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- PDB-8ckl: Semaphorin-5A TSR 3-4 domains in complex with sucrose octasulfate... -

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Basic information

Entry
Database: PDB / ID: 8ckl
TitleSemaphorin-5A TSR 3-4 domains in complex with sucrose octasulfate (SOS)
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
sucrose octasulfate / alpha-D-mannopyranose / Semaphorin-5A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.56 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 sucrose octasulfate (SOS)
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)29,8137
Polymers28,1092
Non-polymers1,7035
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, S-SAD was used for phasing of an isomorphous structure - the molecular replacement template, providing experimental evidence for the position of sulfur atoms within Cys and Met residues.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5910 Å2
ΔGint-30 kcal/mol
Surface area13050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.106, 30.770, 84.172
Angle α, β, γ (deg.)90.000, 99.970, 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
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and ((resid 654 and (name N or name...
d_2ens_1(chain "B" and (resid 654 through 675 or (resid 676...

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1METCYSA1 - 95
d_21ens_1METCYSB1 - 95

NCS oper: (Code: givenMatrix: (-0.966373104628, -0.205420685331, -0.15467826185), (-0.165334894852, 0.0356607335705, 0.985592555078), (-0.196945157836, 0.978023851508, -0.0684247812234)Vector: 19. ...NCS oper: (Code: given
Matrix: (-0.966373104628, -0.205420685331, -0.15467826185), (-0.165334894852, 0.0356607335705, 0.985592555078), (-0.196945157836, 0.978023851508, -0.0684247812234)
Vector: 19.388412939, -26.3025178258, 30.7603935732)

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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
#2: Polysaccharide 2,3,4,6-tetra-O-sulfonato-alpha-D-glucopyranose-(1-2)-1,3,4,6-tetra-O-sulfo-beta-D-fructofuranose


Type: oligosaccharide, Oligosaccharide / Class: Substrate analog / Mass: 982.803 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide with reducing-end-to-reducing-end glycosidic bond
References: sucrose octasulfate
DescriptorTypeProgram
WURCS=2.0/2,2,1/[ha122h-2b_2-5_1*OSO/3=O/3=O_3*OSO/3=O/3=O_4*OSO/3=O/3=O_6*OSO/3=O/3=O][a2122h-1a_1-5_2*OSO/3=O/3=O_3*OSO/3=O/3=O_4*OSO/3=O/3=O_6*OSO/3=O/3=O]/1-2/a2-b1WURCSPDB2Glycan 1.1.0
[][b-D-Fruf1SO33SO34SO36SO3]{[(2+1)][a-D-Glcp2SO33SO34SO36SO3]{}}LINUCSPDB-CARE
#3: 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
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: 2.41 Å3/Da / Density % sol: 48.9 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5 / Details: 8 % PEG 8000, 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: I03 / Wavelength: 0.97625 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 7, 2020
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 2.56→82.9 Å / Num. obs: 5008 / % possible obs: 55.9 % / Redundancy: 6.6 % / Biso Wilson estimate: 73.54 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.143 / Rpim(I) all: 0.061 / Rrim(I) all: 0.156 / Net I/σ(I): 8.2
Reflection shellResolution: 2.561→2.841 Å / Redundancy: 6.6 % / Rmerge(I) obs: 2.67 / Mean I/σ(I) obs: 0.8 / Num. unique obs: 250 / CC1/2: 0.098 / Rpim(I) all: 1.091 / Rrim(I) all: 2.889 / % possible all: 10.7

