetry_vdw_other
ELECTRON MICROSCOPYr_symmetry_hbond_refined
ELECTRON MICROSCOPYr_symmetry_hbond_other
ELECTRON MICROSCOPYr_symmetry_metal_ion_refined
ELECTRON MICROSCOPYr_symmetry_metal_ion_other
ELECTRON MICROSCOPYr_mcbond_it8.5947.1792870
ELECTRON MICROSCOPYr_mcbond_other8.5897.1792870
ELECTRON MICROSCOPYr_mcangle_it13.98912.9043584
ELECTRON MICROSCOPYr_mcangle_other13.98812.9083585
ELECTRON MICROSCOPYr_scbond_it11.0578.4822964
ELECTRON MICROSCOPYr_scbond_other11.0568.4832965
ELECTRON MICROSCOPYr_scangle_it
ELECTRON MICROSCOPYr_scangle_other18.50114.9384356
ELECTRON MICROSCOPYr_long_range_B_refined25.16784.9923857
ELECTRON MICROSCOPYr_long_range_B_other25.16684.9923858
ELECTRON MICROSCOPYr_rigid_bond_restr
ELECTRON MICROSCOPYr_sphericity_free
ELECTRON MICROSCOPYr_sphericity_bonded
LS refinement shellResolution: 3→3.078 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0 0 -
Rwork2.05 4399 -
obs--100 %

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