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Open data
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Basic information
Entry | Database: PDB / ID: 4fom | |||||||||
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Title | Crystal structure of human nectin-3 full ectodomain (D1-D3) | |||||||||
![]() | Poliovirus receptor-related protein 3 | |||||||||
![]() | CELL ADHESION / Immunoglobulin-like domain / Ig domain | |||||||||
Function / homology | ![]() retina morphogenesis in camera-type eye / : / Nectin/Necl trans heterodimerization / establishment of protein localization to plasma membrane / protein localization to cell junction / lens morphogenesis in camera-type eye / cell-cell contact zone / Adherens junctions interactions / fertilization / adherens junction organization ...retina morphogenesis in camera-type eye / : / Nectin/Necl trans heterodimerization / establishment of protein localization to plasma membrane / protein localization to cell junction / lens morphogenesis in camera-type eye / cell-cell contact zone / Adherens junctions interactions / fertilization / adherens junction organization / apical junction complex / heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules / homophilic cell adhesion via plasma membrane adhesion molecules / spermatid development / cell adhesion molecule binding / hippocampal mossy fiber to CA3 synapse / adherens junction / cell-cell junction / axon / dendrite / protein homodimerization activity / identical protein binding / plasma membrane Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Harrison, O.J. / Jin, X. / Brasch, J. / Shapiro, L. | |||||||||
![]() | ![]() Title: Nectin ectodomain structures reveal a canonical adhesive interface. Authors: Harrison, O.J. / Vendome, J. / Brasch, J. / Jin, X. / Hong, S. / Katsamba, P.S. / Ahlsen, G. / Troyanovsky, R.B. / Troyanovsky, S.M. / Honig, B. / Shapiro, L. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 144.7 KB | Display | ![]() |
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PDB format | ![]() | 115.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.6 MB | Display | ![]() |
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Full document | ![]() | 1.7 MB | Display | |
Data in XML | ![]() | 16.6 KB | Display | |
Data in CIF | ![]() | 21.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4fmfC ![]() 4fmkC ![]() 4fn0C ![]() 4fqpC ![]() 4frwC ![]() 4fs0C ![]() 3alpS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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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: 34039.387 Da / Num. of mol.: 1 / Fragment: ectodomain (D1-D3, UNP residues 58-359) Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() | ||||||
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#2: Polysaccharide | Source method: isolated from a genetically manipulated source #3: Polysaccharide | beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | Source method: isolated from a genetically manipulated source #4: Polysaccharide | alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose | Source method: isolated from a genetically manipulated source #5: Sugar | ChemComp-NAG / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 9.13 Å3/Da / Density % sol: 86.52 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 4.6 Details: 4.6 M ammonium acetate, 0.1 M sodium acetate, VAPOR DIFFUSION, HANGING DROP, temperature 293.15K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Jul 1, 2011 | ||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Bent single Si(111) crystal (horizontal focusing and deflection) Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 3.93→40 Å / Num. all: 11776 / Num. obs: 11776 / % possible obs: 98.3 % / Observed criterion σ(I): -3 / Redundancy: 5.9 % / Rsym value: 0.07 / Net I/σ(I): 34 | ||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 3ALP Resolution: 3.93→20 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.907 / SU B: 62.326 / SU ML: 0.467 / Cross valid method: THROUGHOUT / ESU R: 1.721 / ESU R Free: 0.538 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 170.513 Å2
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Refinement step | Cycle: LAST / Resolution: 3.93→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.93→4.029 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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