+Open data
-Basic information
Entry | Database: PDB / ID: 5mr4 | ||||||
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Title | Ligand-receptor complex. | ||||||
Components |
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Keywords | SIGNALING PROTEIN / Complex / Signalling / Receptor | ||||||
Function / homology | Function and homology information glial cell-derived neurotrophic factor receptor activity / glial cell-derived neurotrophic factor receptor binding / glial cell-derived neurotrophic factor receptor signaling pathway / nerve development / heparan sulfate binding / NCAM1 interactions / neural crest cell migration / extrinsic component of membrane / RET signaling / cell surface receptor protein tyrosine kinase signaling pathway ...glial cell-derived neurotrophic factor receptor activity / glial cell-derived neurotrophic factor receptor binding / glial cell-derived neurotrophic factor receptor signaling pathway / nerve development / heparan sulfate binding / NCAM1 interactions / neural crest cell migration / extrinsic component of membrane / RET signaling / cell surface receptor protein tyrosine kinase signaling pathway / growth factor activity / receptor tyrosine kinase binding / MAPK cascade / neuron projection development / nervous system development / RAF/MAP kinase cascade / receptor complex / external side of plasma membrane / axon / signaling receptor binding / extracellular space / extracellular region / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | ||||||
Authors | Sandmark, J. / Oster, L. / Aagaard, A. / Roth, R.G. / Dahl, G. | ||||||
Citation | Journal: J. Biol. Chem. / Year: 2018 Title: Structure and biophysical characterization of the human full-length neurturin-GFRa2 complex: A role for heparan sulfate in signaling. Authors: Sandmark, J. / Dahl, G. / Oster, L. / Xu, B. / Johansson, P. / Akerud, T. / Aagaard, A. / Davidsson, P. / Bigalke, J.M. / Winzell, M.S. / Rainey, G.J. / Roth, R.G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5mr4.cif.gz | 176.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5mr4.ent.gz | 137 KB | Display | PDB format |
PDBx/mmJSON format | 5mr4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5mr4_validation.pdf.gz | 474.2 KB | Display | wwPDB validaton report |
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Full document | 5mr4_full_validation.pdf.gz | 484.4 KB | Display | |
Data in XML | 5mr4_validation.xml.gz | 32 KB | Display | |
Data in CIF | 5mr4_validation.cif.gz | 46 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mr/5mr4 ftp://data.pdbj.org/pub/pdb/validation_reports/mr/5mr4 | HTTPS FTP |
-Related structure data
Related structure data | 5mr5SC 5nmzC 5mr9S 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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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 11706.406 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: NRTN / Production host: Escherichia coli (E. coli) / References: UniProt: Q99748 #2: Protein | Mass: 50932.676 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: GFRA2, GDNFRB, RETL2, TRNR2 / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: O00451 #3: Chemical | ChemComp-PEG / | #4: Chemical | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.16 Å3/Da / Density % sol: 61.1 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 7.5 Details: 8% Tacsimate, 8% PEG MME 5000 and 0.1 M HEPES pH 7.5. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.985 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 11, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.985 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→55.8 Å / Num. obs: 60705 / % possible obs: 99.7 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.098 / Net I/σ(I): 9.4 |
Reflection shell | Resolution: 2.4→2.53 Å / Rmerge(I) obs: 0.75 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5MR5, 5MR9 Resolution: 2.4→49.67 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.94 / SU B: 5.537 / SU ML: 0.126 / Cross valid method: THROUGHOUT / ESU R: 0.215 / ESU R Free: 0.18 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 54.043 Å2
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Refinement step | Cycle: 1 / Resolution: 2.4→49.67 Å
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Refine LS restraints |
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