+Open data
-Basic information
Entry | Database: PDB / ID: 5ftu | ||||||
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Title | Tetrameric complex of Latrophilin 3, Unc5D and FLRT2 | ||||||
Components |
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Keywords | SIGNALING PROTEIN / SIGNALLING PROTEIN / LEUCINE-RICH REPEAT / LRR / UNC5 / APOPTOSIS / UNCOORDINATED-5 / NETRIN RECEPTOR / FLRT / LATROPHILIN / ADHESION / REPULSION / GUIDANCE / BETA PROPELLOR / IMMUNOGLOBULIN / THROMBOSPONDIN / OLFACTOMEDIN / LECTIN / TETRAMER | ||||||
Function / homology | Function and homology information cell adhesion involved in heart morphogenesis / Downstream signaling of activated FGFR1 / netrin receptor activity / locomotion involved in locomotory behavior / basement membrane organization / regulation of neuron migration / cell-cell adhesion via plasma-membrane adhesion molecules / fibroblast growth factor receptor binding / maintenance of postsynaptic specialization structure / chemorepellent activity ...cell adhesion involved in heart morphogenesis / Downstream signaling of activated FGFR1 / netrin receptor activity / locomotion involved in locomotory behavior / basement membrane organization / regulation of neuron migration / cell-cell adhesion via plasma-membrane adhesion molecules / fibroblast growth factor receptor binding / maintenance of postsynaptic specialization structure / chemorepellent activity / pyramidal neuron differentiation / positive regulation of synapse assembly / fibroblast growth factor receptor signaling pathway / heart morphogenesis / synapse assembly / response to cocaine / G protein-coupled receptor activity / axon guidance / synapse organization / neuron migration / Schaffer collateral - CA1 synapse / adenylate cyclase-activating G protein-coupled receptor signaling pathway / cell-cell junction / presynaptic membrane / carbohydrate binding / postsynaptic membrane / cell surface receptor signaling pathway / neuron projection / axon / focal adhesion / glutamatergic synapse / apoptotic process / calcium ion binding / endoplasmic reticulum membrane / cell surface / extracellular space / plasma membrane Similarity search - Function | ||||||
Biological species | RATTUS NORVEGICUS (Norway rat) MUS MUSCULUS (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 6.01 Å | ||||||
Authors | Jackson, V.A. / Mehmood, S. / Chavent, M. / Roversi, P. / Carrasquero, M. / del Toro, D. / Seyit-Bremer, G. / Ranaivoson, F.M. / Comoletti, D. / Sansom, M.S.P. ...Jackson, V.A. / Mehmood, S. / Chavent, M. / Roversi, P. / Carrasquero, M. / del Toro, D. / Seyit-Bremer, G. / Ranaivoson, F.M. / Comoletti, D. / Sansom, M.S.P. / Robinson, C.V. / Klein, R. / Seiradake, E. | ||||||
Citation | Journal: Nat.Commun. / Year: 2016 Title: Super-Complexes of Adhesion Gpcrs and Neural Guidance Receptors Authors: Jackson, V.A. / Mehmood, S. / Chavent, M. / Roversi, P. / Carrasquero, M. / Del Toro, D. / Seyit-Bremer, G. / Ranaivoson, F.M. / Comoletti, D. / Sansom, M.S.P. / Robinson, C.V. / Klein, R. / Seiradake, E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5ftu.cif.gz | 649 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5ftu.ent.gz | 522.6 KB | Display | PDB format |
PDBx/mmJSON format | 5ftu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5ftu_validation.pdf.gz | 518 KB | Display | wwPDB validaton report |
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Full document | 5ftu_full_validation.pdf.gz | 539.4 KB | Display | |
Data in XML | 5ftu_validation.xml.gz | 61.2 KB | Display | |
Data in CIF | 5ftu_validation.cif.gz | 90.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ft/5ftu ftp://data.pdbj.org/pub/pdb/validation_reports/ft/5ftu | HTTPS FTP |
-Related structure data
Related structure data | 5fttSC 4v2cS 5afbS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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3 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper:
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-Components
-Protein , 3 types, 12 molecules AEIBFJCDGHKL
#1: Protein | Mass: 15923.799 Da / Num. of mol.: 3 / Fragment: IMMUNOGLOBULIN-1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) RATTUS NORVEGICUS (Norway rat) / Plasmid: PHLSEC / Cell line (production host): HEK293 / Production host: HOMO SAPIENS (human) / References: UniProt: F1LW30 #2: Protein | Mass: 38411.934 Da / Num. of mol.: 3 / Fragment: LEUCINE-RICH REPEAT DOMAIN Source method: isolated from a genetically manipulated source Source: (gene. exp.) MUS MUSCULUS (house mouse) / Plasmid: PHLSEC / Cell line (production host): HEK293 / Production host: HOMO SAPIENS (human) / References: UniProt: Q8BLU0 #3: Protein | Mass: 43908.012 Da / Num. of mol.: 6 / Fragment: LECTIN AND OLFACTOMEDIN DOMAINS Source method: isolated from a genetically manipulated source Source: (gene. exp.) MUS MUSCULUS (house mouse) / Plasmid: PHLSEC / Cell line (production host): HEK293 / Production host: HOMO SAPIENS (human) / References: UniProt: Q80TS3 |
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-Sugars , 1 types, 9 molecules
#4: Sugar | ChemComp-NAG / |
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-Non-polymers , 2 types, 12 molecules
#5: Chemical | ChemComp-NA / #6: Chemical | ChemComp-CA / |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
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-Sample preparation
Crystal | Density Matthews: 4.33 Å3/Da / Density % sol: 71.62 % / Description: NONE |
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Crystal grow | pH: 6.5 / Details: pH 6.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92 |
Detector | Type: DECTRIS PILATUS / Detector: PIXEL |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.92 Å / Relative weight: 1 |
Reflection | Resolution: 6→92.45 Å / Num. obs: 16120 / % possible obs: 99.8 % / Redundancy: 75.7 % / Biso Wilson estimate: 459.95 Å2 / Rmerge(I) obs: 0.23 / Net I/σ(I): 0.89 |
Reflection shell | Resolution: 6→6.15 Å / Redundancy: 74.9 % / Rmerge(I) obs: 1.5 / Mean I/σ(I) obs: 0.89 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 5FTT, 5AFB, 4V2C Resolution: 6.01→206.73 Å / Cor.coef. Fo:Fc: 0.7473 / Cor.coef. Fo:Fc free: 0.6878 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 2.098
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Displacement parameters | Biso mean: 187.68 Å2
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Refine analyze | Luzzati coordinate error obs: 1.64 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 6.01→206.73 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 6.01→6.42 Å / Total num. of bins used: 8
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