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- PDB-8ckk: Semaphorin-5A TSR 3-4 domains in complex with nitrate -

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Basic information

Entry
Database: PDB / ID: 8ckk
TitleSemaphorin-5A TSR 3-4 domains in complex with nitrate
ComponentsSemaphorin-5A
KeywordsSIGNALING PROTEIN / semaphorin / cell signalling / axon guidance cue / glycosaminoglycan binding protein
Function / homology
Function and homology information


signal clustering / diencephalon development / chondroitin sulfate proteoglycan binding / semaphorin receptor binding / positive regulation of actin filament depolymerization / Defective B3GALTL causes PpS / O-glycosylation of TSR domain-containing proteins / Other semaphorin interactions / negative regulation of axon extension involved in axon guidance / syndecan binding ...signal clustering / diencephalon development / chondroitin sulfate proteoglycan binding / semaphorin receptor binding / positive regulation of actin filament depolymerization / Defective B3GALTL causes PpS / O-glycosylation of TSR domain-containing proteins / Other semaphorin interactions / negative regulation of axon extension involved in axon guidance / syndecan binding / blood vessel endothelial cell proliferation involved in sprouting angiogenesis / positive regulation of axon extension involved in axon guidance / chemorepellent activity / negative regulation of cell adhesion / axon extension / heparan sulfate proteoglycan binding / axonal fasciculation / neural crest cell migration / positive regulation of endothelial cell chemotaxis / positive chemotaxis / semaphorin-plexin signaling pathway / negative regulation of endothelial cell apoptotic process / positive regulation of endothelial cell proliferation / cell chemotaxis / axon guidance / positive regulation of angiogenesis / positive regulation of canonical Wnt signaling pathway / cell-cell signaling / nervous system development / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / cell adhesion / positive regulation of cell migration / extracellular exosome / membrane / plasma membrane
Similarity search - Function
Semaphorin-5A, sema domain / Semaphorin / Plexin repeat / Plexin repeat / Sema domain / semaphorin domain / Sema domain / Sema domain superfamily / Sema domain profile. / Thrombospondin type 1 domain ...Semaphorin-5A, sema domain / Semaphorin / Plexin repeat / Plexin repeat / Sema domain / semaphorin domain / Sema domain / Sema domain superfamily / Sema domain profile. / Thrombospondin type 1 domain / Thrombospondin type-1 (TSP1) repeat superfamily / Thrombospondin type-1 (TSP1) repeat profile. / Thrombospondin type 1 repeats / Thrombospondin type-1 (TSP1) repeat / PSI domain / domain found in Plexins, Semaphorins and Integrins / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
alpha-D-mannopyranose / NITRATE ION / Semaphorin-5A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.56 Å
AuthorsNagy, G.N. / Duman, R. / Harlos, K. / El Omari, K. / Wagner, A. / Jones, E.Y.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom)MR/T000503/1 United Kingdom
CitationJournal: To Be Published
Title: Semaphorin-5A TSR 3-4 domains in complex with nitrate
Authors: Nagy, G.N. / Duman, R. / Harlos, K. / El Omari, K. / Wagner, A. / Jones, E.Y.
History
DepositionFeb 15, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 28, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Semaphorin-5A
B: Semaphorin-5A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,88423
Polymers28,1092
Non-polymers1,77521
Water3,045169
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, S-SAD was used for phasing this crystal structure, providing experimental evidence for the position of sulfur atoms of Cys and Met residues.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)51.894, 68.347, 85.502
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Semaphorin-5A / Semaphorin-F / Sema F


Mass: 14054.702 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: N-terminal 'ET' peptide and C-terminal 'GTLEVLFQ' peptides are recombinant additions encoded by the expression vector.
Source: (gene. exp.) Homo sapiens (human) / Gene: SEMA5A, SEMAF / Cell line (production host): HEK293T / Production host: Homo sapiens (human) / References: UniProt: Q13591
#2: Sugar
ChemComp-MAN / alpha-D-mannopyranose / alpha-D-mannose / D-mannose / mannose / Mannose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H12O6 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DManpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-mannopyranoseCOMMON NAMEGMML 1.0
a-D-ManpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
ManSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Chemical
ChemComp-NO3 / NITRATE ION / Nitrate


