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- PDB-3al8: Plexin A2 / Semaphorin 6A complex -

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Basic information

Entry
Database: PDB / ID: 3al8
TitlePlexin A2 / Semaphorin 6A complex
Components
  • Plexin-A2
  • Semaphorin-6A
KeywordsSIGNALING PROTEIN / beta-propeller / signaling complex
Function / homology
Function and homology information


negative regulation of cell adhesion involved in sprouting angiogenesis / cerebellar granule cell precursor tangential migration / CRMPs in Sema3A signaling / positive regulation of neuron migration / Sema3A PAK dependent Axon repulsion / semaphorin receptor binding / negative regulation of sprouting angiogenesis / negative regulation of axon extension involved in axon guidance / negative regulation of vascular endothelial growth factor signaling pathway / SEMA3A-Plexin repulsion signaling by inhibiting Integrin adhesion ...negative regulation of cell adhesion involved in sprouting angiogenesis / cerebellar granule cell precursor tangential migration / CRMPs in Sema3A signaling / positive regulation of neuron migration / Sema3A PAK dependent Axon repulsion / semaphorin receptor binding / negative regulation of sprouting angiogenesis / negative regulation of axon extension involved in axon guidance / negative regulation of vascular endothelial growth factor signaling pathway / SEMA3A-Plexin repulsion signaling by inhibiting Integrin adhesion / semaphorin-plexin signaling pathway involved in axon guidance / semaphorin receptor complex / limb bud formation / pharyngeal system development / semaphorin receptor activity / chemorepellent activity / negative regulation of cell adhesion / neural tube development / neural crest cell migration / positive regulation of axonogenesis / semaphorin-plexin signaling pathway / centrosome localization / negative chemotaxis / somitogenesis / regulation of GTPase activity / neuron migration / cellular response to vascular endothelial growth factor stimulus / regulation of cell migration / negative regulation of angiogenesis / negative regulation of ERK1 and ERK2 cascade / axon guidance / transmembrane signaling receptor activity / regulation of cell shape / collagen-containing extracellular matrix / cell surface receptor signaling pathway / positive regulation of cell migration / axon / apoptotic process / integral component of plasma membrane / extracellular space / membrane / identical protein binding / plasma membrane
Similarity search - Function
Plexin-A2, sema domain / Semaphorin / Plexin, TIG domain 2 / TIG domain found in plexin / TIG domain / Plexin, TIG domain 1 / 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-A2, sema domain / Semaphorin / Plexin, TIG domain 2 / TIG domain found in plexin / TIG domain / Plexin, TIG domain 1 / 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 superfamily / Sema domain / Sema domain profile. / IPT/TIG domain / Rho GTPase activation protein / ig-like, plexins, transcription factors / domain found in Plexins, Semaphorins and Integrins / PSI domain / IPT domain / YVTN repeat-like/Quinoprotein amine dehydrogenase / Methylamine Dehydrogenase; Chain H / 7 Propeller / Immunoglobulin E-set / WD40/YVTN repeat-like-containing domain superfamily / Immunoglobulin-like fold / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Semaphorin-6A / Plexin-A2
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.6 Å
AuthorsNogi, T. / Yasui, N. / Mihara, E. / Takagi, J.
CitationJournal: Nature / Year: 2010
Title: Structural basis for semaphorin signalling through the plexin receptor.
Authors: Nogi, T. / Yasui, N. / Mihara, E. / Matsunaga, Y. / Noda, M. / Yamashita, N. / Toyofuku, T. / Uchiyama, S. / Goshima, Y. / Kumanogoh, A. / Takagi, J.
History
DepositionJul 28, 2010Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 6, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / 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_ref_seq_dif / 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 / _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 / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Semaphorin-6A
B: Plexin-A2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)125,7968
Polymers123,0492
Non-polymers2,7486
Water0
1
A: Semaphorin-6A
B: Plexin-A2
hetero molecules

A: Semaphorin-6A
B: Plexin-A2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)251,59216
Polymers246,0974
Non-polymers5,49512
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+4/31
2


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2240 Å2
ΔGint-6 kcal/mol
Surface area43340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)240.870, 240.870, 146.745
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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Components

#1: Protein Semaphorin-6A / Semaphorin VIA / Sema VIA / Semaphorin-6A-1 / SEMA6A-1 / Semaphorin Q / Sema Q


Mass: 62863.398 Da / Num. of mol.: 1 / Fragment: sema and PSI domain (UNP RESIDUES 19-570)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Sema6a, Semaq / Plasmid: pSGVH0 / Cell (production host): CHO lec 3.2.8.1 / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: O35464
#2: Protein Plexin-A2 / Plexin-2 / Plex 2


Mass: 60185.113 Da / Num. of mol.: 1 / Fragment: sema and PSI domain (UNP RESIDUES 31-561)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Plxna2, Kiaa0463 / Plasmid: pcDNA3.1/His-Myc / Cell (production host): HEK293S GnTI- / Production host: Homo sapiens (human) / References: UniProt: P70207
#3: 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
#4: 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
#5: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 3
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: 4.99 Å3/Da / Density % sol: 75.37 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 18-25% (wt./vol.) PEG 1000, 0.2-0.3M MgCl2, 0.1M Na-cacodylate pH 5.5-6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Dec 16, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.6→49.15 Å / Num. obs: 29317 / % possible obs: 99.5 % / Observed criterion σ(I): -3 / Redundancy: 6.5 % / Biso Wilson estimate: 59.723 Å2 / Rmerge(I) obs: 0.097 / Net I/σ(I): 17.1
Reflection shellResolution: 3.6→3.79 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.417 / Mean I/σ(I) obs: 4 / Num. unique all: 4222 / % possible all: 99.8

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
MOLREPphasing
REFMAC5.5.0102refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.6→49.15 Å / Cor.coef. Fo:Fc: 0.908 / Cor.coef. Fo:Fc free: 0.854 / SU B: 28.537 / SU ML: 0.422 / Cross valid method: THROUGHOUT / ESU R Free: 0.577 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28733 1483 5.1 %RANDOM
Rwork0.23039 ---
obs0.23316 27830 99.24 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 99.662 Å2
Baniso -1Baniso -2Baniso -3
1-1.62 Å20.81 Å20 Å2
2--1.62 Å20 Å2
3----2.43 Å2
Refinement stepCycle: LAST / Resolution: 3.6→49.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8148 0 181 0 8329
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0228554
X-RAY DIFFRACTIONr_angle_refined_deg1.0981.98211626
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.01251031
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.04923.615379
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.203151381
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.9481552
X-RAY DIFFRACTIONr_chiral_restr0.0730.21308
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0216438
X-RAY DIFFRACTIONr_mcbond_it0.451.55158
X-RAY DIFFRACTIONr_mcangle_it0.82728345
X-RAY DIFFRACTIONr_scbond_it0.61233396
X-RAY DIFFRACTIONr_scangle_it1.134.53281
LS refinement shellResolution: 3.6→3.693 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.328 115 -
Rwork0.29 2008 -
obs--99.77 %

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