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- PDB-6ske: Teneurin 2 in complex with Latrophilin 2 Lec domain -

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Basic information

Entry
Database: PDB / ID: 6ske
TitleTeneurin 2 in complex with Latrophilin 2 Lec domain
Components
  • Adhesion G protein-coupled receptor L2
  • Teneurin-2Teneurin
KeywordsSIGNALING PROTEIN / teneurin / latrophilin / odz / signalling / adhesion / repulsion / synapse / neurons / cell migration / adgrl
Function / homology
Function and homology information


: / positive regulation of synapse assembly / positive regulation of filopodium assembly / heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules / plasma membrane => GO:0005886 / : / neuron development / cell adhesion molecule binding / filopodium / PDZ domain binding ...: / positive regulation of synapse assembly / positive regulation of filopodium assembly / heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules / plasma membrane => GO:0005886 / : / neuron development / cell adhesion molecule binding / filopodium / PDZ domain binding / G protein-coupled receptor activity / axon guidance / synapse organization / response to bacterium / brain development / adenylate cyclase-activating G protein-coupled receptor signaling pathway / cell-cell adhesion / PML body / cell-cell junction / cell junction / growth cone / postsynaptic membrane / carbohydrate binding / dendritic spine / cell surface receptor signaling pathway / neuron projection / protein heterodimerization activity / signaling receptor binding / dendrite / glutamatergic synapse / synapse / calcium ion binding / Golgi apparatus / negative regulation of transcription by RNA polymerase II / endoplasmic reticulum / protein homodimerization activity / nucleus / plasma membrane
Similarity search - Function
Latrophilin-2 / Rhamnose-binding lectin domain (RBL) / Teneurin intracellular, N-terminal / Teneurin Intracellular Region / Teneurin N-terminal domain profile. / Tox-GHH domain / GHH signature containing HNH/Endo VII superfamily nuclease toxin / GPCR, family 2, latrophilin, C-terminal / GPCR, family 2, latrophilin / Latrophilin Cytoplasmic C-terminal region ...Latrophilin-2 / Rhamnose-binding lectin domain (RBL) / Teneurin intracellular, N-terminal / Teneurin Intracellular Region / Teneurin N-terminal domain profile. / Tox-GHH domain / GHH signature containing HNH/Endo VII superfamily nuclease toxin / GPCR, family 2, latrophilin, C-terminal / GPCR, family 2, latrophilin / Latrophilin Cytoplasmic C-terminal region / D-galactoside/L-rhamnose binding SUEL lectin domain superfamily / YD repeat / GAIN domain, N-terminal / GPCR-Autoproteolysis INducing (GAIN) domain / D-galactoside/L-rhamnose binding SUEL lectin domain / Galactose binding lectin domain / SUEL-type lectin domain profile. / Olfactomedin-like domain / Olfactomedin-like domain / Olfactomedin-like domain profile. / Olfactomedin-like domains / Rhs repeat-associated core / Carboxypeptidase-like, regulatory domain superfamily / GPCR proteolysis site, GPS, motif / GPS motif / GPS domain profile. / G-protein-coupled receptor proteolytic site domain / Hormone receptor domain / GPCR, family 2, extracellular hormone receptor domain / G-protein coupled receptors family 2 profile 1. / Domain present in hormone receptors / GPCR family 2, extracellular hormone receptor domain superfamily / Six-bladed beta-propeller, TolB-like / 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) / 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 2. / EGF-like domain signature 1. / EGF-like domain / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Adhesion G protein-coupled receptor L2 / Teneurin-2
Similarity search - Component
Biological speciesGallus gallus (chicken)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.62 Å
AuthorsShahin, M. / Jackson, V.A. / Carrasquero, M. / Lowe, E. / Seiradake, E.
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 / 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 / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Teneurin-2
B: Adhesion G protein-coupled receptor L2
C: Teneurin-2
D: Adhesion G protein-coupled receptor L2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)427,77824
Polymers418,9694
Non-polymers8,80820
Water3,783210
1
A: Teneurin-2
D: Adhesion G protein-coupled receptor L2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)213,88912
Polymers209,4852
Non-polymers4,40410
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Adhesion G protein-coupled receptor L2
C: Teneurin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)213,88912
Polymers209,4852
Non-polymers4,40410
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)90.870, 109.920, 152.210
Angle α, β, γ (deg.)90.19, 93.99, 111.93
Int Tables number1
Space group name H-MP1

