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- PDB-6fb3: Teneurin 2 Partial Extracellular Domain -

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Basic information

Entry
Database: PDB / ID: 6fb3
TitleTeneurin 2 Partial Extracellular Domain
ComponentsTeneurin-2Teneurin
KeywordsCELL ADHESION / TTR / fibronectin / FN-plug / NHL / YD-repeat / antibiotic-binding / colicin / nuclease / cell surface receptor / latrophilin / glycoprotein
Function / homology
Function and homology information


positive regulation of filopodium assembly / heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules / : / neuron development / cell adhesion molecule binding / filopodium / axon guidance / cell-cell adhesion / PML body / cell-cell junction ...positive regulation of filopodium assembly / heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules / : / neuron development / cell adhesion molecule binding / filopodium / axon guidance / cell-cell adhesion / PML body / cell-cell junction / cell junction / growth cone / postsynaptic membrane / dendritic spine / neuron projection / protein heterodimerization activity / signaling receptor binding / dendrite / 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
Teneurin intracellular, N-terminal / Teneurin Intracellular Region / Teneurin N-terminal domain profile. / Tox-GHH domain / GHH signature containing HNH/Endo VII superfamily nuclease toxin / YD repeat / Rhs repeat-associated core / Carboxypeptidase-like, regulatory domain superfamily / Six-bladed beta-propeller, TolB-like / Quinoprotein alcohol dehydrogenase-like superfamily ...Teneurin intracellular, N-terminal / Teneurin Intracellular Region / Teneurin N-terminal domain profile. / Tox-GHH domain / GHH signature containing HNH/Endo VII superfamily nuclease toxin / YD repeat / Rhs repeat-associated core / Carboxypeptidase-like, regulatory domain superfamily / Six-bladed beta-propeller, TolB-like / Quinoprotein alcohol dehydrogenase-like superfamily / 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
Similarity search - Domain/homology
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.38 Å
AuthorsJackson, V.A. / Carrasquero, M. / Lowe, E.D. / Seiradake, E.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Wellcome Trust202827/Z/16/Z United Kingdom
Medical Research Council (United Kingdom)MR/L018039/1 United Kingdom
CitationJournal: Nat Commun / Year: 2018
Title: Structures of Teneurin adhesion receptors reveal an ancient fold for cell-cell interaction.
Authors: Verity A Jackson / Dimphna H Meijer / Maria Carrasquero / Laura S van Bezouwen / Edward D Lowe / Colin Kleanthous / Bert J C Janssen / Elena Seiradake /
Abstract: Teneurins are ancient cell-cell adhesion receptors that are vital for brain development and synapse organisation. They originated in early metazoan evolution through a horizontal gene transfer event ...Teneurins are ancient cell-cell adhesion receptors that are vital for brain development and synapse organisation. They originated in early metazoan evolution through a horizontal gene transfer event when a bacterial YD-repeat toxin fused to a eukaryotic receptor. We present X-ray crystallography and cryo-EM structures of two Teneurins, revealing a ~200 kDa extracellular super-fold in which eight sub-domains form an intricate structure centred on a spiralling YD-repeat shell. An alternatively spliced loop, which is implicated in homophilic Teneurin interaction and specificity, is exposed and thus poised for interaction. The N-terminal side of the shell is 'plugged' via a fibronectin-plug domain combination, which defines a new class of YD proteins. Unexpectedly, we find that these proteins are widespread amongst modern bacteria, suggesting early metazoan receptor evolution from a distinct class of proteins, which today includes both bacterial proteins and eukaryotic Teneurins.
History
DepositionDec 18, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 28, 2018Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2019Group: Data collection / Derived calculations / Other
Category: diffrn_source / pdbx_database_status ...diffrn_source / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop
Item: _diffrn_source.pdbx_synchrotron_site / _pdbx_database_status.process_site
Revision 1.2Jul 10, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
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 / _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_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: Teneurin-2
C: Teneurin-2
D: Teneurin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)853,68048
Polymers835,1794
Non-polymers18,50144
Water3,297183
1
A: Teneurin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)213,42012
Polymers208,7951
Non-polymers4,62511
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Teneurin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)213,42012
Polymers208,7951
Non-polymers4,62511
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Teneurin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)213,42012
Polymers208,7951
Non-polymers4,62511
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Teneurin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)213,42012
Polymers208,7951
Non-polymers4,62511
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)88.560, 452.560, 146.360
Angle α, β, γ (deg.)90.00, 95.12, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 208794.688 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Gene: TENM2, ODZ2, TNM2 / Plasmid: pHLSec / Cell (production host): HEK293T / Production host: Homo sapiens (human) / References: UniProt: Q9DER5
#2: 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.: 4
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
#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.: 20
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: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 20
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
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 183 / Source method: isolated from a natural source / Formula: H2O

