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- PDB-6fkn: Drosophila Plexin A in complex with Semaphorin 1b -

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Basic information

Entry
Database: PDB / ID: 6fkn
TitleDrosophila Plexin A in complex with Semaphorin 1b
Components
  • MIP07328p
  • Plexin A, isoform A
KeywordsSIGNALING PROTEIN / semaphorin / plexin / sema domain / cis interaction
Function / homology
Function and homology information


RHOD GTPase cycle / Sema3A PAK dependent Axon repulsion / CRMPs in Sema3A signaling / SEMA3A-Plexin repulsion signaling by inhibiting Integrin adhesion / guanylate cyclase activator activity / Sema4D induced cell migration and growth-cone collapse / Other semaphorin interactions / embryonic development via the syncytial blastoderm / photoreceptor cell axon guidance / semaphorin receptor binding ...RHOD GTPase cycle / Sema3A PAK dependent Axon repulsion / CRMPs in Sema3A signaling / SEMA3A-Plexin repulsion signaling by inhibiting Integrin adhesion / guanylate cyclase activator activity / Sema4D induced cell migration and growth-cone collapse / Other semaphorin interactions / embryonic development via the syncytial blastoderm / photoreceptor cell axon guidance / semaphorin receptor binding / sensory neuron axon guidance / semaphorin receptor complex / chemorepellent activity / semaphorin receptor activity / negative regulation of cell adhesion / motor neuron axon guidance / axon midline choice point recognition / negative chemotaxis / positive regulation of axonogenesis / semaphorin-plexin signaling pathway / 14-3-3 protein binding / regulation of cell migration / GTPase activator activity / axon guidance / heparin binding / regulation of cell shape / Ras protein signal transduction / positive regulation of cell migration / plasma membrane / cytosol
Similarity search - Function
Semaphorin-1A, sema domain / Semaphorin / Plexin, TIG domain 2 / TIG domain found in plexin / Plexin, TIG domain 1 / TIG domain / Plexin, cytoplasmic RasGAP domain / Plexin, cytoplasmic RhoGTPase-binding domain / Plexin cytoplasmic RasGAP domain / Plexin cytoplasmic RhoGTPase-binding domain ...Semaphorin-1A, sema domain / Semaphorin / Plexin, TIG domain 2 / TIG domain found in plexin / Plexin, TIG domain 1 / TIG domain / Plexin, cytoplasmic RasGAP domain / Plexin, cytoplasmic RhoGTPase-binding domain / Plexin cytoplasmic RasGAP domain / Plexin cytoplasmic RhoGTPase-binding domain / Plexin family / Plexin repeat / Plexin repeat / Sema domain / semaphorin domain / Sema domain / Sema domain superfamily / Sema domain profile. / IPT/TIG domain / ig-like, plexins, transcription factors / Rho GTPase activation protein / PSI domain / domain found in Plexins, Semaphorins and Integrins / IPT domain / Immunoglobulin E-set / WD40/YVTN repeat-like-containing domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
MIP07328p / Plexin A, isoform A
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.801 Å
AuthorsRozbesky, D. / Harlos, K. / Jones, E.Y.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Cancer Research UKB5R00120 United Kingdom
CitationJournal: Embo J. / Year: 2020
Title: Structural basis of semaphorin-plexin cis interaction.
Authors: Rozbesky, D. / Verhagen, M.G. / Karia, D. / Nagy, G.N. / Alvarez, L. / Robinson, R.A. / Harlos, K. / Padilla-Parra, S. / Pasterkamp, R.J. / Jones, E.Y.
History
DepositionJan 24, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 6, 2019Provider: repository / Type: Initial release
Revision 1.1Jun 17, 2020Group: Data collection / Database references / Category: chem_comp / citation / citation_author
Item: _chem_comp.type / _citation.country ..._chem_comp.type / _citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
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 / database_PDB_caveat / 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_chiral / 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.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 / _database_PDB_caveat.text / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_validate_chiral.auth_asym_id / _pdbx_validate_chiral.auth_seq_id / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_2 / _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 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
Revision 2.2Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Plexin A, isoform A
B: MIP07328p
C: Plexin A, isoform A
D: MIP07328p
hetero molecules


Theoretical massNumber of molelcules
Total (without water)290,30814
Polymers285,8244
Non-polymers4,48410
Water00
1
A: Plexin A, isoform A
B: MIP07328p
hetero molecules


Theoretical massNumber of molelcules
Total (without water)144,9117
Polymers142,9122
Non-polymers1,9995
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Plexin A, isoform A
D: MIP07328p
hetero molecules


