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- PDB-8ckg: Semaphorin-5A TSR 3-4 domains in complex with sulfate -

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Basic information

Entry
Database: PDB / ID: 8ckg
TitleSemaphorin-5A TSR 3-4 domains in complex with sulfate
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 / Semaphorin-5A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.714 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 sulfate
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)29,0228
Polymers28,1092
Non-polymers9136
Water1,78399
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, S-SAD was used for phasing, providing experimental evidence for the position of sulfur atoms within Cys and Met residues, and the location of the intermolecular disulfides.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6070 Å2
ΔGint-63 kcal/mol
Surface area13540 Å2
Unit cell
Length a, b, c (Å)105.081, 29.286, 90.429
Angle α, β, γ (deg.)90.00, 100.46, 90.00
Int Tables number5
Space group name H-MC121
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
Components on special symmetry positions
IDModelComponents
11A-942-

HOH

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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
Source: (gene. exp.) Homo sapiens (human) / Gene: SEMA5A, SEMAF / Cell line (production host): HEK293T / Production host: Homo sapiens (human) / References: UniProt: Q13591
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#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
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 99 / 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: 2

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Sample preparation

Crystal
IDDensity Matthews (Å3/Da)Density % sol (%)
12.4349.5
22.4349.5
Crystal grow
Temperature (K)Crystal-IDMethodpHDetails
2931vapor diffusion, sitting drop8.530% PEG 4000, 0.2 M lithium sulfate, 0.1 M Tris
2932vapor diffusion, sitting drop8.530% PEG 4000, 0.2 M lithium sulfate, 0.1 M Tris

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Data collection

Diffraction
IDMean temperature (K)Crystal-IDSerial crystal experiment
11001N
2502N
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONDiamond I2410.9686
SYNCHROTRONDiamond I2322.7552
Detector
TypeIDDetectorDate
DECTRIS PILATUS3 6M1PIXELJan 26, 2020
DECTRIS PILATUS 12M2PIXELMar 2, 2020
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1MSINGLE WAVELENGTHMx-ray1
2MSINGLE WAVELENGTHMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
10.96861
22.75521
Reflection

Entry-ID: 8CKG

Resolution (Å)Num. obs% possible obs (%)Redundancy (%)Biso Wilson estimate (Å2)CC1/2Rmerge(I) obsRpim(I) allDiffraction-IDNet I/σ(I)Rrim(I) all
1.714-88.9252098570.76.229.30.9950.0960.04119.3
2.3-88.71056885.621.456.160.9990.1140.024217.20.117
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allDiffraction-ID% possible allRrim(I) all
1.714-1.8553.71.2110500.3380.7116.9
2.3-2.3819.93.6730.88540.5610.807271.83.769

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Processing

Software
NameVersionClassification
autoPROC1.0.5data processing
CRANK2phasing
PHENIX1.20.1_4487refinement
Coot0.9.6model building
XDS20200417data reduction
Aimless0.7.4data scaling
RefinementMethod to determine structure: SAD / Resolution: 1.714→51.67 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 30.16 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2312 1000 4.77 %
Rwork0.206 --
obs0.2072 20984 70.62 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.714→51.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1645 0 54 99 1798
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071741
X-RAY DIFFRACTIONf_angle_d0.8722365
X-RAY DIFFRACTIONf_dihedral_angle_d12.701646
X-RAY DIFFRACTIONf_chiral_restr0.05247
X-RAY DIFFRACTIONf_plane_restr0.006301
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.714-1.80.377290.3149375X-RAY DIFFRACTION9
1.8-1.910.2671930.28531422X-RAY DIFFRACTION40
1.92-2.070.27811210.23512560X-RAY DIFFRACTION64
2.07-2.270.2421630.22293397X-RAY DIFFRACTION84
2.27-2.60.26741960.23453980X-RAY DIFFRACTION99
2.6-3.280.292140.2184056X-RAY DIFFRACTION100
3.28-51.670.18612040.18354187X-RAY DIFFRACTION100
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)
11.27230.16460.05561.14181.83344.42040.25310.7113-0.1639-1.3790.1066-0.12880.32450.27860.37091.64470.3392-0.11220.6444-0.07250.14829.7229-23.557451.1902
21.9536-3.4212-2.24949.52584.88634.96120.0247-0.13250.26090.12550.268-0.48060.4580.3911-0.23890.20860.053-0.01520.2613-0.01170.26657.6787-6.775.741
33.46833.4025.42865.6634.91049.50110.0068-0.3870.47460.2267-0.20050.3806-0.1475-0.40490.01250.1601-0.01170.02220.2019-0.03670.3305-0.535614.643894.7009
45.1628-2.2773-3.79545.64743.19464.20890.18530.17660.2373-0.07730.0432-0.02690.33110.1357-0.00070.1650.0594-0.03430.24120.01350.24932.5329-0.651278.2639
53.7188-2.735-2.48094.07920.88432.19010.1438-0.49620.42850.10980.1438-0.0158-0.21080.3994-0.35780.0873-0.0136-0.03530.28190.00580.262-12.046510.11488.4611
60.2283-0.76340.03324.01361.61611.24080.40010.3594-0.1844-1.3615-0.55750.6760.623-0.29510.12311.00460.0795-0.17640.5903-0.04970.4165-3.9391-23.407460.9539
73.631-2.1938-2.28485.97214.67946.66120.2182-0.03780.2766-0.0687-0.05850.0176-0.0056-0.2347-0.20680.0995-0.0431-0.03340.2370.03610.3063-8.79255.133187.1861
80.58891.56950.61043.751.44440.44820.0619-0.01420.08320.1103-0.0620.11630.07030.0575-0.03390.235-0.01550.00970.2526-0.02590.26254.182520.421896.738
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 654 through 696 )
2X-RAY DIFFRACTION2chain 'A' and (resid 697 through 707 )
3X-RAY DIFFRACTION3chain 'A' and (resid 708 through 729 )
4X-RAY DIFFRACTION4chain 'A' and (resid 730 through 742 )
5X-RAY DIFFRACTION5chain 'A' and (resid 743 through 763 )
6X-RAY DIFFRACTION6chain 'B' and (resid 654 through 712 )
7X-RAY DIFFRACTION7chain 'B' and (resid 713 through 742 )
8X-RAY DIFFRACTION8chain 'B' and (resid 743 through 772 )

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