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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: 3.5 Å3/Da / Density % sol: 64.83 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion / pH: 8.5
Details: 0.1 M Tris (base)/Bicine (pH 8.5), 20% v/v glycerol, 10% w/v PEG4K, 30 mM di-ethyleneglycol, 30 mM tri-ethyleneglycol, 30 mM tetraethyleneglycol, and 30 mM pentaethyleneglycol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.976 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 6, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 2.38→90.51 Å / Num. obs: 439054 / % possible obs: 96.3 % / Redundancy: 5.6 % / Biso Wilson estimate: 54.02 Å2 / CC1/2: 0.99 / Rrim(I) all: 0.25 / Net I/σ(I): 4.69
Reflection shellResolution: 2.38→2.44 Å / Redundancy: 1.8 % / Mean I/σ(I) obs: 0.39 / Num. unique obs: 29248 / CC1/2: 0.315 / % possible all: 86.8

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 2.38→89.38 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.922 / SU R Cruickshank DPI: 0.303 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.279 / SU Rfree Blow DPI: 0.208 / SU Rfree Cruickshank DPI: 0.218
RfactorNum. reflection% reflectionSelection details
Rfree0.242 21455 4.99 %RANDOM
Rwork0.225 ---
obs0.226 429571 94.3 %-
Displacement parametersBiso mean: 76.85 Å2
Baniso -1Baniso -2Baniso -3
1--5.8554 Å20 Å2-0.9532 Å2
2--8.5928 Å20 Å2
3----2.7374 Å2
Refine analyzeLuzzati coordinate error obs: 0.46 Å
Refinement stepCycle: 1 / Resolution: 2.38→89.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms58012 0 1216 183 59411
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.00760644HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.9982420HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d21156SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes10280HARMONIC5
X-RAY DIFFRACTIONt_it60644HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.35
X-RAY DIFFRACTIONt_other_torsion18.34
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion8168SEMIHARMONIC5
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_contact62202SEMIHARMONIC4
LS refinement shellResolution: 2.38→2.44 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.3191 1318 4.91 %
Rwork0.3066 25518 -
all0.3073 26836 -
obs--79.73 %
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)
10.27380.29490.0182.6393-0.24910.48120.04-0.06260.15310.4913-0.09180.1471-0.11330.02230.05180.1384-0.0739-0.1204-0.00040.01210.12-20.8857-61.1685-66.9857
20.3075-0.27920.07021.7374-0.23490.3492-0.03470.0095-0.01940.1796-0.042-0.26740.11460.02020.07670.32090.0933-0.0799-0.0084-0.0025-0.0213-15.09-165.603-54.6256
30.16570.0012-0.06410.4401-0.09820.1424-0.0126-0.0150.09520.02170.02170.022-0.00790.0017-0.0092-0.0063-0.0272-0.1222-0.04250.03840.0206-58.1069-60.9673-139.2753
40.3105-0.530.17172.3412-0.48240.1211-0.1065-0.0406-0.17530.37240.17650.54180-0.0462-0.070.23130.10060.0695-0.01690.01980.0487-51.5647-165.294-127.0105
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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