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- PDB-8rmj: Drosophila Semaphorin 2b in complex with glycosaminoglycan mimic SOS -

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Basic information

Entry
Database: PDB / ID: 8rmj
TitleDrosophila Semaphorin 2b in complex with glycosaminoglycan mimic SOS
ComponentsFI18622p1
KeywordsSIGNALING PROTEIN / semaphorin / glycosaminoglycan / axon guidance / bridge model
Function / homology
Function and homology information


synaptic target attraction / olfactory bulb axon guidance / dendrite guidance / semaphorin receptor binding / dendrite self-avoidance / regulation of cell-matrix adhesion / chemorepellent activity / negative chemotaxis / semaphorin-plexin signaling pathway / axon guidance ...synaptic target attraction / olfactory bulb axon guidance / dendrite guidance / semaphorin receptor binding / dendrite self-avoidance / regulation of cell-matrix adhesion / chemorepellent activity / negative chemotaxis / semaphorin-plexin signaling pathway / axon guidance / positive regulation of cell migration / plasma membrane
Similarity search - Function
Semaphorin / Sema domain / semaphorin domain / Sema domain / Sema domain superfamily / Sema domain profile. / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
sucrose octasulfate / FI18622p1
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.79 Å
AuthorsNourisanami, F. / Sobol, M. / Rozbesky, D.
Funding support Czech Republic, 1items
OrganizationGrant numberCountry
Czech Science Foundation21-27204M Czech Republic
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2024
Title: Molecular mechanisms of proteoglycan-mediated semaphorin signaling in axon guidance.
Authors: Nourisanami, F. / Sobol, M. / Li, Z. / Horvath, M. / Kowalska, K. / Kumar, A. / Vlasak, J. / Koupilova, N. / Luginbuhl, D.J. / Luo, L. / Rozbesky, D.
History
DepositionJan 8, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 31, 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: FI18622p1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,51710
Polymers74,9211
Non-polymers6,5979
Water00
1
A: FI18622p1
hetero molecules

A: FI18622p1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)163,03520
Polymers149,8412
Non-polymers13,19418
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_544x,x-y-1,-z-1/61
Buried area18280 Å2
ΔGint138 kcal/mol
Surface area57700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)181.489, 181.489, 168.379
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522
Space group name HallP652(x,y,z+1/12)

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Components

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Protein , 1 types, 1 molecules A

#1: Protein FI18622p1 / Semaphorin 2b / isoform A / isoform C


Mass: 74920.625 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly)
Gene: Sema2b, CG30322, CG33960-RA, CG4383, Dmel\CG33960, Sema-2b, sema-2b, sema2b, SemaIIB, CG33960, Dmel_CG33960
Plasmid: pHR-CMV-TetO2-IRES-EmGFP / Cell line (production host): HEK293S / Production host: Homo sapiens (human) / References: UniProt: A1ZAF5

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Sugars , 6 types, 9 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.: 1 / Source method: obtained synthetically
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam 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
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE
#3: Polysaccharide alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-[alpha-D- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1235.105 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3[DManpa1-6]DManpa1-6[DManpa1-3]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,7,6/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3-3-3/a4-b1_b4-c1_c3-d1_c6-e1_e3-f1_e6-g1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#4: Polysaccharide alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]alpha-D- ...alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1559.386 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-2DManpa1-6[DManpa1-3]DManpa1-6[DManpa1-2DManpa1-3]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,9,8/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3-3-3-3-3/a4-b1_b4-c1_c3-d1_c6-f1_d2-e1_f3-g1_f6-h1_h2-i1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{[(2+1)][a-D-Manp]{}}[(6+1)][a-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{[(2+1)][a-D-Manp]{}}}}}}LINUCSPDB-CARE
#5: Polysaccharide alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...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: 748.682 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-6DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3/a4-b1_b4-c1_c6-d1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(6+1)][a-D-Manp]{}}}}LINUCSPDB-CARE
#6: Polysaccharide 1,3,4,6-tetra-O-sulfo-beta-D-fructofuranose-(2-1)-2,3,4,6-tetra-O-sulfonato-alpha-D-glucopyranose


Type: oligosaccharide, Oligosaccharide / Class: Substrate analog / Mass: 982.803 Da / Num. of mol.: 2
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
#7: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 3 / Source method: obtained synthetically / 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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Details

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: 5.35 Å3/Da / Density % sol: 77.03 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: 0.1 M MES pH 6.0, 5% PEG 6000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Aug 3, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.79→157.17 Å / Num. obs: 23325 / % possible obs: 96.4 % / Redundancy: 19.6 % / Biso Wilson estimate: 94.58 Å2 / CC1/2: 1 / Rrim(I) all: 0.086 / Net I/σ(I): 21.6
Reflection shellResolution: 2.79→2.82 Å / Redundancy: 16.1 % / Num. unique obs: 1961 / CC1/2: 0.4 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.19_4092refinement
PHENIX1.19_4092refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.79→45.67 Å / SU ML: 0.3974 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 39.9641
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2738 1193 5.12 %
Rwork0.2463 22111 -
obs0.2478 23304 56.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 91.36 Å2
Refinement stepCycle: LAST / Resolution: 2.79→45.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4935 0 418 0 5353
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00275475
X-RAY DIFFRACTIONf_angle_d0.54597448
X-RAY DIFFRACTIONf_chiral_restr0.0446878
X-RAY DIFFRACTIONf_plane_restr0.0036901
X-RAY DIFFRACTIONf_dihedral_angle_d10.66552126
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.79-2.90.6358210.3995462X-RAY DIFFRACTION10.82
2.9-3.040.3933630.3631132X-RAY DIFFRACTION26.75
3.04-3.20.2947780.33021572X-RAY DIFFRACTION36.69
3.2-3.40.3804910.33351943X-RAY DIFFRACTION45.17
3.4-3.660.30851350.27992272X-RAY DIFFRACTION53.16
3.66-4.030.2931390.25672713X-RAY DIFFRACTION62.87
4.03-4.610.2461890.22943352X-RAY DIFFRACTION77.48
4.61-5.80.26192170.22634071X-RAY DIFFRACTION92.47
5.8-45.670.26952600.24244594X-RAY DIFFRACTION99.73

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