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- PDB-9qe7: Membrane-distal part of extracellular domain of the Fap2 autotran... -
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Open data
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Basic information
Entry | Database: PDB / ID: 9qe7 | ||||||||||||||||||||||||||||||
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Title | Membrane-distal part of extracellular domain of the Fap2 autotransporter adhesin from Fusobacterium nucleatum ATCC23726 | ||||||||||||||||||||||||||||||
![]() | Outer membrane autotransporter barrel domain protein | ||||||||||||||||||||||||||||||
![]() | CELL ADHESION / Type V secretion system / autotransporter / colorectal cancer / bacterial adhesion | ||||||||||||||||||||||||||||||
Function / homology | ![]() | ||||||||||||||||||||||||||||||
Biological species | ![]() | ||||||||||||||||||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.4 Å | ||||||||||||||||||||||||||||||
![]() | Schoepf, F. / Marongiu, G.L. / Milaj, K. / Sprink, T. / Kikhney, J. / Moter, A. / Roderer, D. | ||||||||||||||||||||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Structural basis of Fusobacterium nucleatum adhesin Fap2 interaction with receptors on cancer and immune cells Authors: Schoepf, F. / Marongiu, G.L. / Milaj, K. / Sprink, T. / Kikhney, J. / Moter, A. / Roderer, D. | ||||||||||||||||||||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 293.7 KB | Display | ![]() |
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PDB format | ![]() | 208 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.3 MB | Display | ![]() |
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Full document | ![]() | 1.3 MB | Display | |
Data in XML | ![]() | 64.6 KB | Display | |
Data in CIF | ![]() | 96.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 53049MC C: citing same article ( M: map data used to model this data |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Components
#1: Protein | Mass: 340269.375 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: Extracellular domain of F. nucleatum adhesin Fap2, membrane-distal part Source: (gene. exp.) ![]() ![]() ![]() |
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Has protein modification | N |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
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Sample preparation
Component | Name: Fap2 extracellular domain from F. nucleatum ATCC23726, monomer Type: COMPLEX / Entity ID: all / Source: RECOMBINANT |
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Molecular weight | Value: 0.32 MDa / Experimental value: NO |
Source (natural) | Organism: ![]() |
Source (recombinant) | Organism: ![]() ![]() |
Buffer solution | pH: 7.5 / Details: 20 mM Tris HCl, 200 mM NaCl, pH 7.5 |
Specimen | Conc.: 0.1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 285 K |
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Electron microscopy imaging
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: TFS KRIOS |
Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 81000 X / Nominal defocus max: 2600 nm / Nominal defocus min: 1500 nm / Cs: 2.7 mm / Alignment procedure: ZEMLIN TABLEAU |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Average exposure time: 2 sec. / Electron dose: 58.8 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 12663 |
EM imaging optics | Energyfilter name: GIF Bioquantum / Energyfilter slit width: 20 eV |
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Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 4.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 151825 / Algorithm: FOURIER SPACE / Num. of class averages: 1 / Symmetry type: POINT | ||||||||||||||||||||||||||||||
Atomic model building | Protocol: FLEXIBLE FIT / Space: REAL | ||||||||||||||||||||||||||||||
Atomic model building | Source name: AlphaFold / Type: in silico model | ||||||||||||||||||||||||||||||
Refinement | Highest resolution: 4.4 Å Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS) | ||||||||||||||||||||||||||||||
Refine LS restraints |
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