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Open data
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Basic information
Entry | Database: PDB / ID: 8afo | ||||||
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Title | Structure of fibronectin 2 and 3 of L1CAM at 2.0 Angstrom | ||||||
![]() | Neural cell adhesion molecule L1 | ||||||
![]() | CELL ADHESION / fibronectin / glycans / L1CAM | ||||||
Function / homology | ![]() L1CAM interactions / axon guidance receptor activity / Interaction between L1 and Ankyrins / Basigin interactions / axon development / homophilic cell adhesion via plasma membrane adhesion molecules / Recycling pathway of L1 / positive regulation of axon extension / axonal growth cone / cell-matrix adhesion ...L1CAM interactions / axon guidance receptor activity / Interaction between L1 and Ankyrins / Basigin interactions / axon development / homophilic cell adhesion via plasma membrane adhesion molecules / Recycling pathway of L1 / positive regulation of axon extension / axonal growth cone / cell-matrix adhesion / Signal transduction by L1 / axon guidance / synapse organization / chemotaxis / neuron projection development / cell migration / nervous system development / collagen-containing extracellular matrix / cell adhesion / protein domain specific binding / axon / focal adhesion / neuronal cell body / dendrite / cell surface / plasma membrane Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Guedez, G. / Loew, C. | ||||||
Funding support | 1items
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![]() | ![]() Title: X-ray structure and function of fibronectin domains two and three of the neural cell adhesion molecule L1. Authors: Guedez, G. / Loers, G. / Jeffries, C.M. / Kozak, S. / Meijers, R. / Svergun, D.I. / Schachner, M. / Low, C. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 121.5 KB | Display | ![]() |
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PDB format | ![]() | 80.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.7 MB | Display | ![]() |
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Full document | ![]() | 1.7 MB | Display | |
Data in XML | ![]() | 11.8 KB | Display | |
Data in CIF | ![]() | 16.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8afpC C: citing same article ( |
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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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1 |
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Unit cell |
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Components
#1: Protein | Mass: 24377.211 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() | ||||
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#2: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source | ||||
#3: Sugar | ChemComp-NAG / #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.95 Å3/Da / Density % sol: 58.24 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, sitting drop Details: 150 mM sodium citrate pH 5.5, 10.6% PEG 20.000, 10 mM sodium potassium tartrate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 11, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9762 Å / Relative weight: 1 |
Reflection | Resolution: 1.99→50 Å / Num. obs: 18884 / % possible obs: 94.02 % / Redundancy: 12.4 % / Biso Wilson estimate: 43.43 Å2 / CC1/2: 0.99 / Rrim(I) all: 0.08 / Net I/σ(I): 17.8 |
Reflection shell | Resolution: 1.99→2.1 Å / Num. unique obs: 1022 / CC1/2: 0.69 / Rrim(I) all: 1 |
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Processing
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Refinement | Method to determine structure: ![]() 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: 53.62 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.99→48.52 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: -17.7962692944 Å / Origin y: -24.4805560412 Å / Origin z: 10.7070149513 Å
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Refinement TLS group | Selection details: all |