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- PDB-3ig3: Crystal structure of mouse Plexin A3 intracellular domain -

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Basic information

Entry
Database: PDB / ID: 3ig3
TitleCrystal structure of mouse Plexin A3 intracellular domain
ComponentsPlxna3 protein
KeywordsSIGNALING PROTEIN / MEMBRANE PROTEIN / plexin intracellular GAP RBD inactive / Membrane / Transmembrane
Function / homology
Function and homology information


positive regulation of cytoskeleton organization / CRMPs in Sema3A signaling / Sema3A PAK dependent Axon repulsion / neuron projection guidance / trigeminal nerve structural organization / facial nerve structural organization / branchiomotor neuron axon guidance / SEMA3A-Plexin repulsion signaling by inhibiting Integrin adhesion / semaphorin-plexin signaling pathway involved in axon guidance / negative regulation of axon extension involved in axon guidance ...positive regulation of cytoskeleton organization / CRMPs in Sema3A signaling / Sema3A PAK dependent Axon repulsion / neuron projection guidance / trigeminal nerve structural organization / facial nerve structural organization / branchiomotor neuron axon guidance / SEMA3A-Plexin repulsion signaling by inhibiting Integrin adhesion / semaphorin-plexin signaling pathway involved in axon guidance / negative regulation of axon extension involved in axon guidance / pyramidal neuron development / semaphorin receptor complex / semaphorin receptor activity / negative regulation of cell adhesion / neuron projection extension / negative chemotaxis / positive regulation of axonogenesis / regulation of GTPase activity / plasma membrane => GO:0005886 / regulation of cell migration / axon guidance / hippocampus development / regulation of cell shape
Similarity search - Function
GTPase Activation - p120GAP; domain 1 / GTPase Activation - p120gap; domain 1 / Plexin, TIG domain 2 / TIG domain found in plexin / Plexin, TIG domain 1 / TIG domain / Plexin, cytoplasmic RasGAP domain / Plexin cytoplasmic RasGAP domain / Plexin family / Plexin repeat ...GTPase Activation - p120GAP; domain 1 / GTPase Activation - p120gap; domain 1 / Plexin, TIG domain 2 / TIG domain found in plexin / Plexin, TIG domain 1 / TIG domain / Plexin, cytoplasmic RasGAP domain / Plexin cytoplasmic RasGAP domain / Plexin family / Plexin repeat / Plexin repeat / Sema domain / semaphorin domain / Sema domain / Sema domain superfamily / Sema domain profile. / IPT/TIG domain / ig-like, plexins, transcription factors / Rho GTPase activation protein / PSI domain / domain found in Plexins, Semaphorins and Integrins / IPT domain / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Ubiquitin-like (UB roll) / Immunoglobulin E-set / WD40/YVTN repeat-like-containing domain superfamily / Roll / Immunoglobulin-like fold / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Plexin-A3 / Plexin-A3
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.99 Å
AuthorsHe, H. / Zhang, X.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2009
Title: Crystal structure of the plexin A3 intracellular region reveals an autoinhibited conformation through active site sequestration.
Authors: He, H. / Yang, T. / Terman, J.R. / Zhang, X.
History
DepositionJul 27, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 25, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Dec 14, 2016Group: Structure summary
Revision 1.3Nov 1, 2017Group: Refinement description / Category: software
Revision 1.4Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Plxna3 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,0942
Polymers72,0021
Non-polymers921
Water6,539363
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)147.789, 47.203, 101.178
Angle α, β, γ (deg.)90.000, 118.690, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Plxna3 protein


Mass: 72002.117 Da / Num. of mol.: 1 / Fragment: UNP residues 1170-1795
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Plxna3 / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): ArcticExpress / References: UniProt: A5D6Q5, UniProt: P70208*PLUS
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 363 / Source method: isolated from a natural source / Formula: H2O

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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: 2.15 Å3/Da / Density % sol: 42.79 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.75
Details: 100 mM Bis-Tris Propane, 200 mM NaNO3 and 20% PEG3350, pH 7.75, vapor diffusion, hanging drop, temperature 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONAPS 19-BM10.97926
SYNCHROTRONAPS 19-BM20.97926
Detector
TypeIDDetectorDate
CUSTOM-MADE1CCDJan 1, 2008
CUSTOM-MADE2CCDJan 1, 2008
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SADMx-ray1
Radiation wavelengthWavelength: 0.97926 Å / Relative weight: 1
ReflectionRedundancy: 9.3 % / Av σ(I) over netI: 26.27 / Number: 150460 / Rmerge(I) obs: 0.111 / Χ2: 1.15 / D res high: 2.75 Å / D res low: 50 Å / Num. obs: 16221 / % possible obs: 99.8
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
5.925098.210.0671.8359.5
4.75.9299.810.0881.3548.5
4.114.710010.0821.2899.2
3.734.1110010.0991.239.4
3.463.7399.910.1141.2259.5
3.263.4699.910.1451.119.5
3.13.2610010.2050.9589.5
2.963.110010.2750.8749.5
2.852.9610010.3820.8069.3
2.752.8599.910.4580.7918.8
ReflectionResolution: 1.99→50 Å / Num. obs: 41961 / % possible obs: 99.6 % / Redundancy: 4.7 % / Rmerge(I) obs: 0.05 / Χ2: 0.995 / Net I/σ(I): 15.7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.99-2.073.70.35540610.9951,297.4
2.07-2.154.60.27641901.0391,2100
2.15-2.254.80.19741450.9441,2100
2.25-2.374.80.14741980.9881,2100
2.37-2.524.90.11341911.0171,2100
2.52-2.714.90.0941741.0021,2100
2.71-2.994.90.06242221.0271,2100
2.99-3.424.80.04842291.0061,2100
3.42-4.314.80.03942490.9091,2100
4.31-504.50.03243021.021,299

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIXrefinement
PDB_EXTRACT3.005data extraction
HKL-2000data collection
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.99→34.082 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.832 / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflectionSelection details
Rfree0.223 2007 4.99 %random
Rwork0.188 ---
obs0.19 40238 95.1 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 49.273 Å2 / ksol: 0.351 e/Å3
Displacement parametersBiso max: 129.53 Å2 / Biso mean: 44.828 Å2 / Biso min: 18.74 Å2
Baniso -1Baniso -2Baniso -3
1--9.691 Å20 Å2-2.525 Å2
2--8.719 Å2-0 Å2
3---0.956 Å2
Refinement stepCycle: LAST / Resolution: 1.99→34.082 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4479 0 6 363 4848
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0044567
X-RAY DIFFRACTIONf_angle_d0.7196183
X-RAY DIFFRACTIONf_chiral_restr0.051716
X-RAY DIFFRACTIONf_plane_restr0.003784
X-RAY DIFFRACTIONf_dihedral_angle_d16.9061675
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.99-2.0410.2541060.232223232978
2.041-2.0970.2411370.2252516265389
2.097-2.1580.271450.212637278293
2.158-2.2280.2331430.2062644278793
2.228-2.3070.2271350.1962677281294
2.307-2.40.2671340.2022776291097
2.4-2.5090.2391540.2012767292197
2.509-2.6410.2471540.22772292697
2.641-2.8070.2651380.22791292997
2.807-3.0230.2571290.1992835296498
3.023-3.3270.2251560.1942866302299
3.327-3.8080.2221330.17128993032100
3.808-4.7960.1661790.15228753054100
4.796-34.0870.1951640.182953311799

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