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- PDB-9gqn: Cryo-EM map of dimeric AvrSr35 -

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Basic information

Entry
Database: PDB / ID: 9gqn
TitleCryo-EM map of dimeric AvrSr35
ComponentsAvirulence factor
KeywordsANTIFUNGAL PROTEIN / Dimer / plant immunity
Function / homologyAvirulence factor
Function and homology information
Biological speciesPuccinia graminis f. sp. tritici (fungus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsMacha, A. / Gunkel, M. / Lawson, A.W. / Schulze-Lefert, P. / Behrmann, E.
Funding support Germany, 2items
OrganizationGrant numberCountry
German Research Foundation (DFG)INST 216/949-1 FUGG Germany
German Research Foundation (DFG)INST 216/512/1 FUGG Germany
CitationJournal: To Be Published
Title: A versatile protocol for purifying recombinant proteins from Nicotiana benthamiana
Authors: Lawson, A.W. / Macha, A. / Neumann, U. / Gunkel, M. / Chai, J.J. / Behrmann, E. / Schulze-Lefert, P.
History
DepositionSep 9, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 24, 2025Provider: repository / Type: Initial release
Revision 1.0Sep 24, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Sep 24, 2025Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Sep 24, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Sep 24, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Sep 24, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Sep 24, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Sep 24, 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: Avirulence factor
B: Avirulence factor


Theoretical massNumber of molelcules
Total (without water)142,4272
Polymers142,4272
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 Avirulence factor


Mass: 71213.438 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Puccinia graminis f. sp. tritici (fungus)
Gene: PGT21_019944, PGTUg99_030428 / Production host: Nicotiana benthamiana (plant) / References: UniProt: A0A5B0N367
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: Dimeric complex of wheat stem rust effector AvrSr35 / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 0.12 MDa / Experimental value: NO
Source (natural)Organism: Puccinia graminis f. sp. tritici (fungus)
Source (recombinant)Organism: Nicotiana benthamiana (plant)
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: monodisperse sample
Specimen supportGrid material: COPPER / Grid mesh size: 400 divisions/in. / Grid type: C-flat-1.2/1.3
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: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 96000 X / Nominal defocus max: 2500 nm / Nominal defocus min: 500 nm / Cs: 2.7 mm / C2 aperture diameter: 70 µm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 43 sec. / Electron dose: 42 e/Å2 / Detector mode: COUNTING / Film or detector model: FEI FALCON III (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 4004

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Processing

EM software
IDNameVersionCategoryDetails
1cryoSPARC4.4particle selectionblob picker > template picker
2EPU2.12.1.2782RELimage acquisition
4cryoSPARC4.4CTF correctionpatchCTF
7Coot0.9.4model fitting
9cryoSPARC4.4initial Euler assignmentab initio
10cryoSPARC4.4final Euler assignmentnon-uniform refinement
12cryoSPARC4.43D reconstructionnon-uniform refinement
13PHENIX1.21-5207model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 4190952
SymmetryPoint symmetry: C2 (2 fold cyclic)
3D reconstructionResolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 250926 / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL
Atomic model buildingPDB-ID: 7XDS

7xds


Accession code: 7XDS / Source name: PDB / Type: experimental model
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0036882
ELECTRON MICROSCOPYf_angle_d0.7769256
ELECTRON MICROSCOPYf_dihedral_angle_d2.912872
ELECTRON MICROSCOPYf_chiral_restr0.0461016
ELECTRON MICROSCOPYf_plane_restr0.0041162

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