+Open data
-Basic information
Entry | Database: PDB / ID: 5b21 | ||||||
---|---|---|---|---|---|---|---|
Title | Dimer structure of murine Nectin-1 D1 | ||||||
Components | murine Nectin-1 D1 | ||||||
Keywords | CELL ADHESION / Cell Adhesion Molecules / CAM / Immunoglobulin-like domains | ||||||
Function / homology | Function and homology information Nectin/Necl trans heterodimerization / desmosome organization / protein localization to cell junction / Adherens junctions interactions / lens morphogenesis in camera-type eye / growth cone membrane / enamel mineralization / camera-type eye morphogenesis / cell-cell contact zone / virion binding ...Nectin/Necl trans heterodimerization / desmosome organization / protein localization to cell junction / Adherens junctions interactions / lens morphogenesis in camera-type eye / growth cone membrane / enamel mineralization / camera-type eye morphogenesis / cell-cell contact zone / virion binding / heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules / regulation of synapse assembly / apical junction complex / homophilic cell adhesion via plasma membrane adhesion molecules / cell adhesion molecule binding / axon guidance / adherens junction / cell-cell adhesion / retina development in camera-type eye / presynaptic membrane / signaling receptor activity / iron ion transport / carbohydrate binding / membrane => GO:0016020 / neuron projection / symbiont entry into host cell / axon / intracellular membrane-bounded organelle / synapse / dendrite / protein-containing complex binding / virion attachment to host cell / protein homodimerization activity / identical protein binding / plasma membrane Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.24 Å | ||||||
Authors | Sangawa, T. / Takebe, K. / Suzuki, M. | ||||||
Citation | Journal: To Be Published Title: Dimer structure of murine Nectin-1 D1 Authors: Sangawa, T. / Takebe, K. / Suzuki, M. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 5b21.cif.gz | 104.7 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb5b21.ent.gz | 79.9 KB | Display | PDB format |
PDBx/mmJSON format | 5b21.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b2/5b21 ftp://data.pdbj.org/pub/pdb/validation_reports/b2/5b21 | HTTPS FTP |
---|
-Related structure data
Related structure data | 3alpS S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 12689.452 Da / Num. of mol.: 2 / Fragment: UNP residues 31-144 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Pvrl1, Hvec, Prr1 / Plasmid: pFastBac-1 / Cell line (production host): Sf-9 / Organ (production host): ovary / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q9JKF6 #2: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.49 Å3/Da / Density % sol: 50.64 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: 40% PEG3350, 70 mM Na-citrate pH 5.0 / PH range: 5.0-7.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å |
Detector | Type: BRUKER SMART 6500 / Detector: CCD / Date: Jul 8, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 2.24→39.16 Å / Num. obs: 12470 / % possible obs: 100 % / Redundancy: 7 % / Rmerge(I) obs: 0.162 / Net I/σ(I): 7.3 |
Reflection shell | Resolution: 2.238→2.318 Å / Redundancy: 7 % / % possible all: 100 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3ALP Resolution: 2.24→39.16 Å / SU ML: 0.4 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 24.77 / Stereochemistry target values: ML
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.24→39.16 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / % reflection obs: 100 %
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|