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- PDB-6fkk: Drosophila Semaphorin 1b, extracellular domains 1-2 -

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Basic information

Entry
Database: PDB / ID: 6fkk
TitleDrosophila Semaphorin 1b, extracellular domains 1-2
ComponentsMIP07328p
KeywordsSIGNALING PROTEIN / semaphorin / sema domain / axon guidance cue / cell cell signaling
Function / homology
Function and homology information


Sema3A PAK dependent Axon repulsion / CRMPs in Sema3A signaling / SEMA3A-Plexin repulsion signaling by inhibiting Integrin adhesion / Sema4D induced cell migration and growth-cone collapse / Other semaphorin interactions / embryonic development via the syncytial blastoderm / semaphorin receptor binding / negative regulation of axon extension involved in axon guidance / chemorepellent activity / neural crest cell migration ...Sema3A PAK dependent Axon repulsion / CRMPs in Sema3A signaling / SEMA3A-Plexin repulsion signaling by inhibiting Integrin adhesion / Sema4D induced cell migration and growth-cone collapse / Other semaphorin interactions / embryonic development via the syncytial blastoderm / semaphorin receptor binding / negative regulation of axon extension involved in axon guidance / chemorepellent activity / neural crest cell migration / negative chemotaxis / semaphorin-plexin signaling pathway / axon guidance / positive regulation of cell migration / plasma membrane / cytosol
Similarity search - Function
Semaphorin-1A, sema domain / Semaphorin / Sema domain / semaphorin domain / Sema domain / Sema domain superfamily / Sema domain profile. / YVTN repeat-like/Quinoprotein amine dehydrogenase / 7 Propeller / Methylamine Dehydrogenase; Chain H ...Semaphorin-1A, sema domain / Semaphorin / Sema domain / semaphorin domain / Sema domain / Sema domain superfamily / Sema domain profile. / YVTN repeat-like/Quinoprotein amine dehydrogenase / 7 Propeller / Methylamine Dehydrogenase; Chain H / WD40/YVTN repeat-like-containing domain superfamily / Mainly Beta
Similarity search - Domain/homology
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.78 Å
AuthorsRozbesky, D. / Harlos, K. / Jones, E.Y.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Cancer Research UKB5R00120 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
DepositionJan 24, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 6, 2019Provider: repository / Type: Initial release
Revision 1.1Aug 21, 2019Group: Data collection / Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Aug 28, 2019Group: Data collection / Database references / Category: citation / citation_author
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_symm_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.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_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.type_symbol / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_validate_symm_contact.auth_asym_id_2 / _pdbx_validate_symm_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 17, 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

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Assembly

Deposited unit
A: MIP07328p
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,9635
Polymers64,2121
Non-polymers2,7504
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: assay for oligomerization, SEC-MALS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3180 Å2
ΔGint46 kcal/mol
Surface area25630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)163.256, 163.256, 140.403
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/6
#3: y,-x+y,z+5/6
#4: -y,x-y,z+1/3
#5: -x+y,-x,z+2/3
#6: x-y,-y,-z
#7: -x,-x+y,-z+2/3
#8: -x,-y,z+1/2
#9: y,x,-z+1/3
#10: -y,-x,-z+5/6
#11: -x+y,y,-z+1/2
#12: x,x-y,-z+1/6

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Components

#1: Protein MIP07328p / Sema-1b / isoform A / isoform B / isoform C / Semaphorin-like


Mass: 64212.426 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly)
Gene: Sema1b, Sema-1b, Sema-1b-RB, semaphorin-like, CG6446, Dmel_CG6446
Plasmid: pHLSec / Cell line (production host): HEK293T / Production host: Homo sapiens (human) / References: UniProt: Q7KK54
#2: Polysaccharide alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D- ...alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]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: 1559.386 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-2DManpa1-2DManpa1-3[DManpa1-3[DManpa1-6]DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam 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-g1_d2-e1_e2-f1_g3-h1_g6-i1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{[(2+1)][a-D-Manp]{[(2+1)][a-D-Manp]{}}}[(6+1)][a-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}}}}}LINUCSPDB-CARE
#3: Polysaccharide alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...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: 748.682 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam 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_c3-d1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#4: 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.: 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: 4.51 Å3/Da / Density % sol: 72.75 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.2 M trisodium citrate and 20% (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 8, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.78→81.628 Å / Num. obs: 27778 / % possible obs: 96.74 % / Redundancy: 11.7 % / Biso Wilson estimate: 63.91 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.117 / Net I/σ(I): 10.93
Reflection shellResolution: 2.78→2.88 Å / Rmerge(I) obs: 1.641

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Processing

Software
NameVersionClassification
PHENIX(1.13rc2_2986: ???)refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3OKY

3oky


Resolution: 2.78→81.628 Å / SU ML: 0.35 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 26.81
RfactorNum. reflection% reflection
Rfree0.2475 1141 5.05 %
Rwork0.2061 --
obs0.2082 22592 79.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.78→81.628 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4034 0 183 0 4217
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0034337
X-RAY DIFFRACTIONf_angle_d0.6195921
X-RAY DIFFRACTIONf_dihedral_angle_d10.9432615
X-RAY DIFFRACTIONf_chiral_restr0.044703
X-RAY DIFFRACTIONf_plane_restr0.004734
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7802-2.90670.3402670.34221380X-RAY DIFFRACTION42
2.9067-3.060.3436900.30441735X-RAY DIFFRACTION53
3.06-3.25170.34891100.28722294X-RAY DIFFRACTION69
3.2517-3.50280.32761740.26462793X-RAY DIFFRACTION85
3.5028-3.85530.26991670.2333129X-RAY DIFFRACTION94
3.8553-4.41310.23581800.1813278X-RAY DIFFRACTION98
4.4131-5.55990.17481650.16023350X-RAY DIFFRACTION98
5.5599-81.66320.23491880.18973492X-RAY DIFFRACTION97
Refinement TLS params.Method: refined / Origin x: 48.6252 Å / Origin y: 39.8763 Å / Origin z: -6.0814 Å
111213212223313233
T0.2925 Å2-0.0104 Å2-0.012 Å2-0.2435 Å20.1117 Å2--0.6254 Å2
L1.858 °2-1.0743 °2-0.4237 °2-2.3444 °20.4215 °2--3.4965 °2
S-0.0269 Å °0.0067 Å °-0.0132 Å °-0.2845 Å °0.0423 Å °0.1578 Å °0.2181 Å °-0.4568 Å °0.0011 Å °
Refinement TLS groupSelection details: all

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