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- PDB-1q47: Structure of the Semaphorin 3A Receptor-Binding Module -

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Basic information

Entry
Database: PDB / ID: 1q47
TitleStructure of the Semaphorin 3A Receptor-Binding Module
ComponentsSemaphorin 3A
KeywordsSIGNALING PROTEIN / beta propeller
Function / homology
Function and homology information


neural crest cell migration involved in sympathetic nervous system development / regulation of axon extension involved in axon guidance / synaptic target recognition / CRMPs in Sema3A signaling / basal dendrite arborization / Sema3A PAK dependent Axon repulsion / dichotomous subdivision of terminal units involved in salivary gland branching / semaphorin receptor binding / epithelial cell migration / ventral trunk neural crest cell migration ...neural crest cell migration involved in sympathetic nervous system development / regulation of axon extension involved in axon guidance / synaptic target recognition / CRMPs in Sema3A signaling / basal dendrite arborization / Sema3A PAK dependent Axon repulsion / dichotomous subdivision of terminal units involved in salivary gland branching / semaphorin receptor binding / epithelial cell migration / ventral trunk neural crest cell migration / sympathetic neuron projection guidance / facioacoustic ganglion development / trigeminal ganglion development / cerebellar climbing fiber to Purkinje cell synapse / 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 / SEMA3A-Plexin repulsion signaling by inhibiting Integrin adhesion / maintenance of synapse structure / axon extension involved in axon guidance / negative regulation of axon extension involved in axon guidance / sympathetic neuron projection extension / negative regulation of epithelial cell migration / sympathetic ganglion development / axonogenesis involved in innervation / 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 / negative regulation of neuron projection development / nervous system development / axon / dendrite / glutamatergic synapse / extracellular space / extracellular region
Similarity search - Function
Semaphorin-3A, sema domain / IL-1Ra-like, immunoglobulin domain / Immunoglobulin domain / Semaphorin / Sema domain / semaphorin domain / Sema domain / Sema domain superfamily / Sema domain profile. / PSI domain ...Semaphorin-3A, sema domain / IL-1Ra-like, immunoglobulin domain / Immunoglobulin domain / Semaphorin / Sema domain / semaphorin domain / Sema domain / Sema domain superfamily / Sema domain profile. / PSI domain / domain found in Plexins, Semaphorins and Integrins / YVTN repeat-like/Quinoprotein amine dehydrogenase / 7 Propeller / Methylamine Dehydrogenase; Chain H / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / Immunoglobulin-like fold / Mainly Beta
Similarity search - Domain/homology
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.8 Å
AuthorsAntipenko, A. / Himanen, J.-P. / van Leyen, K. / Nardi-Dei, V. / Lesniak, J. / Barton, W.A. / Rajashankar, K.R. / Lu, M. / Hoemme, C. / Puschel, A. / Nikolov, D.
CitationJournal: Neuron / Year: 2003
Title: Structure of the semaphorin-3A receptor binding module.
Authors: Antipenko, A. / Himanen, J.-P. / van Leyen, K. / Nardi-Dei, V. / Lesniak, J. / Barton, W.A. / Rajashankar, K.R. / Lu, M. / Hoemme, C. / Puschel, A.W. / Nikolov, D.B.
History
DepositionAug 1, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 3, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Feb 1, 2017Group: Database references / Structure summary
Revision 1.4Jul 29, 2020Group: Advisory / Data collection ...Advisory / Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_validate_close_contact / struct_conn / struct_conn_type / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Semaphorin 3A
B: Semaphorin 3A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)113,8126
Polymers112,9272
Non-polymers8854
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4030 Å2
ΔGint-6 kcal/mol
Surface area43000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)218.791, 59.733, 122.715
Angle α, β, γ (deg.)90, 109.007, 90
Int Tables number5
Space group name H-MC121
DetailsThe biological assembly is a dimer which is found in the asymmetric unit.

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Components

#1: Protein Semaphorin 3A / Semaphorin III / Sema III / Semaphorin D / Sema D


Mass: 56463.582 Da / Num. of mol.: 2 / Fragment: Sema-3A 65k (residues 26-520)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Cell line (production host): SF9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: O08665
#2: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.36 Å3/Da / Density % sol: 63.34 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: Tris, PEG 8000, heptyl-beta-D thioglucoside, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 8-BM / Wavelength: 0.97, 0.964
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 2, 2003
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.971
20.9641
ReflectionResolution: 2.8→30 Å / Num. all: 278233 / Num. obs: 277955 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 2.8→2.93 Å / % possible all: 100

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
MLPHAREphasing
CNS1refinement
RefinementMethod to determine structure: MAD / Resolution: 2.8→20 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.294 7016 random
obs0.249 70534 -
all-72166 -
Refinement stepCycle: LAST / Resolution: 2.8→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7863 0 60 0 7923

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