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- PDB-6qp7: Drosophila Semaphorin 2a -

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Basic information

Entry
Database: PDB / ID: 6qp7
TitleDrosophila Semaphorin 2a
ComponentsSemaphorin-2A
KeywordsSIGNALING PROTEIN / axon guidance cue / developmental protein / cell signalling / semaphorin / signalling protein
Function / homology
Function and homology information


flight behavior / olfactory bulb axon guidance / Other semaphorin interactions / dendrite guidance / synaptic target inhibition / Sema4D induced cell migration and growth-cone collapse / semaphorin receptor binding / visual behavior / sensory neuron axon guidance / negative regulation of axon extension involved in axon guidance ...flight behavior / olfactory bulb axon guidance / Other semaphorin interactions / dendrite guidance / synaptic target inhibition / Sema4D induced cell migration and growth-cone collapse / semaphorin receptor binding / visual behavior / sensory neuron axon guidance / negative regulation of axon extension involved in axon guidance / drinking behavior / chemorepellent activity / negative chemotaxis / adult behavior / semaphorin-plexin signaling pathway / endomembrane system / axon guidance / positive regulation of cell migration / extracellular space / extracellular region / cytosol
Similarity search - Function
Semaphorin / Sema domain / semaphorin domain / Sema domain / Sema domain superfamily / Sema domain profile. / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain ...Semaphorin / Sema domain / semaphorin domain / Sema domain / Sema domain superfamily / Sema domain profile. / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.96 Å
AuthorsRobinson, R.A. / Rozbesky, D. / Harlos, K. / Siebold, C. / Jones, E.Y.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Cancer Research UKC375/A17721 United Kingdom
Medical Research Council (United Kingdom)MR/M000141/1 United Kingdom
CitationJournal: Nat Commun / Year: 2019
Title: Diversity of oligomerization in Drosophila semaphorins suggests a mechanism of functional fine-tuning.
Authors: Rozbesky, D. / Robinson, R.A. / Jain, V. / Renner, M. / Malinauskas, T. / Harlos, K. / Siebold, C. / Jones, E.Y.
History
DepositionFeb 13, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 21, 2019Provider: repository / Type: Initial release
Revision 1.1Aug 28, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_validate_close_contact / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _atom_site_anisotrop.id / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Jan 24, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Semaphorin-2A
B: Semaphorin-2A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)159,49935
Polymers150,7362
Non-polymers8,76433
Water14,286793
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: assay for oligomerization, analytical ultracentrifugation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18610 Å2
ΔGint147 kcal/mol
Surface area53290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.804, 109.977, 134.793
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Semaphorin-2A / Semaphorin-II / Sema II


Mass: 75367.805 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: Sema2a, Sema-2a, CG4700 / Cell line (production host): HEK293S-GnTI- / Production host: Homo sapiens (human) / References: UniProt: Q24323

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Sugars , 6 types, 11 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.: 4
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam 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
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#3: Polysaccharide alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D- ...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: 1072.964 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-6DManpa1-6[DManpa1-3]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,6,5/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3-3/a4-b1_b4-c1_c3-d1_c6-e1_e6-f1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+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-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1397.245 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-2DManpa1-6[DManpa1-3]DManpa1-6[DManpa1-3]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,8,7/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3-3-3-3/a4-b1_b4-c1_c3-d1_c6-e1_e3-f1_e6-g1_g2-h1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-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]{[(2+1)][a-D-Manp]{}}}}}}}LINUCSPDB-CARE
#5: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}}LINUCSPDB-CARE
#6: 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-Glycam 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
[]{[(4+1)][b-D-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
#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 / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
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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Non-polymers , 3 types, 815 molecules

#8: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: C2H6O2
#9: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#10: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 793 / Source method: isolated from a natural source / Formula: H2O

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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: 54.51 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 0.1 M Bis-Tris (pH 6.5) and 20% (w/v) PEG 5000 MME

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.9785 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 15, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 1.96→57.464 Å / Num. obs: 110704 / % possible obs: 99.6 % / Redundancy: 14.8 % / CC1/2: 0.998 / Rmerge(I) obs: 0.175 / Net I/σ(I): 11.51
Reflection shellResolution: 1.96→1.9823 Å

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Processing

Software
NameVersionClassification
PHENIX(dev_3386: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1OLZ

