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- PDB-9gos: CryoEM structure of the native Chlamydomonas reinhardtii Flagella... -

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Basic information

Entry
Database: PDB / ID: 9gos
TitleCryoEM structure of the native Chlamydomonas reinhardtii Flagella Membrane Glycoprotein 1B.
ComponentsFlagella Membrane Glycoprotein 1B
KeywordsMEMBRANE PROTEIN / Mucin / Glycoprotein / Glycocalyx
Biological speciesChlamydomonas reinhardtii (plant)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsNievergelt, A.P. / Hoepfner, L.M. / Matrino, F. / Scholz, M. / Foster, H.E. / Rodenfels, J. / von Appen, A. / Hippler, M. / Pigino, G.
Funding support France, European Union, Germany, 4items
OrganizationGrant numberCountry
Human Frontier Science Program (HFSP)LT000515/2019 France
European Molecular Biology Organization (EMBO)ALTF 891-2018European Union
European Research Council (ERC)819826European Union
German Research Foundation (DFG)HI 739/12-4 Germany
CitationJournal: To Be Published
Title: CryoEM structure of the native Chlamydomonas reinhardtii Flagella Membrane Glycoprotein 1B.
Authors: Nievergelt, A.P. / Hoepfner, L.M. / Matrino, F. / Scholz, M. / Foster, H.E. / Rodenfels, J. / von Appen, A. / Hippler, M. / Pigino, G.
History
DepositionSep 6, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 7, 2025Provider: repository / Type: Initial release
Revision 1.0May 7, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
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Revision 1.0May 7, 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: Flagella Membrane Glycoprotein 1B


Theoretical massNumber of molelcules
Total (without water)448,2271
Polymers448,2271
Non-polymers00
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 Flagella Membrane Glycoprotein 1B


Mass: 448226.625 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / Strain: CC-124 32M fmg1a
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: Flagella Membrane Glycoprotein 1B / Type: ORGANELLE OR CELLULAR COMPONENT
Details: Material purified from endogenous Chlamydomonas cilia by lectin affinity chromatography.
Entity ID: all / Source: NATURAL
Molecular weightValue: 0.55 MDa / Experimental value: YES
Source (natural)Organism: Chlamydomonas reinhardtii (plant) / Strain: CC-124 32M fmg1a / Cellular location: Ciliary membrane / Organelle: Cilia
Buffer solutionpH: 7.3
Buffer component
IDConc.NameFormulaBuffer-ID
110 mM4-(2-hydroxyethyl)-1-piperazineethanesulfonic acidHEPES1
2300 mMsodium chlorideNaCl1
31
SpecimenConc.: 0.2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Details: The is sample lightly clusters but can be separated due to the large size
Specimen supportDetails: Grids were washed in chloroform before discharge. / Grid material: COPPER / Grid mesh size: 400 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: LEICA EM GP / Cryogen name: ETHANE / Humidity: 90 % / Chamber temperature: 297 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: 81000 X / Calibrated magnification: 81000 X / Nominal defocus max: 2200 nm / Nominal defocus min: 750 nm / Calibrated defocus min: 750 nm / Calibrated defocus max: 2200 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Temperature (max): 77 K / Temperature (min): 77 K
Image recordingElectron dose: 70 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 8100
EM imaging opticsEnergyfilter name: TFS Selectris X / Energyfilter slit width: 10 eV
Image scansWidth: 4096 / Height: 4096

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Processing

EM softwareName: PHENIX / Version: 1.21.2_5419 / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 6500000
3D reconstructionResolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 583765 / Algorithm: FOURIER SPACE / Num. of class averages: 10 / Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 63.55 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.003127240
ELECTRON MICROSCOPYf_angle_d0.583437509
ELECTRON MICROSCOPYf_chiral_restr0.04495042
ELECTRON MICROSCOPYf_plane_restr0.00514725
ELECTRON MICROSCOPYf_dihedral_angle_d6.47074057

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