+Open data
-Basic information
Entry | Database: PDB / ID: 8be3 | ||||||
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Title | Crystal structure of KRasG12V-Nanobody84 | ||||||
Components |
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Keywords | SIGNALING PROTEIN / Complex / Stabilizer | ||||||
Function / homology | small monomeric GTPase / Ca2+ pathway / GUANOSINE-5'-DIPHOSPHATE / Isoform 2B of GTPase KRas Function and homology information | ||||||
Biological species | Lama glama (llama) Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å | ||||||
Authors | Fischer, B. / Wohlkonig, A. / Steyaert, J. | ||||||
Funding support | Belgium, 1items
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Citation | Journal: Nat Commun / Year: 2024 Title: Allosteric nanobodies to study the interactions between SOS1 and RAS. Authors: Fischer, B. / Uchanski, T. / Sheryazdanova, A. / Gonzalez, S. / Volkov, A.N. / Brosens, E. / Zogg, T. / Kalichuk, V. / Ballet, S. / Versees, W. / Sablina, A.A. / Pardon, E. / Wohlkonig, A. / Steyaert, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8be3.cif.gz | 136.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8be3.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 8be3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8be3_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 8be3_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 8be3_validation.xml.gz | 24.6 KB | Display | |
Data in CIF | 8be3_validation.cif.gz | 35.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/be/8be3 ftp://data.pdbj.org/pub/pdb/validation_reports/be/8be3 | HTTPS FTP |
-Related structure data
Related structure data | 8be2C 8be4C 8be5C 4l9sS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Antibody | Mass: 13519.057 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Lama glama (llama) / Production host: Escherichia coli (E. coli) #2: Protein | Mass: 21675.314 Da / Num. of mol.: 2 / Mutation: G12V Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: KRAS, KRAS2, RASK2 / Production host: Escherichia coli (E. coli) / References: UniProt: P01116-2, small monomeric GTPase #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | Has ligand of interest | N | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.3 Å3/Da / Density % sol: 46.62 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: PEG 3350 21%, MES 0.1 M pH 6.0, NaCl 150mM |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97857 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 4, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97857 Å / Relative weight: 1 |
Reflection | Resolution: 1.84→42.3 Å / Num. obs: 54015 / % possible obs: 98.6 % / Redundancy: 4.7 % / Biso Wilson estimate: 33.43 Å2 / CC1/2: 0.99 / Net I/σ(I): 10.7 |
Reflection shell | Resolution: 1.85→1.96 Å / Num. unique obs: 38376 / CC1/2: 0.66 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4L9S Resolution: 1.85→42.3 Å / SU ML: 0.232 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 24.8998 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 41.19 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.85→42.3 Å
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Refine LS restraints |
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LS refinement shell |
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