+Open data
-Basic information
Entry | Database: PDB / ID: 7zau | ||||||
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Title | Fascin-1 in complex with Nb 3E11 | ||||||
Components |
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Keywords | STRUCTURAL PROTEIN / Nanobody / actin-bundling inhibitor | ||||||
Function / homology | Function and homology information microspike / parallel actin filament bundle assembly / regulation of microvillus assembly / positive regulation of extracellular matrix disassembly / establishment of apical/basal cell polarity / microspike assembly / cell projection membrane / podosome / positive regulation of podosome assembly / cell-cell junction assembly ...microspike / parallel actin filament bundle assembly / regulation of microvillus assembly / positive regulation of extracellular matrix disassembly / establishment of apical/basal cell polarity / microspike assembly / cell projection membrane / podosome / positive regulation of podosome assembly / cell-cell junction assembly / positive regulation of filopodium assembly / establishment or maintenance of cell polarity / actin filament bundle assembly / microvillus / positive regulation of lamellipodium assembly / stress fiber / ruffle / filopodium / cell motility / regulation of actin cytoskeleton organization / cell-cell junction / actin filament binding / actin cytoskeleton / cell migration / lamellipodium / protein-macromolecule adaptor activity / actin binding / cell cortex / actin cytoskeleton organization / growth cone / Interleukin-4 and Interleukin-13 signaling / cytoskeleton / cadherin binding / RNA binding / extracellular exosome / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) Lama glama (llama) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Burgess, S.G. / Bayliss, R. | ||||||
Funding support | United Kingdom, 1items
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Citation | Journal: Open Biology / Year: 2024 Title: A nanobody inhibitor of Fascin-1 actin-bundling activity and filopodia formation. Authors: Burgess, S.G. / Paul, N.R. / Richards, M.W. / Ault, J.R. / Askenatzis, L. / Claydon, S.G. / Corbyn, R. / Machesky, L.M. / Bayliss, R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7zau.cif.gz | 493.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7zau.ent.gz | 392 KB | Display | PDB format |
PDBx/mmJSON format | 7zau.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7zau_validation.pdf.gz | 514.4 KB | Display | wwPDB validaton report |
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Full document | 7zau_full_validation.pdf.gz | 537.8 KB | Display | |
Data in XML | 7zau_validation.xml.gz | 93.5 KB | Display | |
Data in CIF | 7zau_validation.cif.gz | 130.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/za/7zau ftp://data.pdbj.org/pub/pdb/validation_reports/za/7zau | HTTPS FTP |
-Related structure data
Related structure data | 2x1oS 3llpS S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 55079.340 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: FSCN1, FAN1, HSN, SNL / Plasmid: pBDDP-SPR3 / Production host: Escherichia coli (E. coli) / References: UniProt: Q16658 #2: Antibody | Mass: 14723.501 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Lama glama (llama) / Production host: Escherichia coli (E. coli) #3: Chemical | ChemComp-EDO / #4: Chemical | ChemComp-PEG / #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: 2.82 Å3/Da / Density % sol: 56.32 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop Details: 0.02 M D-glucose, D-mannose, D-galactose, L-fucose, D-xylose, N-acetyl-D-glucosamine; 0.1 M MES/imidazole pH 6.5, 10% PEG 8000, 20% ethylene glycol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å |
Detector | Type: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Dec 7, 2017 |
Radiation | Monochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→105.16 Å / Num. obs: 155971 / % possible obs: 99.86 % / Redundancy: 3.3 % / Biso Wilson estimate: 46.67 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.065 / Rpim(I) all: 0.042 / Rrim(I) all: 0.077 / Net I/σ(I): 7.7 |
Reflection shell | Resolution: 2.2→2.24 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.611 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 7600 / CC1/2: 0.599 / Rpim(I) all: 0.427 / Rrim(I) all: 0.748 / % possible all: 97.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3LLP, 2X1O Resolution: 2.2→59.44 Å / SU ML: 0.4285 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 42.7365 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 60.78 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→59.44 Å
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Refine LS restraints |
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LS refinement shell |
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