Mass: 62.005 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: NO3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 169 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.7 Å3/Da / Density % sol: 54.4 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 0.1 M BIS-TRIS propane, 6 M ammonium nitrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9686 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jan 26, 2020
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9686 Å / Relative weight: 1
ReflectionResolution: 1.557→53.39 Å / Num. obs: 24530 / % possible obs: 55.4 % / Redundancy: 12.7 % / Biso Wilson estimate: 22.67 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.123 / Rpim(I) all: 0.036 / Rrim(I) all: 0.128 / Net I/σ(I): 11.2
Reflection shellResolution: 1.557→1.768 Å / Redundancy: 12.2 % / Rmerge(I) obs: 1.564 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 1226 / CC1/2: 0.624 / Rpim(I) all: 0.465 / Rrim(I) all: 1.633 / % possible all: 8.9

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Processing

Software
NameVersionClassification
autoPROC1.0.5data processing
PHENIX1.20.1_4487refinement
Coot0.9.6model building
XDSdata reduction
Aimless0.7.4data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.56→42.75 Å / SU ML: 0.1976 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 31.5736
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2292 1194 4.87 %
Rwork0.1966 23334 -
obs0.1981 24526 55.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 35.52 Å2
Refinement stepCycle: LAST / Resolution: 1.56→42.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1808 0 112 169 2089
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00241967
X-RAY DIFFRACTIONf_angle_d0.62922660
X-RAY DIFFRACTIONf_chiral_restr0.0412271
X-RAY DIFFRACTIONf_plane_restr0.0043356
X-RAY DIFFRACTIONf_dihedral_angle_d10.2727711
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.56-1.620.589470.3437144X-RAY DIFFRACTION3.11
1.62-1.690.3836200.3228365X-RAY DIFFRACTION8
1.69-1.780.3124470.2842814X-RAY DIFFRACTION17.68
1.78-1.890.2668730.25851406X-RAY DIFFRACTION30.37
1.89-2.040.25831110.23882427X-RAY DIFFRACTION51.79
2.04-2.250.27632090.22693897X-RAY DIFFRACTION84.14
2.25-2.570.27092160.22754639X-RAY DIFFRACTION98.6
2.57-3.240.24282610.20234717X-RAY DIFFRACTION99.94
3.24-42.750.19142500.16694925X-RAY DIFFRACTION99.94
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)
11.22424270158-1.050901529010.09213392072314.07098284168-2.855047797822.913196500220.03319560103050.0933901716630.0765465174073-0.4162692705210.1128968958470.1493946264270.17844383198-0.045149911832-0.06251260590080.235665185474-0.0370732885249-0.06525954163560.134741354135-0.003352463540710.1425703473443.6856262710936.597228209865.1143625678
20.1524377148360.478111246127-0.5642472472019.22172796697-2.185487074230.1637900416090.0352989513255-0.003459281627410.02965287105190.148708012546-0.04834935141090.116849501523-0.08858404757430.04450181449670.01056080257030.248621026678-0.0475034344409-0.09888470114940.1811889630680.03073065793040.1179700471894.9053562527225.25863350470.5963818389
30.9970709495962.15689832839-0.3275957024685.133732906011.301543748587.60262002103-0.213258973314-1.76498869892-1.249738313330.910653215753-0.128271167908-0.3443184470571.43877755615-0.04262287517920.2329797333270.352669602016-0.007498810847890.1186701852850.4087215755140.3036837140630.5126949303832.54725456995-25.534288752388.3111959387
41.319823431152.14968087652-0.7170042792177.05528736577-3.246855846582.67960128292-0.0702107970945-0.0344329767277-0.176856916618-0.0392033822253-0.147057215018-0.345904474711-0.179334275326-0.02904963014920.187137786840.1234230218880.01636196028960.003452411087790.153597892910.02025832765470.1294145978051.81145903367-4.8711717374680.1467627901
