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- PDB-3okt: Mouse Plexin A2, extracellular domains 1-4 -

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Basic information

Entry
Database: PDB / ID: 3okt
TitleMouse Plexin A2, extracellular domains 1-4
ComponentsPlexin-A2
KeywordsSIGNALING PROTEIN / Transmembrane / receptor / sema-domain / Cell-cell signalling / Semaphorin-6A
Function / homology
Function and homology information


cerebellar granule cell precursor tangential migration / CRMPs in Sema3A signaling / Sema3A PAK dependent Axon repulsion / limb bud formation / SEMA3A-Plexin repulsion signaling by inhibiting Integrin adhesion / semaphorin receptor complex / pharyngeal system development / semaphorin receptor activity / negative regulation of cell adhesion / neural tube development ...cerebellar granule cell precursor tangential migration / CRMPs in Sema3A signaling / Sema3A PAK dependent Axon repulsion / limb bud formation / SEMA3A-Plexin repulsion signaling by inhibiting Integrin adhesion / semaphorin receptor complex / pharyngeal system development / semaphorin receptor activity / negative regulation of cell adhesion / neural tube development / centrosome localization / positive regulation of axonogenesis / semaphorin-plexin signaling pathway / somitogenesis / regulation of cell migration / regulation of cell shape / collagen-containing extracellular matrix / cell surface receptor signaling pathway / identical protein binding / plasma membrane
Similarity search - Function
Plexin-A2, sema domain / Plexin, TIG domain 2 / TIG domain found in plexin / Plexin, TIG domain 1 / TIG domain / Plexin, cytoplasmic RasGAP domain / Plexin, cytoplasmic RhoGTPase-binding domain / Plexin cytoplasmic RasGAP domain / Plexin cytoplasmic RhoGTPase-binding domain / Plexin family ...Plexin-A2, sema domain / Plexin, TIG domain 2 / TIG domain found in plexin / Plexin, TIG domain 1 / TIG domain / Plexin, cytoplasmic RasGAP domain / Plexin, cytoplasmic RhoGTPase-binding domain / Plexin cytoplasmic RasGAP domain / Plexin cytoplasmic RhoGTPase-binding 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 / YVTN repeat-like/Quinoprotein amine dehydrogenase / 7 Propeller / Methylamine Dehydrogenase; Chain H / Immunoglobulin E-set / 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 / MOLECULAR REPLACEMENT / Resolution: 2.296 Å
AuthorsJanssen, B.J.C. / Robinson, R.A. / Bell, C.H. / Siebold, C. / Jones, E.Y.
CitationJournal: Nature / Year: 2010
Title: Structural basis of semaphorin-plexin signalling.
Authors: Janssen, B.J. / Robinson, R.A. / Perez-Branguli, F. / Bell, C.H. / Mitchell, K.J. / Siebold, C. / Jones, E.Y.
History
DepositionAug 25, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 13, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Author supporting evidence / Category: pdbx_struct_assembly_auth_evidence
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / 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 / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
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: Plexin-A2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,50313
Polymers75,9351
Non-polymers1,56812
Water3,279182
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: light scattering, equilibrium centrifugation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Plexin-A2
hetero molecules

A: Plexin-A2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)155,00626
Polymers151,8702
Non-polymers3,13724
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,y,-z1
Buried area7500 Å2
ΔGint-33 kcal/mol
Surface area56850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)157.860, 92.903, 62.904
Angle α, β, γ (deg.)90.00, 102.87, 90.00
Int Tables number5
Space group name H-MC121
DetailsAuthors have confirmed that the quaternary structure is a monomer, experimentally by multi-angle light scattering and also by analytical utracentrifugation.

