+Open data
-Basic information
Entry | Database: PDB / ID: 4gz8 | |||||||||
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Title | Mouse Semaphorin 3A, domains Sema-PSI-IG | |||||||||
Components | Semaphorin-3A | |||||||||
Keywords | SIGNALING PROTEIN / sema / multi-domain / cell-cell signaling / plexin / glycosilated / extracellular | |||||||||
Function / homology | Function and homology information neural crest cell migration involved in sympathetic nervous system development / regulation of axon extension involved in axon guidance / CRMPs in Sema3A signaling / Sema3A PAK dependent Axon repulsion / basal dendrite arborization / dichotomous subdivision of terminal units involved in salivary gland branching / semaphorin receptor binding / ventral trunk neural crest cell migration / sympathetic neuron projection guidance / facioacoustic ganglion development ...neural crest cell migration involved in sympathetic nervous system development / regulation of axon extension involved in axon guidance / CRMPs in Sema3A signaling / Sema3A PAK dependent Axon repulsion / basal dendrite arborization / dichotomous subdivision of terminal units involved in salivary gland branching / semaphorin receptor binding / ventral trunk neural crest cell migration / sympathetic neuron projection guidance / facioacoustic ganglion development / trigeminal ganglion development / epithelial cell migration / trigeminal nerve structural organization / facial nerve structural organization / gonadotrophin-releasing hormone neuronal migration to the hypothalamus / branchiomotor neuron axon guidance / positive regulation of male gonad development / cerebellar climbing fiber to Purkinje cell synapse / SEMA3A-Plexin repulsion signaling by inhibiting Integrin adhesion / maintenance of synapse structure / negative regulation of axon extension involved in axon guidance / axon extension involved in axon guidance / synaptic target recognition / sympathetic neuron projection extension / negative regulation of epithelial cell migration / axonogenesis involved in innervation / sympathetic ganglion development / neural crest cell migration involved in autonomic nervous system development / negative regulation of axon extension / nerve development / positive regulation of neuron migration / olfactory bulb development / neuropilin binding / chemorepellent activity / axon extension / motor neuron axon guidance / axonal fasciculation / dendrite morphogenesis / neural crest cell migration / negative chemotaxis / semaphorin-plexin signaling pathway / regulation of heart rate / axon guidance / neuron migration / nervous system development / positive regulation of cell migration / axon / glutamatergic synapse / dendrite / extracellular space / extracellular region / plasma membrane Similarity search - Function | |||||||||
Biological species | Mus musculus (house mouse) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 Å | |||||||||
Authors | Janssen, B.J.C. / Malinauskas, T. / Siebold, C. / Jones, E.Y. | |||||||||
Citation | Journal: Nat.Struct.Mol.Biol. / Year: 2012 Title: Neuropilins lock secreted semaphorins onto plexins in a ternary signaling complex. Authors: Janssen, B.J.C. / Malinauskas, T. / Weir, G.A. / Cader, M.Z. / Siebold, C. / Jones, E.Y. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4gz8.cif.gz | 235.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4gz8.ent.gz | 185.8 KB | Display | PDB format |
PDBx/mmJSON format | 4gz8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4gz8_validation.pdf.gz | 1.3 MB | Display | wwPDB validaton report |
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Full document | 4gz8_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | 4gz8_validation.xml.gz | 40.4 KB | Display | |
Data in CIF | 4gz8_validation.cif.gz | 55.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gz/4gz8 ftp://data.pdbj.org/pub/pdb/validation_reports/gz/4gz8 | HTTPS FTP |
-Related structure data
Related structure data | 4gz9C 4gzaC 1q47S 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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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: ASN / Beg label comp-ID: ASN / End auth comp-ID: UNK / End label comp-ID: UNK / Refine code: _
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 72416.078 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 21-675 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Sema3a, Semad, SemD / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: O08665 |
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-Sugars , 4 types, 4 molecules
#2: Polysaccharide | alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-3)-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 |
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#3: Polysaccharide | 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-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-6)-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 |
#7: Sugar | ChemComp-NAG / |
-Non-polymers , 2 types, 7 molecules
#5: Chemical | ChemComp-CA / #6: Chemical | |
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-Details
Sequence details | (1) THE SEQUENCE IS BASED ON NCBI REFERENCE SEQUENCE: NP_033178.2. RESIDUE 475 IS A VAL IN THIS ...(1) THE SEQUENCE IS BASED ON NCBI REFERENCE SEQUENCE: NP_033178.2. RESIDUE 475 IS A VAL IN THIS DATABASE SEQUENCE. (2) RESIDUES 551 AND 555 WERE BOTH MUTATED FROM ARG TO ALA TO PREVENT PROTEOLYTI |
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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: 3.43 Å3/Da / Density % sol: 64.18 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: 0.1M sodium cacodylate, 0.1M calcium acetate, 12% w/v PEG 8000, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9173 Å |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Apr 14, 2011 |
Radiation | Monochromator: Single bounce monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9173 Å / Relative weight: 1 |
Reflection | Resolution: 3.3→99.42 Å / Num. all: 30776 / Num. obs: 29876 / % possible obs: 97.7 % / Observed criterion σ(F): -3 / Observed criterion σ(I): 0 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1Q47 Resolution: 3.3→77 Å / Cor.coef. Fo:Fc: 0.896 / Cor.coef. Fo:Fc free: 0.867 / SU B: 23.111 / SU ML: 0.375 / Cross valid method: THROUGHOUT / σ(F): -3 / ESU R Free: 0.503 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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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: 55.898 Å2
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Refinement step | Cycle: LAST / Resolution: 3.3→77 Å
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Refine LS restraints |
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Refine LS restraints NCS | Ens-ID: 1 / Number: 33450 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.07 Å / Weight position: 0.05
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LS refinement shell | Resolution: 3.3→3.386 Å / Total num. of bins used: 20
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