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- PDB-3oky: Plexin A2 in complex with Semaphorin 6A -

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Basic information

Entry
Database: PDB / ID: 3oky
TitlePlexin A2 in complex with Semaphorin 6A
Components
  • Plexin-A2
  • Putative uncharacterized protein
KeywordsSIGNALING PROTEIN / Transmembrane / ligand / sema-domain / Cell-cell signalling
Function / homology
Function and homology information


negative regulation of cell adhesion involved in sprouting angiogenesis / cerebellar granule cell precursor tangential migration / CRMPs in Sema3A signaling / Sema3A PAK dependent Axon repulsion / semaphorin receptor binding / negative regulation of sprouting angiogenesis / SEMA3A-Plexin repulsion signaling by inhibiting Integrin adhesion / semaphorin-plexin signaling pathway involved in axon guidance / negative regulation of vascular endothelial growth factor signaling pathway / negative regulation of axon extension involved in axon guidance ...negative regulation of cell adhesion involved in sprouting angiogenesis / cerebellar granule cell precursor tangential migration / CRMPs in Sema3A signaling / Sema3A PAK dependent Axon repulsion / semaphorin receptor binding / negative regulation of sprouting angiogenesis / SEMA3A-Plexin repulsion signaling by inhibiting Integrin adhesion / semaphorin-plexin signaling pathway involved in axon guidance / negative regulation of vascular endothelial growth factor signaling pathway / negative regulation of axon extension involved in axon guidance / limb bud formation / semaphorin receptor complex / positive regulation of neuron migration / pharyngeal system development / chemorepellent activity / semaphorin receptor activity / negative regulation of cell adhesion / neural tube development / neural crest cell migration / centrosome localization / negative chemotaxis / positive regulation of axonogenesis / semaphorin-plexin signaling pathway / cellular response to vascular endothelial growth factor stimulus / somitogenesis / regulation of cell migration / negative regulation of angiogenesis / axon guidance / neuron migration / negative regulation of ERK1 and ERK2 cascade / transmembrane signaling receptor activity / nervous system development / regulation of cell shape / collagen-containing extracellular matrix / cell differentiation / cell surface receptor signaling pathway / axon / apoptotic process / membrane / identical protein binding / plasma membrane
Similarity search - Function
Plexin-A2, sema domain / Semaphorin / Plexin, TIG domain 2 / TIG domain found in plexin / Plexin, TIG domain 1 / TIG domain / Plexin, cytoplasmic RhoGTPase-binding domain / Plexin cytoplasmic RhoGTPase-binding domain / Plexin, cytoplasmic RasGAP domain / Plexin cytoplasmic RasGAP domain ...Plexin-A2, sema domain / Semaphorin / Plexin, TIG domain 2 / TIG domain found in plexin / Plexin, TIG domain 1 / TIG domain / Plexin, cytoplasmic RhoGTPase-binding domain / Plexin cytoplasmic RhoGTPase-binding domain / Plexin, cytoplasmic RasGAP domain / Plexin cytoplasmic RasGAP domain / ligand-binding face of the semaphorins, domain 2 / ligand-binding face of the semaphorins, domain 2 / 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 / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Semaphorin-6A / Plexin-A2 / Sema domain-containing protein
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.195 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 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.id / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _chem_comp.name / _chem_comp.type / _pdbx_entity_nonpoly.entity_id / _pdbx_entity_nonpoly.name / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_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

Downloads & links

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Assembly

Deposited unit
A: Plexin-A2
B: Putative uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)142,11314
Polymers139,9002
Non-polymers2,21212
Water7,008389
1
A: Plexin-A2
B: Putative uncharacterized protein
hetero molecules

A: Plexin-A2
B: Putative uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)284,22528
Polymers279,8014
Non-polymers4,42424
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z+1/21
Buried area5960 Å2
ΔGint12 kcal/mol
Surface area46530 Å2
Unit cell
Length a, b, c (Å)155.544, 159.596, 139.256
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Details-x+1,y,-z+1/2

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Components

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Protein , 2 types, 2 molecules AB

#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: Kiaa0463, Plxna2 / Plasmid: pHLsec / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: P70207
#2: Protein Putative uncharacterized protein


Mass: 63965.582 Da / Num. of mol.: 1 / Fragment: extracellular domains 1-2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Sema6a / Plasmid: pHLsec / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: Q8BUT0, UniProt: O35464*PLUS

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Sugars , 2 types, 7 molecules

#3: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#4: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 6
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 , 2 types, 394 molecules

#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 389 / 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: 3.09 Å3/Da / Density % sol: 60.18 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 2-Methyl-2,4-Pentanediol 12.4% v/v, MES 124mM pH 6.0, ethyl acetate 1% v/v, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 8, 2009
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.195→55 Å / Num. all: 88386 / Num. obs: 82704 / % possible obs: 94.4 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3