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Components

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Protein / Sugars , 2 types, 6 molecules A

#1: Protein Plexin-A2 / Plexin-2 / Plex 2


Mass: 75934.914 Da / Num. of mol.: 1 / Fragment: residues 33-703, extracellular domains 1-4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Plxna2, Kiaa0463 / Plasmid: PHLsec / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: P70207
#2: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 5
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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Non-polymers , 4 types, 189 molecules

#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 182 / 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: 2.96 Å3/Da / Density % sol: 58.46 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: Polyethylene Glycol 6000 12.8% w/v, Magnesium Chloride 128mM, HEPES 64mM pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.975 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 27, 2009
RadiationMonochromator: SI [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.975 Å / Relative weight: 1
ReflectionResolution: 2.296→50 Å / Num. all: 39628 / Num. obs: 38566 / % possible obs: 97.9 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3

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Processing

Software
NameVersionClassification
DNAdata collection
PHASERphasing
PHENIX(phenix.refine: 1.6_289)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.296→44.907 Å / SU ML: 0.37 / σ(F): 1.35 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2506 1940 5.03 %random
Rwork0.1958 ---
all0.1986 39628 --
obs0.1986 38550 97.28 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 32.832 Å2 / ksol: 0.362 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.501 Å20 Å211.7196 Å2
2---2.7475 Å20 Å2
3---3.2485 Å2
Refinement stepCycle: LAST / Resolution: 2.296→44.907 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5138 0 97 182 5417
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0055370
X-RAY DIFFRACTIONf_angle_d0.9197266
X-RAY DIFFRACTIONf_dihedral_angle_d15.6491939
X-RAY DIFFRACTIONf_chiral_restr0.06811
X-RAY DIFFRACTIONf_plane_restr0.004930
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2961-2.35360.34181420.28922535X-RAY DIFFRACTION96
2.3536-2.41720.31651330.27372645X-RAY DIFFRACTION98
2.4172-2.48830.32261320.26832636X-RAY DIFFRACTION99
2.4883-2.56860.31871420.26592629X-RAY DIFFRACTION98
2.5686-2.66040.32181390.24412620X-RAY DIFFRACTION98
2.6604-2.76690.29681510.23782620X-RAY DIFFRACTION98
2.7669-2.89280.28661300.21022619X-RAY DIFFRACTION98
2.8928-3.04530.26521300.2042634X-RAY DIFFRACTION98
3.0453-3.23610.26741490.19722580X-RAY DIFFRACTION97
3.2361-3.48580.26321300.17852635X-RAY DIFFRACTION97
3.4858-3.83640.22571260.16582609X-RAY DIFFRACTION97
3.8364-4.39120.19391440.14342591X-RAY DIFFRACTION96
4.3912-5.53080.16981300.13922624X-RAY DIFFRACTION97
5.5308-44.91530.22331620.18352633X-RAY DIFFRACTION96
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.53490.1831-0.54951.4551-0.41270.9968-0.06860.0534-0.20940.04620.01690.06830.06-0.0324-00.1793-0.0250.0010.1589-0.03750.153547.666353.704220.3194
20.04840.0158-0.05260.0672-0.01890.055-0.01640.0643-0.0850.11370.11970.1285-0.0547-0.2939-00.2412-0.0747-0.04150.4139-0.01580.197268.637668.4379-8.8934
30.3175-0.1060.10520.1524-0.13110.21030.2261-0.11210.5042-0.3066-0.088-0.2097-0.2840.0640.00140.3076-0.0660.07250.3032-0.02990.35884.157184.1877-19.0327
40.07170.0019-0.02970.06950.00090.0324-0.0161-0.17290.25210.3078-0.2408-0.39520.2619-0.046300.334-0.07240.02120.39430.04090.4979110.199291.5934-17.7626
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A and (resseq 1:509 or resseq 1000:1509)
2X-RAY DIFFRACTION2chain A and (resseq 510:559 or resseq 1510:1559)
3X-RAY DIFFRACTION3chain A and (resseq 560:655 or resseq 1560:1655)
4X-RAY DIFFRACTION4chain A and (resseq 656:707 or resseq 1656:1707)

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