+Open data
-Basic information
Entry | Database: PDB / ID: 4v2a | ||||||
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Title | human Unc5A ectodomain | ||||||
Components | NETRIN RECEPTOR UNC5A | ||||||
Keywords | APOPTOSIS / UNCOORDINATED-5 / UNC5A / NETRIN RECEPTOR / FLRT | ||||||
Function / homology | Function and homology information netrin receptor activity / neuron projection membrane / : / anterior/posterior axon guidance / netrin-activated signaling pathway / Netrin-1 signaling / Netrin mediated repulsion signals / Caspase activation via Dependence Receptors in the absence of ligand / neuronal cell body membrane / axon guidance ...netrin receptor activity / neuron projection membrane / : / anterior/posterior axon guidance / netrin-activated signaling pathway / Netrin-1 signaling / Netrin mediated repulsion signals / Caspase activation via Dependence Receptors in the absence of ligand / neuronal cell body membrane / axon guidance / neuron projection development / membrane => GO:0016020 / membrane raft / apoptotic process / plasma membrane Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | ||||||
Authors | Seiradake, E. / del Toro, D. / Nagel, D. / Cop, F. / Haertl, R. / Ruff, T. / Seyit-Bremer, G. / Harlos, K. / Border, E.C. / Acker-Palmer, A. ...Seiradake, E. / del Toro, D. / Nagel, D. / Cop, F. / Haertl, R. / Ruff, T. / Seyit-Bremer, G. / Harlos, K. / Border, E.C. / Acker-Palmer, A. / Jones, E.Y. / Klein, R. | ||||||
Citation | Journal: Neuron / Year: 2014 Title: Flrt Structure: Balancing Repulsion and Cell Adhesion in Cortical and Vascular Development Authors: Seiradake, E. / Del Toro, D. / Nagel, D. / Cop, F. / Haertl, R. / Ruff, T. / Seyit-Bremer, G. / Harlos, K. / Border, E.C. / Acker-Palmer, A. / Jones, E.Y. / Klein, R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4v2a.cif.gz | 109.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4v2a.ent.gz | 89.1 KB | Display | PDB format |
PDBx/mmJSON format | 4v2a.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/v2/4v2a ftp://data.pdbj.org/pub/pdb/validation_reports/v2/4v2a | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 33561.012 Da / Num. of mol.: 1 / Fragment: ECTODOMAIN, UNP RESIDUES 1-303 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PHLSEC / Production host: HOMO SAPIENS (human) / References: UniProt: Q6ZN44 |
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#2: Sugar | ChemComp-NAG / |
#3: Water | ChemComp-HOH / |
Sequence details | N-TERMINUS IS PROTEOLYTI |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.26 Å3/Da / Density % sol: 45.57 % / Description: NONE |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 1.0401 |
Detector | Type: PILATUS / Detector: PIXEL |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0401 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→44 Å / Num. obs: 11029 / % possible obs: 86.8 % / Redundancy: 6.6 % / Biso Wilson estimate: 68.17 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 13.88 |
Reflection shell | Resolution: 2.4→2.46 Å / Redundancy: 4.9 % / Mean I/σ(I) obs: 0.61 / % possible all: 46.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: NONE Resolution: 2.4→43.88 Å / Cor.coef. Fo:Fc: 0.8292 / Cor.coef. Fo:Fc free: 0.7943 / SU R Cruickshank DPI: 0.62 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.657 / SU Rfree Blow DPI: 0.358 / SU Rfree Cruickshank DPI: 0.357
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Displacement parameters | Biso mean: 80.49 Å2
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Refine analyze | Luzzati coordinate error obs: 1.062 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.4→43.88 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.4→2.63 Å / Total num. of bins used: 6
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Refinement TLS params. | Method: refined / Origin x: 3.2411 Å / Origin y: -24.3785 Å / Origin z: -18.0082 Å
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Refinement TLS group | Selection details: CHAIN A |