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- PDB-3okw: Mouse Semaphorin 6A, extracellular domains 1-2 -

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Basic information

Entry
Database: PDB / ID: 3okw
TitleMouse Semaphorin 6A, extracellular domains 1-2
ComponentsSemaphorin-6A
KeywordsSIGNALING PROTEIN / Transmembrane / ligand / sema-domain / Cell-cell signalling / Plexin A2
Function / homology
Function and homology information


negative regulation of cell adhesion involved in sprouting angiogenesis / semaphorin receptor binding / negative regulation of sprouting angiogenesis / negative regulation of vascular endothelial growth factor signaling pathway / negative regulation of axon extension involved in axon guidance / positive regulation of neuron migration / chemorepellent activity / neural crest cell migration / centrosome localization / negative chemotaxis ...negative regulation of cell adhesion involved in sprouting angiogenesis / semaphorin receptor binding / negative regulation of sprouting angiogenesis / negative regulation of vascular endothelial growth factor signaling pathway / negative regulation of axon extension involved in axon guidance / positive regulation of neuron migration / chemorepellent activity / neural crest cell migration / centrosome localization / negative chemotaxis / semaphorin-plexin signaling pathway / cellular response to vascular endothelial growth factor stimulus / negative regulation of angiogenesis / axon guidance / neuron migration / negative regulation of ERK1 and ERK2 cascade / transmembrane signaling receptor activity / cell surface receptor signaling pathway / axon / apoptotic process / membrane / identical protein binding / plasma membrane
Similarity search - Function
Semaphorin / ligand-binding face of the semaphorins, domain 2 / ligand-binding face of the semaphorins, domain 2 / Plexin repeat / Plexin repeat / Sema domain / semaphorin domain / Sema domain / Sema domain superfamily / Sema domain profile. ...Semaphorin / ligand-binding face of the semaphorins, domain 2 / ligand-binding face of the semaphorins, domain 2 / Plexin repeat / Plexin repeat / Sema domain / semaphorin domain / Sema domain / Sema domain superfamily / Sema domain profile. / YVTN repeat-like/Quinoprotein amine dehydrogenase / 7 Propeller / Methylamine Dehydrogenase; Chain H / WD40/YVTN repeat-like-containing domain superfamily / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
CITRIC ACID / Semaphorin-6A
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.299 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: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / database_PDB_caveat / 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 / pdbx_validate_chiral / pdbx_validate_close_contact / 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_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.type_symbol / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.src_method / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_validate_chiral.auth_asym_id / _pdbx_validate_chiral.auth_seq_id / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_2 / _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_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_comp_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: Semaphorin-6A
B: Semaphorin-6A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)132,09520
Polymers127,9312
Non-polymers4,16418
Water5,008278
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8400 Å2
ΔGint29 kcal/mol
Surface area47900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.036, 97.036, 153.055
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Semaphorin-6A / Semaphorin VIA / Sema VIA / Semaphorin-6A-1 / SEMA6A-1 / Semaphorin Q / Sema Q


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

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Sugars , 3 types, 7 molecules

#2: 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.: 4
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
#3: Polysaccharide alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-3)-[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


Type: oligosaccharide / Mass: 910.823 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3[DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,5,4/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3/a4-b1_b4-c1_c3-d1_c6-e1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}}}}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.: 2
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 , 3 types, 289 molecules

#5: Chemical ChemComp-CIT / CITRIC ACID / Citric acid


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#6: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 278 / 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: 3.25 Å3/Da / Density % sol: 62.18 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.4
Details: Polyethylene Glycol 3350 20% w/v, di-ammonium Hydrogen Citrate 200mM, 6% D-galactose, pH 7.4, 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: Apr 9, 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: 2.299→37 Å / Num. all: 71753 / Num. obs: 71409 / % possible obs: 99.6 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3