54.48151554313-3.230782741951.312368976767.01281589347-0.6640539107162.051732103530.127269682085-0.418283101801-0.2354552111970.27690610373-0.151518883592-0.3564858581150.4514815140540.2775189310710.1099339431940.121377766638-0.0365805976679-0.0527433138140.2145324585170.07209605656870.21335139839915.7780738575-15.187327429187.2987747357
61.933454588351.6317185107-0.6264252499668.783861625150.1098024057671.71669651527-0.0139020920938-0.0114885396765-0.1641874285380.589042518060.253076303403-0.8640541599380.1741431405690.0830009952327-0.1784614266470.2132854055470.00814650835828-0.09701993670950.164935322344-0.02385358424580.2487359162318.444751676339.222515855275.541011002
70.2689929190510.593263802647-0.3616215167373.495957536510.3013314384811.21550755244-0.03061029188380.115238847836-0.0378594690995-0.3196203637630.1096668194140.1732443032760.0532399260401-0.121126123026-0.04196129233190.214245906555-0.0245833365186-0.06884164277050.2166777849010.01442108299540.26422799438615.908730489745.816906734272.8133289114
81.32278281362-0.0657897281079-0.5687943463643.48892832946-0.737385166621.650651723-0.229720842348-0.2029448446670.335369340571-0.5542246190830.262425057526-0.53077253905-0.110765442945-0.0698747570854-0.01573750935580.2186174308740.017621578006-0.02099256800040.1640973667050.02170698155560.28947829275813.60684748034.8889997617281.0182859902
96.361066248230.220628868989-0.1816144249840.0518365635357-0.5164188269756.050519217570.1799574703740.524977021034-1.40453925153-0.335880901787-0.0516938087681-0.05078556489031.97303821125-0.373683951080.1580126822930.5842217928090.0208734972314-0.1100730659240.3915321617820.2191538213830.58496072093910.5378491203-25.803702373989.2501843388
101.59106562068-0.8703625702060.5885108244173.03757197229-0.5159703110751.57718523116-0.0693234047747-0.1817396848230.1050375455720.2237631202820.0554234559236-0.275656622186-0.284190651747-0.05344487026160.04463875883740.161183319026-0.00975520151845-0.01740793923590.1780117984910.05853719865680.21433369006711.4027344522-4.656275405883.9920476539
112.241220327941.906882362460.6797147561063.058248307630.06698643319640.6885357727640.127472885516-0.1416283682740.3215591304480.654003565046-0.07720644156570.530012503254-0.178175393659-0.0226714754833-0.02556307786190.1939736657420.03981008373760.103342542220.191520895870.03783465118120.223266074526-0.574428294274-5.4879129243785.0886444837
123.51821287127-1.26743764169-2.350531565878.640393618321.09240583331.73746517960.1408864356430.325905973044-0.374510952555-0.5786771153160.08135764768580.9336664135271.068558296970.0236188798731-0.1450989764360.4719233960210.0244482425368-0.09142136703620.300598293443-0.06486174208440.216917338210.551886833863-31.438255720181.0865144187
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 651 through 677 )AA651 - 6771 - 27
22chain 'A' and (resid 678 through 712 )AA678 - 71228 - 62
33chain 'A' and (resid 713 through 722 )AA713 - 72263 - 72
44chain 'A' and (resid 723 through 742 )AA723 - 74273 - 92
55chain 'A' and (resid 743 through 763 )AA743 - 76393 - 113
66chain 'B' and (resid 652 through 677 )BB652 - 6771 - 26
77chain 'B' and (resid 678 through 696 )BB678 - 69627 - 45
88chain 'B' and (resid 697 through 712 )BB697 - 71246 - 61
99chain 'B' and (resid 713 through 722 )BB713 - 72262 - 71
1010chain 'B' and (resid 723 through 742 )BB723 - 74272 - 91
1111chain 'B' and (resid 743 through 752 )BB743 - 75292 - 101
1212chain 'B' and (resid 753 through 772 )BB753 - 772102 - 121

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