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Components

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Protein , 2 types, 4 molecules ACBD

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


Mass: 197234.719 Da / Num. of mol.: 2
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 L2 / Calcium-independent alpha-latrotoxin receptor 2 / CIRL-2 / Latrophilin-2


Mass: 12249.954 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Adgrl2, Kiaa0786, Lphn2 / Production host: Homo sapiens (human) / References: UniProt: Q8JZZ7

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Sugars , 3 types, 20 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.: 2
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.: 10
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-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 8
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, 210 molecules

#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 210 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 3.36 Å3/Da / Density % sol: 63.35 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 0.1 M calcium acetate, 0.1 M sodium acetate pH 4.5, 10% (w/v) PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97956 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 1, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97956 Å / Relative weight: 1
ReflectionResolution: 3.6→84 Å / Num. obs: 59561 / % possible obs: 96 % / Redundancy: 1.8 % / Biso Wilson estimate: 71.31 Å2 / CC1/2: 0.97 / Net I/σ(I): 3.5
Reflection shellResolution: 3.6→3.71 Å / Num. unique obs: 4393 / CC1/2: 0.25

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.62→84 Å / Cor.coef. Fo:Fc: 0.734 / Cor.coef. Fo:Fc free: 0.737 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.666
RfactorNum. reflection% reflectionSelection details
Rfree0.269 2997 5.03 %RANDOM
Rwork0.27 ---
obs0.27 59561 96 %-
Displacement parametersBiso mean: 99.36 Å2
Baniso -1Baniso -2Baniso -3
1--36.2218 Å2-39.883 Å2-32.954 Å2
2---7.2958 Å2-15.6347 Å2
3---43.5176 Å2
Refine analyzeLuzzati coordinate error obs: 1.03 Å
Refinement stepCycle: 1 / Resolution: 3.62→84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms29198 0 580 210 29988
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.00730486HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.9741430HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d10658SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes5182HARMONIC5
X-RAY DIFFRACTIONt_it30486HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.19
X-RAY DIFFRACTIONt_other_torsion18.25
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion4106SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact30994SEMIHARMONIC4
LS refinement shellResolution: 3.62→3.64 Å / Total num. of bins used: 50
RfactorNum. reflection% reflection
Rfree0.284 -3.78 %
Rwork0.2828 1147 -
all0.2829 1192 -
obs--96.19 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.2556-0.1496-0.63960.1977-0.18610.9746-0.03520.0793-0.2041-0.1276-0.0849-0.0291-0.1258-0.00720.12010.16450.2329-0.07980.1010.00060.007221.8383-1.4978-38.8038
21.5990.8178-3.03348.3662-1.29937.8388-0.02040.00390.17410.037-0.06680.1410.1176-0.19480.08720.27370.0597-0.11290.3575-0.11570.2807-11.862579.598950.8364
30.07740.0622-0.65410.924-0.76791.2729-0.133-0.0794-0.1157-0.0287-0.0265-0.22180.0655-0.15340.15940.34320.0591-0.0355-0.18450.0149-0.107618.79955.972229.4547
45.0629-2.6739-1.90522.9213-4.13587.55250.056-0.02790.1833-0.10980.0452-0.0954-0.14410.1931-0.10130.4365-0.1089-0.19210.19370.07340.281827.779736.8518-60.186
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }
3X-RAY DIFFRACTION3{ C|* }
4X-RAY DIFFRACTION4{ D|* }

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