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
autoPROC1.0.5data processing
PHASERphasing
Coot0.9.6model building
XDSBUILT 20200417data reduction
Aimless0.7.4data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.56→82.9 Å / SU ML: 0.4093 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 33.0547
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.285 239 4.78 %
Rwork0.2554 4757 -
obs0.2566 4996 55.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 82.26 Å2
Refinement stepCycle: LAST / Resolution: 2.56→82.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1515 0 99 0 1614
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00181659
X-RAY DIFFRACTIONf_angle_d0.56152276
X-RAY DIFFRACTIONf_chiral_restr0.0387243
X-RAY DIFFRACTIONf_plane_restr0.0047276
X-RAY DIFFRACTIONf_dihedral_angle_d11.3601595
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 2.02253170192 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.56-3.230.4658580.36581066X-RAY DIFFRACTION25.52
3.23-82.90.26631810.24643691X-RAY DIFFRACTION85.06
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)
11.719245669941.473052993552.055233310232.833523715611.839190440182.945323017680.1382743252010.390479039256-0.293424696103-0.6127199547950.850817471483-0.8568305546880.1170763079050.321191987897-0.4360469883091.825820981440.009338675960260.08539437419390.44792438039-0.1029148989140.72596027250617.2682087471-18.01416519235.6666472594
22.21320650762-0.4039882890450.07519578781491.84116584775-0.3999721535182.555398853690.0520329750878-0.04861741983130.191737349373-0.3485126130530.2417666870480.5559965387020.119095407738-0.4635675247091.26601769977-0.0728713055955-0.02289640697910.1126343215330.324781384550.1352357232790.5315159482477.8736941139113.271978937339.0085533747
30.9799614839420.540157538322-0.2846752168970.9731998537350.7437469322161.29264068898-0.3163578646790.185952589907-0.417806253097-0.5715602452380.1178447708950.02275857479421.138849217210.0380395670593-1.03941657621.413747010940.081558896538-0.1230805368990.141104356629-0.03057608848360.202407917582.88797220546-21.660640139912.1327869904
42.417369370861.07077683525-1.905181899567.01918507715-1.096919200041.513914101180.2962526427990.145637617249-0.928324392009-1.91327994948-0.1125718874120.2261802589840.6201920470510.1897168970120.2520390810151.99839709590.2791824682680.07979638709760.5692150709540.2782616581370.9993643303538.22987257275-34.01123335584.67639196455
54.89354835861-0.693858371385-0.4579228533734.95321295272-1.267357697890.495112314565-0.6838624622370.207023339119-1.05859569228-1.44014380787-0.03819429885140.1306424063930.335585840222-0.05587025872030.5548194002371.92334844781-0.161080604603-0.3715618065670.4807335383870.121562259581.089904311014.77734998988-17.78114075099.87989246279
61.85054579377-1.27148524277-1.456074351274.37180465007-0.9928101439822.26989704194-0.02591106451630.293307453429-0.093594547116-0.846503144742-0.3495251660130.1746722864330.61392711395-0.44102785975-0.1008861307790.0007863802664110.076294245431-0.01105313953380.5238077836430.1154562714320.5360804853480.4789072579054.4573679872231.4319241723
74.75309776715-3.10931219047-2.408122924653.81166041774-1.252353493925.736762186920.0213876996729-0.1753344421061.172876251210.4662093027160.8919353960130.301640708997-0.3950610198640.1724379857050.09941376904990.1882139062320.0701072745130.03725973372660.5065785705370.1726685044440.78916802684-3.3324704305622.180739594349.5217633871
80.4730800473441.100456424171.486544694824.32184148812.047430647545.76375393343-0.1282524173890.19328241339-1.17668328923-0.1578095513640.177310369591-0.01014383227761.45574113776-0.02722619259470.03088409651750.399822265951-0.01959496898610.07422424545180.279106032007-0.03323089144680.7720658213753.523554475414.1256378849432.4803268055
93.60475243451.712178055843.122538687762.570672077940.674192246453.085141054390.180975614545-0.0650865233004-0.5427865024160.1084882108330.1512145526850.1591193891570.299745078942-0.3368260293990.4246983945210.0904619354133-0.0633990143880.02428301535440.511727192958-0.1399342868690.32203157772811.050792154911.336557071644.4747060422
101.53707634179-0.330272601917-0.059609015920.163652149164-0.2215491964150.8948258357310.3001313830010.1882297237690.0382859571483-0.06963788909730.041236671329-0.0282232313347-0.027786131290.1245657814841.102250919930.135081469590.1342562235450.0425597487850.600244658772-0.1853547014980.62261954835317.085788888245.201362484951.6573449824
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 654 through 696 )AA654 - 6961 - 43
22chain 'A' and (resid 697 through 756 )AA697 - 75644 - 96
33chain 'B' and (resid 654 through 677 )BB654 - 6771 - 24
44chain 'B' and (resid 678 through 690 )BB678 - 69025 - 37
55chain 'B' and (resid 691 through 696 )BB691 - 69638 - 43
66chain 'B' and (resid 697 through 712 )BB697 - 71244 - 59
77chain 'B' and (resid 713 through 729 )BB713 - 72960 - 69
88chain 'B' and (resid 730 through 742 )BB730 - 74270 - 82
99chain 'B' and (resid 743 through 752 )BB743 - 75283 - 92
1010chain 'B' and (resid 753 through 773 )BB753 - 77393 - 101

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