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

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Basic information

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


RHOD GTPase cycle / semaphorin-plexin signaling pathway involved in regulation of photoreceptor cell axon guidance / Sema3A PAK dependent Axon repulsion / CRMPs in Sema3A signaling / G alpha (12/13) signalling events / SEMA3A-Plexin repulsion signaling by inhibiting Integrin adhesion / Other semaphorin interactions / guanylate cyclase activator activity / Sema4D induced cell migration and growth-cone collapse / embryonic development via the syncytial blastoderm ...RHOD GTPase cycle / semaphorin-plexin signaling pathway involved in regulation of photoreceptor cell axon guidance / Sema3A PAK dependent Axon repulsion / CRMPs in Sema3A signaling / G alpha (12/13) signalling events / SEMA3A-Plexin repulsion signaling by inhibiting Integrin adhesion / Other semaphorin interactions / guanylate cyclase activator activity / Sema4D induced cell migration and growth-cone collapse / embryonic development via the syncytial blastoderm / semaphorin receptor binding / sensory neuron axon guidance / semaphorin-plexin signaling pathway involved in axon guidance / negative regulation of axon extension involved in axon guidance / semaphorin receptor complex / positive regulation of guanylate cyclase activity / chemorepellent activity / semaphorin receptor activity / negative regulation of cell adhesion / axon midline choice point recognition / negative chemotaxis / positive regulation of axonogenesis / regulation of GTPase activity / semaphorin-plexin signaling pathway / regulation of cell migration / GTPase activator activity / 14-3-3 protein binding / axon guidance / heparin binding / regulation of cell shape / Ras protein signal transduction / positive regulation of cell migration / membrane / 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 RhoGTPase-binding domain / Plexin cytoplasmic RhoGTPase-binding domain / Plexin, cytoplasmic RasGAP domain / Plexin cytoplasmic RasGAP domain ...Semaphorin-1A, sema domain / Semaphorin / Plexin, TIG domain 2 / TIG domain found in plexin / Plexin, TIG domain 1 / TIG domain / Plexin, cytoplasmic RhoGTPase-binding domain / Plexin cytoplasmic RhoGTPase-binding domain / Plexin, cytoplasmic RasGAP domain / Plexin cytoplasmic RasGAP domain / ligand-binding face of the semaphorins, domain 2 / ligand-binding face of the semaphorins, domain 2 / 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 / YVTN repeat-like/Quinoprotein amine dehydrogenase / 7 Propeller / Methylamine Dehydrogenase; Chain H / Immunoglobulin E-set / WD40/YVTN repeat-like-containing domain superfamily / Immunoglobulin-like fold / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
MIP07328p / Plexin A, isoform A
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.96 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: 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_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 / _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 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)145,6188
Polymers142,9122
Non-polymers2,7066
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4620 Å2
ΔGint31 kcal/mol
Surface area46270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)130.940, 195.090, 124.840
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2

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Components

#1: Protein Plexin A, isoform A


Mass: 78699.383 Da / Num. of mol.: 1
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 line (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.: 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
#3: 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
#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 / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 4
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: 3.86 Å3/Da / Density % sol: 68.86 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 0.1 M HEPES (pH 7.0) and 8% (w/v) PEG 8000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 1.072 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 3, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.072 Å / Relative weight: 1
ReflectionResolution: 2.96→76.864 Å / Num. obs: 31584 / % possible obs: 93.78 % / Redundancy: 4.6 % / Biso Wilson estimate: 69.89 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.174 / Net I/σ(I): 8.86
Reflection shellResolution: 2.96→3.07 Å / Rmerge(I) obs: 0.634

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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, 6FKK

3oky

6fkk


Resolution: 2.96→76.864 Å / SU ML: 0.44 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 26.8
RfactorNum. reflection% reflection
Rfree0.2462 1515 4.8 %
Rwork0.1862 --
obs0.1891 31582 93.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.96→76.864 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7941 0 178 0 8119
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0058327
X-RAY DIFFRACTIONf_angle_d0.75511348
X-RAY DIFFRACTIONf_dihedral_angle_d9.7975023
X-RAY DIFFRACTIONf_chiral_restr0.0481323
X-RAY DIFFRACTIONf_plane_restr0.0051440
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.96-3.05560.35421110.28182409X-RAY DIFFRACTION84
3.0556-3.16480.30381110.2782424X-RAY DIFFRACTION84
3.1648-3.29150.35871310.2662522X-RAY DIFFRACTION87
3.2915-3.44130.32631300.22362823X-RAY DIFFRACTION98
3.4413-3.62270.30441520.21342821X-RAY DIFFRACTION98
3.6227-3.84970.26971390.19992854X-RAY DIFFRACTION98
3.8497-4.14690.24141370.17582833X-RAY DIFFRACTION98
4.1469-4.56420.20391350.13942834X-RAY DIFFRACTION97
4.5642-5.22450.18291670.13382820X-RAY DIFFRACTION97
5.2245-6.58180.23421410.18022855X-RAY DIFFRACTION96
6.5818-76.88960.22531610.18642872X-RAY DIFFRACTION94
Refinement TLS params.Method: refined / Origin x: 43.7609 Å / Origin y: -9.6535 Å / Origin z: -38.6108 Å
111213212223313233
T0.372 Å20.0005 Å20.0115 Å2-0.4388 Å20.0288 Å2--0.4022 Å2
L0.3656 °2-0.3485 °2-0.1263 °2-2.6613 °20.579 °2--0.5762 °2
S-0.08 Å °-0.0125 Å °-0.0118 Å °0.0941 Å °0.0698 Å °0.1503 Å °0.0041 Å °-0.0626 Å °0.0216 Å °
Refinement TLS groupSelection details: all

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