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Processing

Software
NameVersionClassification
GDAdata collection
PHASERphasing
PHENIX(phenix.refine: 1.6.2_432)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.299→32.434 Å / SU ML: 0.37 / σ(F): 1.96 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2187 3610 5.06 %random
Rwork0.1841 ---
all0.1858 71753 --
obs0.1858 71381 99.55 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 45 Å2 / ksol: 0.348 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--1.7959 Å20 Å20 Å2
2---1.7959 Å20 Å2
3---3.5918 Å2
Refinement stepCycle: LAST / Resolution: 2.299→32.434 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8443 0 274 278 8995
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0088939
X-RAY DIFFRACTIONf_angle_d1.12312071
X-RAY DIFFRACTIONf_dihedral_angle_d18.3423360
X-RAY DIFFRACTIONf_chiral_restr0.0711338
X-RAY DIFFRACTIONf_plane_restr0.0041526
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2986-2.32880.33981340.32822551X-RAY DIFFRACTION98
2.3288-2.36070.37591380.31852614X-RAY DIFFRACTION100
2.3607-2.39440.28921370.29182598X-RAY DIFFRACTION100
2.3944-2.43020.3561260.27922662X-RAY DIFFRACTION100
2.4302-2.46810.31711610.25122586X-RAY DIFFRACTION100
2.4681-2.50860.25151310.23012567X-RAY DIFFRACTION100
2.5086-2.55180.29371530.23782665X-RAY DIFFRACTION100
2.5518-2.59820.24971370.22422582X-RAY DIFFRACTION100
2.5982-2.64820.29411570.22872581X-RAY DIFFRACTION100
2.6482-2.70220.26541360.20772634X-RAY DIFFRACTION100
2.7022-2.76090.27621300.19742626X-RAY DIFFRACTION100
2.7609-2.82510.2431360.1842578X-RAY DIFFRACTION100
2.8251-2.89570.22061420.18872623X-RAY DIFFRACTION100
2.8957-2.9740.22871440.18322605X-RAY DIFFRACTION100
2.974-3.06140.23781240.18692646X-RAY DIFFRACTION100
3.0614-3.16010.23711290.18192630X-RAY DIFFRACTION100
3.1601-3.2730.21051480.18452592X-RAY DIFFRACTION100
3.273-3.40390.19911540.17992597X-RAY DIFFRACTION100
3.4039-3.55860.22291480.18132662X-RAY DIFFRACTION100
3.5586-3.7460.18681110.17872648X-RAY DIFFRACTION100
3.746-3.98030.18531300.16552618X-RAY DIFFRACTION100
3.9803-4.2870.19881540.14992588X-RAY DIFFRACTION100
4.287-4.71720.13691350.12852599X-RAY DIFFRACTION100
4.7172-5.39710.21911330.14712654X-RAY DIFFRACTION100
5.3971-6.78950.24111410.19422592X-RAY DIFFRACTION100
6.7895-32.43710.18651410.19022473X-RAY DIFFRACTION94
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)
11.8575-0.01550.08921.128-0.41581.30260.02740.22210.206-0.1491-0.0529-0.02910.0451-0.1189-00.18310.00610.00830.0912-0.01180.1755-21.936582.1329-0.8543
20.39740.25440.1440.2053-0.02210.3296-0.25210.09140.0542-0.3948-0.03990.4112-0.36730.2296-0.00030.4744-0.0464-0.14390.55080.00250.3787-51.380778.2907-20.1157
31.7945-0.1259-0.15332.2009-1.40992.4802-0.1219-0.2048-0.04280.66020.1341-0.0369-0.428-0.17160.00010.35820.09130.00230.1108-0.04170.1406-33.623129.9876-3.9415
40.04510.0363-0.04660.0263-0.03550.0466-0.0478-0.0668-0.48020.31790.0260.49830.4288-0.314700.7720.19770.34661.15990.26920.6452-62.1657119.76213.58
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 510:570 or resseq 1510:1570)
3X-RAY DIFFRACTION3chain B and (resseq 1:509 or resseq 1000:1509)
4X-RAY DIFFRACTION4chain B and (resseq 510:570 or resseq 1510:1570)

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