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Processing

Software
NameVersionClassification
GDAdata collection
PHASERphasing
PHENIX(phenix.refine)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.195→39.899 Å / SU ML: 0.32 / σ(F): 1.33 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.23 4197 5.08 %
Rwork0.1896 --
all0.1916 88386 -
obs0.1916 82680 93.61 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 49.756 Å2 / ksol: 0.356 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-13.7873 Å2-0 Å2-0 Å2
2---4.8816 Å2-0 Å2
3----8.9057 Å2
Refinement stepCycle: LAST / Resolution: 2.195→39.899 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9069 0 142 389 9600
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0059454
X-RAY DIFFRACTIONf_angle_d0.91912786
X-RAY DIFFRACTIONf_dihedral_angle_d17.1393443
X-RAY DIFFRACTIONf_chiral_restr0.0621417
X-RAY DIFFRACTIONf_plane_restr0.0031637
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1954-2.22040.35111050.30042419X-RAY DIFFRACTION86
2.2204-2.24650.33281510.28562667X-RAY DIFFRACTION96
2.2465-2.27390.30461390.28532638X-RAY DIFFRACTION96
2.2739-2.30270.28841440.25082643X-RAY DIFFRACTION96
2.3027-2.3330.30711420.23922648X-RAY DIFFRACTION96
2.333-2.36490.2641380.23522656X-RAY DIFFRACTION95
2.3649-2.39870.26991410.23662658X-RAY DIFFRACTION96
2.3987-2.43450.28361480.23352624X-RAY DIFFRACTION95
2.4345-2.47250.26411330.22162643X-RAY DIFFRACTION95
2.4725-2.51310.24631400.22042648X-RAY DIFFRACTION95
2.5131-2.55640.29211410.21932590X-RAY DIFFRACTION94
2.5564-2.60290.27991500.21312623X-RAY DIFFRACTION95
2.6029-2.65290.24871440.21792660X-RAY DIFFRACTION95
2.6529-2.7070.27271450.2252607X-RAY DIFFRACTION95
2.707-2.76590.27581300.20612614X-RAY DIFFRACTION94
2.7659-2.83020.25841470.19752603X-RAY DIFFRACTION94
2.8302-2.9010.24071260.19112638X-RAY DIFFRACTION94
2.901-2.97940.22341430.19542623X-RAY DIFFRACTION94
2.9794-3.0670.26081640.19292608X-RAY DIFFRACTION94
3.067-3.1660.2431400.18982611X-RAY DIFFRACTION94
3.166-3.27910.21781650.17632600X-RAY DIFFRACTION94
3.2791-3.41030.24891440.17142622X-RAY DIFFRACTION94
3.4103-3.56540.21791360.16682606X-RAY DIFFRACTION93
3.5654-3.75330.20011400.16912603X-RAY DIFFRACTION93
3.7533-3.98820.20271410.16632639X-RAY DIFFRACTION93
3.9882-4.29580.19251200.15472602X-RAY DIFFRACTION92
4.2958-4.72750.16551270.12472554X-RAY DIFFRACTION90
4.7275-5.41020.14381390.13632573X-RAY DIFFRACTION91
5.4102-6.81070.19971440.16762628X-RAY DIFFRACTION92
6.8107-39.90560.19781300.17782635X-RAY DIFFRACTION88
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)
10.3616-0.1058-0.1910.7335-0.15351.188-0.08980.008-0-0.07980.0406-0.03940.25820.06520.04260.2264-0.00290.01170.1568-0.01990.153252.6402-33.162.0074
21.0362-0.20640.9630.59920.3416-0.1021-0.0517-0.35150.01540.4281-0.0622-0.00550.154-0.17230.06750.66420.11610.0380.41040.07660.345154.0335-50.391196.3124
30.4418-0.40330.31011.11710.1554-0.01820.0026-0.2959-0.17710.8992-0.18870.00880.2003-0.04370.20221.02690.0809-0.0510.4570.28850.458460.3902-65.8455114.075
40.6723-0.3367-0.30751.3981-0.17040.71010.06490.130.0151-0.2151-0.06340.002-0.0378-0.1149-0.00230.19980.0049-0.01060.20590.0130.146253.62364.107530.4679
50.6929-0.0687-0.30720.7119-0.25950.4559-0.02640.33750.2485-0.6413-0.5491-0.42010.23630.41830.31740.66480.22950.22050.65870.39710.556560.586932.43879.4482
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 560:657 or resseq 1560:1657)
4X-RAY DIFFRACTION4chain B and (resseq 1:512 or resseq 1000:1512)
5X-RAY DIFFRACTION5chain B and (resseq 513:580 or resseq 1513:1580)

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