1olz


Resolution: 1.96→57.464 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 24.07
RfactorNum. reflection% reflection
Rfree0.2178 5611 5.07 %
Rwork0.1829 --
obs0.1847 110627 99.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.96→57.464 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10004 0 576 793 11373
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00310789
X-RAY DIFFRACTIONf_angle_d0.61314587
X-RAY DIFFRACTIONf_dihedral_angle_d12.5156508
X-RAY DIFFRACTIONf_chiral_restr0.0461673
X-RAY DIFFRACTIONf_plane_restr0.0031828
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.96-1.98230.37911730.34733383X-RAY DIFFRACTION97
1.9823-2.00560.34061840.30253423X-RAY DIFFRACTION99
2.0056-2.03010.34272040.30313431X-RAY DIFFRACTION100
2.0301-2.05580.30131840.27183425X-RAY DIFFRACTION99
2.0558-2.08280.28142170.25663427X-RAY DIFFRACTION99
2.0828-2.11130.28982120.24063451X-RAY DIFFRACTION100
2.1113-2.14150.28541690.23753459X-RAY DIFFRACTION100
2.1415-2.17350.28551840.22883520X-RAY DIFFRACTION99
2.1735-2.20740.2411850.22133457X-RAY DIFFRACTION99
2.2074-2.24360.28421680.2163461X-RAY DIFFRACTION100
2.2436-2.28230.24732000.21983465X-RAY DIFFRACTION100
2.2823-2.32380.27371830.20653494X-RAY DIFFRACTION100
2.3238-2.36850.24291950.21133463X-RAY DIFFRACTION100
2.3685-2.41690.27991970.2113464X-RAY DIFFRACTION100
2.4169-2.46940.25791830.19963508X-RAY DIFFRACTION100
2.4694-2.52690.2541930.20583470X-RAY DIFFRACTION100
2.5269-2.59010.22031740.1953486X-RAY DIFFRACTION100
2.5901-2.66010.23381690.18863532X-RAY DIFFRACTION100
2.6601-2.73840.24121730.1863517X-RAY DIFFRACTION100
2.7384-2.82670.2171750.18413498X-RAY DIFFRACTION100
2.8267-2.92780.20181970.18293500X-RAY DIFFRACTION100
2.9278-3.0450.22821930.18063514X-RAY DIFFRACTION100
3.045-3.18360.21981810.17663522X-RAY DIFFRACTION100
3.1836-3.35140.18641990.16593545X-RAY DIFFRACTION100
3.3514-3.56130.20571690.15863553X-RAY DIFFRACTION100
3.5613-3.83630.19931760.15463541X-RAY DIFFRACTION100
3.8363-4.22220.17212030.14553563X-RAY DIFFRACTION100
4.2222-4.83290.1411770.13443589X-RAY DIFFRACTION100
4.8329-6.08790.18632010.16083613X-RAY DIFFRACTION100
6.0879-57.48910.21481930.18773742X-RAY DIFFRACTION99
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)
19.0994-0.6829-4.17070.42530.80492.5651-1.15160.8917-0.3347-0.61060.55440.12320.5111-0.50690.58871.2105-0.1777-0.07670.94030.11930.8551-0.7296-9.8452-31.5253
20.940.0495-0.10660.65140.12821.0825-0.0103-0.0601-0.09510.00570.03390.01670.0026-0.0633-0.01940.15430.0135-0.00940.1690.03650.1939-16.3418-24.54360.352
36.29352.4989-0.94668.53111.03468.1938-0.260.58630.0721-0.32730.21280.08670.07080.07680.06540.15540.0020.00010.24250.05780.230310.6935-17.2874-23.3056
43.1192-0.7651-0.16016.3353-3.46816.36080.19160.02310.39590.0855-0.0657-0.1051-0.35570.0735-0.16830.38490.0177-0.00190.20870.04770.361110.50653.9147-32.528
53.57134.70363.79996.23445.03134.05680.6377-0.97380.1820.7982-0.3476-0.51170.26530.15-0.28750.7678-0.04730.06520.9284-0.00560.53951.023525.2939-21.1239
60.91990.3191-0.24231.07290.07382.59720.0394-0.08210.1219-0.08080.0204-0.0504-0.5120.3119-0.02830.2722-0.06970.04310.2449-0.03820.2264-6.328324.203815.0988
73.7051.81721.11327.29340.23196.6735-0.16090.3240.2391-0.03420.1968-0.0174-1.0368-0.269-0.06870.44830.05950.05880.30510.03290.254-13.333231.3922-19.8491
83.5095-0.84930.17386.99941.26394.7730.06970.6221-0.4767-0.2971-0.09470.3010.3113-0.11780.04220.3106-0.03680.04960.4462-0.05910.3324-9.725113.7821-35.2614
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A and (resseq 31:41)
2X-RAY DIFFRACTION2chain A and (resseq 58:524 or resseq 1000:1001 or resseq 2000 or resseq 3000:3008 or resseq 4000:4008)
3X-RAY DIFFRACTION3chain A and (resseq 525:570 or resseq 5000)
4X-RAY DIFFRACTION4chain A and (resseq 571:662)
5X-RAY DIFFRACTION5chain B and (resseq 32:41)
6X-RAY DIFFRACTION6chain B and (resseq 56:524 or resseq 1000 or resseq 2000:2008 or resseq 3000:3002 or resseq 4000 or resseq 5000:5008)
7X-RAY DIFFRACTION7chain B and (resseq 525:570 or resseq 6000:6001)
8X-RAY DIFFRACTION8chain B and (resseq 571:663)

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