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- PDB-6ska: Teneurin 2 in complex with Latrophilin 1 Lec-Olf domains -

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Basic information

Entry
Database: PDB / ID: 6ska
TitleTeneurin 2 in complex with Latrophilin 1 Lec-Olf domains
Components
  • Adhesion G protein-coupled receptor L1
  • Teneurin-2
KeywordsSIGNALING PROTEIN / adhesion / Odz / Lphn / synapse / neurons / repulsion / olfactomedin / lectin / YD-repeat / complex
Function / homology
Function and homology information


latrotoxin receptor activity / positive regulation of synapse assembly / positive regulation of filopodium assembly / toxic substance binding / neuron development / cell adhesion molecule binding / filopodium / cell-cell adhesion / PML body / G protein-coupled receptor activity ...latrotoxin receptor activity / positive regulation of synapse assembly / positive regulation of filopodium assembly / toxic substance binding / neuron development / cell adhesion molecule binding / filopodium / cell-cell adhesion / PML body / G protein-coupled receptor activity / cell-cell junction / cell junction / growth cone / carbohydrate binding / presynaptic membrane / dendritic spine / postsynaptic membrane / cell surface receptor signaling pathway / neuron projection / G protein-coupled receptor signaling pathway / protein heterodimerization activity / signaling receptor binding / axon / calcium ion binding / synapse / dendrite / glutamatergic synapse / negative regulation of transcription by RNA polymerase II / endoplasmic reticulum / Golgi apparatus / signal transduction / protein homodimerization activity / nucleus / plasma membrane
Similarity search - Function
Latrophilin-1 / Rhamnose-binding lectin domain (RBL) / : / : / Teneurin intracellular, N-terminal / : / : / Teneurin Intracellular Region / Teneurin-3-like, galactose-binding domain-like / Teneurin antibiotic-binding-like domain ...Latrophilin-1 / Rhamnose-binding lectin domain (RBL) / : / : / Teneurin intracellular, N-terminal / : / : / Teneurin Intracellular Region / Teneurin-3-like, galactose-binding domain-like / Teneurin antibiotic-binding-like domain / Teneurin 1-4, FN-plug domain / Teneurin TTR-like domain / Teneurin NHL domain / Teneurin N-terminal domain profile. / GPCR, family 2, latrophilin, C-terminal / GPCR, family 2, latrophilin / Tox-GHH domain / : / Latrophilin Cytoplasmic C-terminal region / GHH signature containing HNH/Endo VII superfamily nuclease toxin / D-galactoside/L-rhamnose binding SUEL lectin domain superfamily / D-galactoside/L-rhamnose binding SUEL lectin domain / D-galactoside/L-rhamnose binding SUEL lectin domain / SUEL-type lectin domain profile. / GAIN domain, N-terminal / AGRL2-4 GAIN subdomain A / : / Teneurin YD-shell / Olfactomedin-like domain / Olfactomedin-like domain / Olfactomedin-like domain profile. / Olfactomedin-like domains / YD repeat / Teneurin EGF domain / Rhs repeat-associated core / Carboxypeptidase-like, regulatory domain superfamily / GPCR proteolysis site, GPS, motif / GAIN domain superfamily / : / GPS motif / G-protein-coupled receptor proteolytic site domain / GAIN-B domain profile. / GPCR, family 2, extracellular hormone receptor domain / G-protein coupled receptors family 2 profile 1. / Domain present in hormone receptors / Hormone receptor domain / GPCR family 2, extracellular hormone receptor domain superfamily / G-protein coupled receptors family 2 signature 2. / GPCR, family 2, secretin-like, conserved site / GPCR, family 2, secretin-like / 7 transmembrane receptor (Secretin family) / Six-bladed beta-propeller, TolB-like / Quinoprotein alcohol dehydrogenase-like superfamily / GPCR, family 2-like / G-protein coupled receptors family 2 profile 2. / EGF-like calcium-binding domain / Calcium-binding EGF-like domain / Epidermal growth factor-like domain. / EGF-like domain profile. / EGF-like domain signature 1. / EGF-like domain signature 2. / EGF-like domain / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Adhesion G protein-coupled receptor L1 / Teneurin-2
Similarity search - Component
Biological speciesGallus gallus (chicken)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.86 Å
AuthorsChu, A. / Carrasquero, M.A. / Lowe, E. / Seiradake, E.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Wellcome Trust United Kingdom
CitationJournal: Cell / Year: 2020
Title: Structural Basis of Teneurin-Latrophilin Interaction in Repulsive Guidance of Migrating Neurons.
Authors: Del Toro, D. / Carrasquero-Ordaz, M.A. / Chu, A. / Ruff, T. / Shahin, M. / Jackson, V.A. / Chavent, M. / Berbeira-Santana, M. / Seyit-Bremer, G. / Brignani, S. / Kaufmann, R. / Lowe, E. / ...Authors: Del Toro, D. / Carrasquero-Ordaz, M.A. / Chu, A. / Ruff, T. / Shahin, M. / Jackson, V.A. / Chavent, M. / Berbeira-Santana, M. / Seyit-Bremer, G. / Brignani, S. / Kaufmann, R. / Lowe, E. / Klein, R. / Seiradake, E.
History
DepositionAug 15, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 12, 2020Provider: repository / Type: Initial release
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 / pdbx_struct_conn_angle / 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 / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _struct_conn.conn_type_id / _struct_conn.id / _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_atom_id / _struct_conn.ptnr2_label_comp_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 23, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification / _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: Teneurin-2
D: Adhesion G protein-coupled receptor L1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)250,74114
Polymers246,0752
Non-polymers4,66512
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: surface plasmon resonance
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8580 Å2
ΔGint75 kcal/mol
Surface area89240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.260, 96.260, 809.220
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number95
Space group name H-MP4322

