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- PDB-8ckm: Semaphorin-5A TSR 3-4 domains -

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Basic information

Entry
Database: PDB / ID: 8ckm
TitleSemaphorin-5A TSR 3-4 domains
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
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.72 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
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


Theoretical massNumber of molelcules
Total (without water)28,1092
Polymers28,1092
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, S-SAD was used for phasing an isomorphous crystal structure providing experimental evidence of sulfur atoms in Cys and Met residues
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4460 Å2
ΔGint-36 kcal/mol
Surface area13060 Å2
Unit cell
Length a, b, c (Å)104.110, 27.650, 92.240
Angle α, β, γ (deg.)90.000, 99.100, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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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 / Plasmid: pHL-sec / Cell line (production host): HEK293T / Production host: Homo sapiens (human) / References: UniProt: Q13591

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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: 2.33 Å3/Da / Density % sol: 47.3 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: 38 % PEG 200, 0.1 M sodium citrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9999 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 12, 2021
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9999 Å / Relative weight: 1
ReflectionResolution: 2.72→51.41 Å / Num. obs: 7316 / % possible obs: 99.8 % / Redundancy: 6.1 % / Biso Wilson estimate: 73.79 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.114 / Rpim(I) all: 0.073 / Rrim(I) all: 0.136 / Net I/σ(I): 7.1
Reflection shellResolution: 2.72→2.77 Å / Rmerge(I) obs: 5.129 / Mean I/σ(I) obs: 0.3 / Num. unique obs: 382 / CC1/2: 0.467 / Rpim(I) all: 3.725 / Rrim(I) all: 6.373

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Processing

Software
NameVersionClassification
autoPROC1.0.5data processing
PHENIX1.19rc5_4047refinement
Coot0.9.6model building
XDS20200417data reduction
Aimless0.7.4data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.72→51.4 Å / SU ML: 0.514 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 46.7273
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.3311 334 4.64 %
Rwork0.2878 6858 -
obs0.29 7192 98.1 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 146.2 Å2
Refinement stepCycle: LAST / Resolution: 2.72→51.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1571 0 0 0 1571
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00251615
X-RAY DIFFRACTIONf_angle_d0.5062203
X-RAY DIFFRACTIONf_chiral_restr0.0361227
X-RAY DIFFRACTIONf_plane_restr0.004290
X-RAY DIFFRACTIONf_dihedral_angle_d10.9383573
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.72-3.430.44911570.43243329X-RAY DIFFRACTION96.43
3.43-51.40.30951770.26093529X-RAY DIFFRACTION99.73
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)
12.170233344961.681573416640.5778661731691.401052185610.5757924890481.35268220083-1.787596350981.007406276350.672664311955-1.439920363164.581015746393.33271304912-3.13121625229-0.0242804537818-1.179793994662.104114592890.5615712972710.3783569246962.56448282411-0.4600447554031.5846845901514.615-23.61551.257
25.00089605728-0.4732424633430.61660924564.29990156294.665632702638.54167181968-0.644935971905-1.30192043601-0.0575648798594-0.3182024250391.15852584970.1404561147710.8811299459330.12763154484-1.182739313051.766746889940.450613699454-0.1427729607441.864010803390.01410457469751.101623365769.36-20.95157.408
36.057738459090.5069605687620.3928946343993.715487389874.149825189354.603060573770.023960437953-0.1856668662990.775388011467-0.06603697081-1.042832954530.231221610911-0.218056769628-0.7627581434610.6665995201390.7788285201550.06512177388110.05855197024211.167018142320.125981736851.263805745612.46110.75993.998
49.14966770846-2.95791598439-0.9444447621193.789208650034.466913808176.6292651368-2.33151462681.22968342119-0.251514254568-0.5949954942172.106603111452.49053135419-1.29554741934.780081933550.5686035303310.8283356097350.002382036299340.05308593805921.740286866630.4709175022351.336198336393.596-0.78285.68
56.38882101835-1.47755015374-0.1206871659324.239489133597.173604159753.921505755990.3158638860032.437659371620.5141125573790.268934034715-0.7256597748750.3230389755260.267723288816-2.06509747847-0.4271628934960.9321051082890.2571226459260.0889519549010.9264635034210.2574367707080.91372200174-5.1846.07884.223
61.918351201840.4817682850750.5038225997613.233934704030.5005672193046.43620230918-0.537099928266-0.829922937122-0.82077029121.30241333549-1.564539069333.409182691291.22535743411-1.286268105812.69110865032.019231097550.0436104618770.3314966097451.20232976973-0.1245110418331.49943085026-5.622-33.67954.011
70.466229231103-2.13833266350.192434691740.4706034989820.563024861142-0.3016760418680.4800944423660.197278729368-0.362325942859-0.2816239422160.190151293063-1.171849788741.052300497741.15491000147-0.08453226392012.173221227830.3829867373070.05756250920531.33054136776-0.02400288737271.16566814771-2.089-25.23458.319
88.04264794624-1.29544013959-0.8751069867676.195471622-0.248210404365.5386607164-0.271650433298-0.1573347794031.949284344910.457524620574-0.2990843029520.154338786923-0.1726336943330.844389056302-0.2234217811730.680464444398-0.02568491085740.106255997240.950393406090.193272969791.65649123994-9.1578.01193.985
92.66577561915-0.485597618830.6404938691926.068927470214.051877354498.844284227890.04260753028230.5734065704530.457296573452-0.0101895841289-0.1905781914630.146352877010.796634327790.1612688220650.3542735385260.8984810193670.09385799814460.22045304381.456307835550.3525199448240.987562051675-1.042-0.1586.124
100.5907867104280.8251910553171.809778465693.5841278717-1.226817461741.91542734505-0.941704911749-1.420060574733.464147139042.14513514469-3.306267383432.6355335634-5.775239125670.633161120982-0.384519145362.18360160923-0.324685503753-0.5080923294131.35004512356-0.5356431937543.425403020315.45523.202104.492
114.45100557161-1.86196423447-4.33860713353.164430428910.4757528132224.82262937462-0.253326372114-0.818006279842-0.593879857578-1.381992972391.05770213728-1.212606720610.5509113618961.17930826614-0.2156369431821.038390969610.0730447065443-0.03701509337041.60650972272-0.0583798162681.186344383689.87836.878100.765
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 656:663 )A656 - 663
2X-RAY DIFFRACTION2( CHAIN A AND RESID 664:702 )A664 - 702
3X-RAY DIFFRACTION3( CHAIN A AND RESID 703:729 )A703 - 729
4X-RAY DIFFRACTION4( CHAIN A AND RESID 730:736 )A730 - 736
5X-RAY DIFFRACTION5( CHAIN A AND RESID 737:755 )A737 - 755
6X-RAY DIFFRACTION6( CHAIN B AND RESID 655:663 )B655 - 663
7X-RAY DIFFRACTION7( CHAIN B AND RESID 664:702 )B664 - 702
8X-RAY DIFFRACTION8( CHAIN B AND RESID 703:728 )B703 - 728
9X-RAY DIFFRACTION9( CHAIN B AND RESID 729:752 )B729 - 752
10X-RAY DIFFRACTION10( CHAIN B AND RESID 753:764 )B753 - 764
11X-RAY DIFFRACTION11( CHAIN B AND RESID 765:772 )B765 - 772

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