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- PDB-5l5n: Plexin A4 full extracellular region, domains 1 to 7 modeled, data... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5l5n | ||||||
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Title | Plexin A4 full extracellular region, domains 1 to 7 modeled, data to 8.5 angstrom, spacegroup P4(3)22 | ||||||
![]() | Plexin-A4 | ||||||
![]() | SIGNALING PROTEIN / receptor / signaling / axon guidance | ||||||
Function / homology | ![]() glossopharyngeal nerve morphogenesis / chemorepulsion of branchiomotor axon / regulation of negative chemotaxis / vagus nerve morphogenesis / cranial nerve morphogenesis / trigeminal nerve morphogenesis / anterior commissure morphogenesis / regulation of axon extension involved in axon guidance / postganglionic parasympathetic fiber development / facial nerve morphogenesis ...glossopharyngeal nerve morphogenesis / chemorepulsion of branchiomotor axon / regulation of negative chemotaxis / vagus nerve morphogenesis / cranial nerve morphogenesis / trigeminal nerve morphogenesis / anterior commissure morphogenesis / regulation of axon extension involved in axon guidance / postganglionic parasympathetic fiber development / facial nerve morphogenesis / sympathetic neuron axon guidance / CRMPs in Sema3A signaling / Sema3A PAK dependent Axon repulsion / trigeminal nerve structural organization / facial nerve structural organization / branchiomotor neuron axon guidance / cerebellar climbing fiber to Purkinje cell synapse / SEMA3A-Plexin repulsion signaling by inhibiting Integrin adhesion / maintenance of synapse structure / sympathetic nervous system development / semaphorin-plexin signaling pathway involved in axon guidance / semaphorin receptor activity / negative regulation of cell adhesion / embryonic heart tube development / semaphorin receptor complex / motor neuron axon guidance / positive regulation of axonogenesis / semaphorin-plexin signaling pathway / regulation of cell migration / neuron projection morphogenesis / axon guidance / nervous system development / regulation of cell shape / plasma membrane Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Janssen, B.J.C. / Kong, Y. / Malinauskas, T. / Vangoor, V.R. / Coles, C.H. / Kaufmann, R. / Ni, T. / Gilbert, R.J.C. / Padilla-Parra, S. / Pasterkamp, R.J. / Jones, E.Y. | ||||||
![]() | ![]() Title: Structural Basis for Plexin Activation and Regulation. Authors: Kong, Y. / Janssen, B.J. / Malinauskas, T. / Vangoor, V.R. / Coles, C.H. / Kaufmann, R. / Ni, T. / Gilbert, R.J. / Padilla-Parra, S. / Pasterkamp, R.J. / Jones, E.Y. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 178.9 KB | Display | ![]() |
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PDB format | ![]() | 130 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 448.4 KB | Display | ![]() |
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Full document | ![]() | 566.1 KB | Display | |
Data in XML | ![]() | 46.1 KB | Display | |
Data in CIF | ![]() | 62.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5l56SC ![]() 5l59C ![]() 5l5cC ![]() 5l5gC ![]() 5l5kC ![]() 5l5lC ![]() 5l5mC ![]() 5l74C ![]() 5l7nC S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 134813.844 Da / Num. of mol.: 1 / Fragment: UNP residues 36-1229 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density % sol: 83 % |
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Crystal grow | Temperature: 293.5 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 1.5 lithium sulfate, 100 mM TRIS, pH 8.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 22, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9763 Å / Relative weight: 1 |
Reflection | Resolution: 8.5→71 Å / Num. obs: 4374 / % possible obs: 99.7 % / Redundancy: 5.8 % / Rmerge(I) obs: 0.33 / Net I/σ(I): 4.2 |
Reflection shell | Highest resolution: 8.5 Å / Rmerge(I) obs: 1.17 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5L56 Resolution: 8.502→70.367 Å / SU ML: 1.89 / Cross valid method: FREE R-VALUE / σ(F): 1.12 / Phase error: 45.03 Details: THE AUTHORS STATE THAT DUE TO THE LOW RESOLUTION OF THE DIFFRACTION DATA THE STRUCTURE WAS ONLY SUBJECTED TO RIGID BODY REFINEMENT WITH EACH DOMAIN AS RIGID BODY. THE STRUCTURE IS BASED ON A ...Details: THE AUTHORS STATE THAT DUE TO THE LOW RESOLUTION OF THE DIFFRACTION DATA THE STRUCTURE WAS ONLY SUBJECTED TO RIGID BODY REFINEMENT WITH EACH DOMAIN AS RIGID BODY. THE STRUCTURE IS BASED ON A HOMOLOGY MODEL GENERATED WITH PDB ENTRY 5L56 AS TEMPLATE (53% SEQUENCE IDENTITY). THE AUTHORS HAVE NOT FURTHER REFINED THE RESULTING COORDINATES NOR CORRECTED RESULTING CLASHES BETWEEN ATOMS AND DEVIATING PEPTIDE LINKAGES BETWEEN DOMAINS.
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 8.502→70.367 Å
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Refine LS restraints |
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LS refinement shell |
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