+Open data
-Basic information
Entry | Database: PDB / ID: 8afp | ||||||
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Title | Structure of fibronectin 2 and 3 of L1CAM at 3.0 Angstrom | ||||||
Components | Neural cell adhesion molecule L1 | ||||||
Keywords | CELL ADHESION / fibronectin / glycans | ||||||
Function / homology | Function and homology information 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 | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å | ||||||
Authors | Guedez, G. / Loew, C. | ||||||
Funding support | 1items
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Citation | Journal: Faseb J. / Year: 2023 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8afp.cif.gz | 114.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8afp.ent.gz | 76.7 KB | Display | PDB format |
PDBx/mmJSON format | 8afp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8afp_validation.pdf.gz | 1.4 MB | Display | wwPDB validaton report |
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Full document | 8afp_full_validation.pdf.gz | 1.4 MB | Display | |
Data in XML | 8afp_validation.xml.gz | 10.4 KB | Display | |
Data in CIF | 8afp_validation.cif.gz | 12.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/af/8afp ftp://data.pdbj.org/pub/pdb/validation_reports/af/8afp | HTTPS FTP |
-Related structure data
Related structure data | 8afoC 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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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.) Homo sapiens (human) / Gene: L1CAM, CAML1, MIC5 / Cell line (production host): HEK293F / Production host: Homo sapiens (human) / References: UniProt: P32004 | ||
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#2: Sugar | ChemComp-NAG / Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.09 Å3/Da / Density % sol: 60.14 % |
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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: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.9762 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jun 14, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9762 Å / Relative weight: 1 |
Reflection | Resolution: 2.95→50 Å / Num. obs: 11342 / % possible obs: 97.3 % / Redundancy: 13.9 % / Biso Wilson estimate: 74.86 Å2 / CC1/2: 0.99 / Rrim(I) all: 0.16 / Net I/σ(I): 12.1 |
Reflection shell | Resolution: 2.95→3.25 Å / Num. unique obs: 548 / CC1/2: 0.98 / Rrim(I) all: 1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 3→35.8 Å / SU ML: 0.2727 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 34.2545 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: 83.91 Å2 | ||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3→35.8 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: -17.6869627417 Å / Origin y: -26.4588455953 Å / Origin z: 11.9783920516 Å
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Refinement TLS group | Selection details: all |