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- PDB-6qp9: Drosophila Semaphorin 1a, extracellular domains 1-2 -

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Basic information

Entry
Database: PDB / ID: 6qp9
TitleDrosophila Semaphorin 1a, extracellular domains 1-2
ComponentsSemaphorin-1A
KeywordsSIGNALING PROTEIN / axon guidance cue / developmental protein / cell signalling / semaphorin / signalling protein
Function / homology
Function and homology information


semaphorin-plexin signaling pathway involved in regulation of photoreceptor cell axon guidance / Other semaphorin interactions / Sema4D induced cell migration and growth-cone collapse / synaptic target recognition / semaphorin receptor binding / negative regulation of axon extension involved in axon guidance / chemorepellent activity / negative regulation of cell size / motor neuron axon guidance / axon midline choice point recognition ...semaphorin-plexin signaling pathway involved in regulation of photoreceptor cell axon guidance / Other semaphorin interactions / Sema4D induced cell migration and growth-cone collapse / synaptic target recognition / semaphorin receptor binding / negative regulation of axon extension involved in axon guidance / chemorepellent activity / negative regulation of cell size / motor neuron axon guidance / axon midline choice point recognition / dendrite morphogenesis / negative chemotaxis / semaphorin-plexin signaling pathway / synapse assembly / axon guidance / heparin binding / membrane => GO:0016020 / positive regulation of cell migration / extracellular space / plasma membrane
Similarity search - Function
Semaphorin-1A, sema domain / Semaphorin / Plexin repeat / Plexin repeat / Sema domain / semaphorin domain / Sema domain / Sema domain superfamily / Sema domain profile. / PSI domain ...Semaphorin-1A, sema domain / Semaphorin / Plexin repeat / Plexin repeat / Sema domain / semaphorin domain / Sema domain / Sema domain superfamily / Sema domain profile. / PSI domain / domain found in Plexins, Semaphorins and Integrins / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.6 Å
AuthorsRozbesky, D. / Robinson, R.A. / 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: Atomic model / Data collection ...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 / 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_seq_id / _atom_site.label_asym_id / _atom_site.label_entity_id / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _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_entity_nonpoly.entity_id / _pdbx_entity_nonpoly.name / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_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 / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Semaphorin-1A
B: Semaphorin-1A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)121,1836
Polymers119,8922
Non-polymers1,2914
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: assay for oligomerization, analytical ultracentrifugation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3390 Å2
ΔGint12 kcal/mol
Surface area50290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.476, 99.476, 150.131
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32

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Components

#1: Protein Semaphorin-1A / Semaphorin-I / Sema I


Mass: 59945.953 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: Sema1a, Dsema-I, Sema-1a, CG18405 / Production host: Homo sapiens (human) / References: UniProt: Q24322
#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.: 2
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: 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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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.58 Å3/Da / Density % sol: 65.61 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 0.1 M Tris-HCl (pH 8.0), 0.2 M ammonium sulphate, 25% PEG 3350

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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 PILATUS3 S 6M / Detector: PIXEL / Date: Jan 27, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 3.6→49.74 Å / Num. obs: 19133 / % possible obs: 96.98 % / Redundancy: 6.1 % / Rmerge(I) obs: 0.233 / Net I/σ(I): 5
Reflection shellResolution: 3.6→3.82 Å

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6FKK

6fkk


Resolution: 3.6→49.738 Å / SU ML: 0.36 / Cross valid method: THROUGHOUT / σ(F): 135.19 / Phase error: 53.32
RfactorNum. reflection% reflection
Rfree0.3226 786 5.14 %
Rwork0.2875 --
obs0.2934 15300 79.49 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.6→49.738 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7916 0 84 0 8000
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0028205
X-RAY DIFFRACTIONf_angle_d0.57511169
X-RAY DIFFRACTIONf_dihedral_angle_d12.4884922
X-RAY DIFFRACTIONf_chiral_restr0.0431245
X-RAY DIFFRACTIONf_plane_restr0.0051458
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.6-3.82510.4003810.35121036X-RAY DIFFRACTION32
3.8251-4.11960.30251080.31361608X-RAY DIFFRACTION51
4.1196-4.53270.24851530.29952736X-RAY DIFFRACTION85
4.5327-5.18510.36021630.27883004X-RAY DIFFRACTION94
5.1851-6.51960.32071560.2833028X-RAY DIFFRACTION95
6.5196-28.35420.35961180.28713079X-RAY DIFFRACTION96
Refinement TLS params.Method: refined / Origin x: 105.2393 Å / Origin y: -3.7203 Å / Origin z: -21.6492 Å
111213212223313233
T-0.0623 Å20.087 Å20.0802 Å2-0.1253 Å20.0062 Å2--0.223 Å2
L0.7033 °20.2536 °20.299 °2-1.6268 °2-0.215 °2--2.8561 °2
S0.2094 Å °-0.025 Å °-0.163 Å °-0.2651 Å °-0.0305 Å °-0.2956 Å °0.0008 Å °-0.0276 Å °0.0376 Å °
Refinement TLS groupSelection details: all

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