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Components

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Protein , 2 types, 2 molecules AD

#1: Protein Teneurin-2 / Ten-2 / Neurestin / Protein Odd Oz/ten-m homolog 2 / Tenascin-M2 / Ten-m2 / Teneurin transmembrane protein 2


Mass: 206155.812 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Gene: TENM2, ODZ2, TNM2 / Production host: Homo sapiens (human) / References: UniProt: Q9DER5
#2: Protein Adhesion G protein-coupled receptor L1 / Calcium-independent alpha-latrotoxin receptor 1 / CIRL-1 / Latrophilin-1 / Lectomedin-2


Mass: 39919.430 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Adgrl1, Kiaa0821, Lec2, Lphn1 / Production host: Homo sapiens (human) / References: UniProt: Q80TR1

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Sugars , 3 types, 11 molecules

#3: 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)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1397.245 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-2DManpa1-2DManpa1-3[DManpa1-3DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,8,7/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3-3-3-3/a4-b1_b4-c1_c3-d1_c6-g1_d2-e1_e2-f1_g3-h1WURCSPDB2Glycan 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]{}}}}}}LINUCSPDB-CARE
#4: 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.: 5
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
#5: 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.: 5
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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Non-polymers , 1 types, 1 molecules

#6: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca

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Details

Has ligand of interestN
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: 3.81 Å3/Da / Density % sol: 67.71 %
Crystal growTemperature: 293 K / Method: evaporation
Details: 0.1M potassium chloride, 0.1M HEPES pH7.5, 15% (w/v) PEG6000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97624 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Apr 28, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97624 Å / Relative weight: 1
ReflectionResolution: 3.86→202.306 Å / Num. obs: 34296 / % possible obs: 91.22 % / Redundancy: 12.83 % / Biso Wilson estimate: 80.18 Å2 / CC1/2: 0.9932 / Net I/σ(I): 6.187
Reflection shellResolution: 3.86→4.046 Å / Num. unique obs: 1716 / CC1/2: 0.446

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Processing

Software
NameClassification
BUSTERrefinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.86→52.09 Å / Cross valid method: FREE R-VALUE /
Num. reflection% reflection
obs34267 91 %
Refinement stepCycle: LAST / Resolution: 3.86→52.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17313 0 305 0 17618

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