Theoretical massNumber of molelcules
Total (without water)145,3977
Polymers142,9122
Non-polymers2,4855
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)153.630, 153.630, 425.370
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
Symmetry operation#1: x,y,z
#2: x-y,x,z+5/6
#3: y,-x+y,z+1/6
#4: -y,x-y,z+2/3
#5: -x+y,-x,z+1/3
#6: x-y,-y,-z
#7: -x,-x+y,-z+1/3
#8: -x,-y,z+1/2
#9: y,x,-z+2/3
#10: -y,-x,-z+1/6
#11: -x+y,y,-z+1/2
#12: x,x-y,-z+5/6
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
12
22

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111(chain B and (resid 53 through 292 or resid 295...
211(chain D and (resid 53 through 292 or resid 295...
112chain A
212(chain C and (resid 62 through 126 or resid 128 through 1003))

NCS ensembles :
ID
1
2

NCS oper:
IDCodeMatrixVector
1given(-0.978135125924, 0.044070146626, 0.203247380329), (-0.0197492321061, 0.953190655836, -0.301724280524), (-0.207030537036, -0.299141096814, -0.931478910621)-11.9052323741, 9.85824068066, 9.69741043937
2given(-0.985522480265, 0.0382711563491, 0.165168881704), (-0.0126434639888, 0.954888016128, -0.296696847765), (-0.169072717225, -0.294489720105, -0.940579726043)-10.5783105889, 9.69696305674, 10.018559383

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Components

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Protein , 2 types, 4 molecules ACBD

#1: Protein Plexin A, isoform A


Mass: 78699.383 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly)
Gene: PlexA, BcDNA:GM05237, D-Plex A, Dmel\CG11081, DPlexA, lincRNA.927, plex, plex A, Plex1, plexA, PlexA1, CG11081, Dmel_CG11081
Variant: isoform A / Plasmid: pHLSec / Cell (production host): HEK293T / Production host: Homo sapiens (human) / References: UniProt: Q9V491
#2: Protein MIP07328p / Sema-1b / isoform A / isoform B / isoform C / Semaphorin-like


Mass: 64212.426 Da / Num. of mol.: 2
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 (production host): HEK293T / Production host: Homo sapiens (human) / References: UniProt: Q7KK54

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Sugars , 4 types, 10 molecules

#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: 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
#5: Polysaccharide alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-3)-[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: 910.823 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3[DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,5,4/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3/a4-b1_b4-c1_c3-d1_c6-e1WURCSPDB2Glycan 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]{}}}}}LINUCSPDB-CARE
#6: 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.: 6
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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Details

Has protein modificationY

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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: 3.24 Å3/Da / Density % sol: 62.01 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 0.1 M MES and 12% (w/v) PEG 20 000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 1.0719 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Oct 1, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0719 Å / Relative weight: 1
ReflectionResolution: 4.801→133.047 Å / Num. obs: 15309 / % possible obs: 99.9 % / Redundancy: 20.9 % / Biso Wilson estimate: 217.36 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.339 / Net I/σ(I): 7.41
Reflection shellResolution: 4.801→4.97 Å

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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: 6KFM

6kfm


Resolution: 4.801→133.047 Å / SU ML: 0.58 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 29.76 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.297 819 5.35 %
Rwork0.2848 --
obs0.2854 15307 99.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 4.801→133.047 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15305 0 295 0 15600
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00515984
X-RAY DIFFRACTIONf_angle_d0.81121770
X-RAY DIFFRACTIONf_dihedral_angle_d12.0565915
X-RAY DIFFRACTIONf_chiral_restr0.0632540
X-RAY DIFFRACTIONf_plane_restr0.0052760
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11B3736X-RAY DIFFRACTIONPOSITIONAL
12D3736X-RAY DIFFRACTIONPOSITIONAL0.946
21A3965X-RAY DIFFRACTIONPOSITIONAL
22C3965X-RAY DIFFRACTIONPOSITIONAL0.002
Refinement TLS params.Method: refined / Origin x: -2.4413 Å / Origin y: 43.7016 Å / Origin z: 1.2018 Å
111213212223313233
T2.2291 Å2-0.0028 Å2-0.1705 Å2-2.3678 Å20.1186 Å2--2.32 Å2
L0.5064 °2-0.046 °2-0.4969 °2-0.7743 °20.198 °2--1.1783 °2
S-0.0218 Å °0.0953 Å °-0.0219 Å °0.2378 Å °-0.0047 Å °0.2411 Å °0.0811 Å °-0.3514 Å °0.073 Å °
Refinement TLS groupSelection details: all

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