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- PDB-5oj6: Crystal structure of the chicken MDGA1 ectodomain in complex with... -

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Basic information

Entry
Database: PDB / ID: 5oj6
TitleCrystal structure of the chicken MDGA1 ectodomain in complex with the human neuroligin 1 (NL1(-A-B)) cholinesterase domain.
Components
  • MAM domain-containing glycosylphosphatidylinositol anchor protein 1
  • Neuroligin-1
KeywordsCELL ADHESION / neuroligin-neurexin / synapse formation / austism spectrum disorders (ASDs) / synaptic transmission
Function / homology
Function and homology information


neurexin clustering involved in presynaptic membrane assembly / asymmetric, glutamatergic, excitatory synapse / cytoskeletal matrix organization at active zone / cell-cell adhesion involved in synapse maturation / positive regulation of circadian sleep/wake cycle, wakefulness / protein complex involved in cell-cell adhesion / positive regulation of neuromuscular synaptic transmission / terminal button organization / neuron to neuron synapse / positive regulation of synaptic vesicle exocytosis ...neurexin clustering involved in presynaptic membrane assembly / asymmetric, glutamatergic, excitatory synapse / cytoskeletal matrix organization at active zone / cell-cell adhesion involved in synapse maturation / positive regulation of circadian sleep/wake cycle, wakefulness / protein complex involved in cell-cell adhesion / positive regulation of neuromuscular synaptic transmission / terminal button organization / neuron to neuron synapse / positive regulation of synaptic vesicle exocytosis / neuronal signal transduction / excitatory synapse assembly / postsynaptic density protein 95 clustering / negative regulation of dendritic spine morphogenesis / postsynaptic membrane assembly / synapse maturation / presynaptic membrane assembly / maintenance of synapse structure / synaptic vesicle targeting / inhibitory synapse / synaptic vesicle clustering / neuron cell-cell adhesion / presynapse assembly / neurexin family protein binding / receptor localization to synapse / filopodium tip / protein localization to synapse / NMDA glutamate receptor clustering / neuron projection arborization / positive regulation of synaptic vesicle endocytosis / calcium-dependent cell-cell adhesion via plasma membrane cell adhesion molecules / regulation of AMPA receptor activity / AMPA glutamate receptor clustering / postsynaptic specialization membrane / Neurexins and neuroligins / positive regulation of synapse assembly / positive regulation of ruffle assembly / regulation of NMDA receptor activity / positive regulation of intracellular signal transduction / positive regulation of filopodium assembly / heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules / regulation of neuron differentiation / positive regulation of dendritic spine development / positive regulation of excitatory postsynaptic potential / synaptic vesicle endocytosis / excitatory synapse / GABA-ergic synapse / protein targeting / synaptic cleft / cell adhesion molecule binding / synapse assembly / cellular response to calcium ion / positive regulation of synaptic transmission, glutamatergic / neuron projection morphogenesis / PDZ domain binding / positive regulation of synaptic transmission, GABAergic / neuron migration / modulation of chemical synaptic transmission / neuromuscular junction / establishment of protein localization / positive regulation of neuron projection development / neuron projection development / rhythmic process / presynapse / signaling receptor activity / nervous system development / amyloid-beta binding / scaffold protein binding / postsynapse / chemical synaptic transmission / postsynaptic membrane / dendritic spine / postsynaptic density / receptor complex / glutamatergic synapse / synapse / dendrite / Golgi apparatus / cell surface / membrane / identical protein binding / plasma membrane
Similarity search - Function
Neuroligin / Domain in meprin, A5, receptor protein tyrosine phosphatase mu (and others) / MAM domain, meprin/A5/mu / MAM domain / MAM domain profile. / Carboxylesterase type B, conserved site / Carboxylesterases type-B signature 2. / Carboxylesterase, type B / Carboxylesterase family / Immunoglobulin domain ...Neuroligin / Domain in meprin, A5, receptor protein tyrosine phosphatase mu (and others) / MAM domain, meprin/A5/mu / MAM domain / MAM domain profile. / Carboxylesterase type B, conserved site / Carboxylesterases type-B signature 2. / Carboxylesterase, type B / Carboxylesterase family / Immunoglobulin domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / Alpha/Beta hydrolase fold, catalytic domain / Concanavalin A-like lectin/glucanase domain superfamily / Immunoglobulin subtype / Immunoglobulin / Alpha/Beta hydrolase fold / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
MAM domain-containing glycosylphosphatidylinositol anchor protein 1 / Neuroligin-1
Similarity search - Component
Biological speciesHomo sapiens (human)
Gallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 Å
AuthorsElegheert, J. / Clayton, A.J. / Aricescu, A.R.
Funding support United Kingdom, Canada, United States, 13items
OrganizationGrant numberCountry
Medical Research Council (United Kingdom)G0700232 United Kingdom
Medical Research Council (United Kingdom)L009609 United Kingdom
Medical Research Council (United Kingdom)MC_UP_1201/15 United Kingdom
CIHRFDN- 143206 Canada
CIHRNDD-144222 Canada
National Institutes of HealthR00 DC013805 United States
European Molecular Biology OrganizationALTF 1116-2012 United Kingdom
Marie CurieFP7-328531 United Kingdom
Cancer Research UKC375/A10976 United Kingdom
National Institutes of HealthMH085926 United States
National Institutes of HealthGM105730 United States
National Institutes of HealthF32NS093753 United States
Wellcome Trust090532/Z/09/Z United Kingdom
CitationJournal: Neuron / Year: 2017
Title: Structural Mechanism for Modulation of Synaptic Neuroligin-Neurexin Signaling by MDGA Proteins.
Authors: Elegheert, J. / Cvetkovska, V. / Clayton, A.J. / Heroven, C. / Vennekens, K.M. / Smukowski, S.N. / Regan, M.C. / Jia, W. / Smith, A.C. / Furukawa, H. / Savas, J.N. / de Wit, J. / Begbie, J. ...Authors: Elegheert, J. / Cvetkovska, V. / Clayton, A.J. / Heroven, C. / Vennekens, K.M. / Smukowski, S.N. / Regan, M.C. / Jia, W. / Smith, A.C. / Furukawa, H. / Savas, J.N. / de Wit, J. / Begbie, J. / Craig, A.M. / Aricescu, A.R.
History
DepositionJul 20, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 23, 2017Provider: repository / Type: Initial release
Revision 1.1Aug 30, 2017Group: Database references / Category: citation
Item: _citation.journal_id_ISSN / _citation.page_last ..._citation.journal_id_ISSN / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Sep 20, 2017Group: Database references / Category: struct_ref_seq_dif / Item: _struct_ref_seq_dif.details
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / 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_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_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 / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Neuroligin-1
B: MAM domain-containing glycosylphosphatidylinositol anchor protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)168,89711
Polymers166,5412
Non-polymers2,3569
Water0
1
A: Neuroligin-1
B: MAM domain-containing glycosylphosphatidylinositol anchor protein 1
hetero molecules

A: Neuroligin-1
B: MAM domain-containing glycosylphosphatidylinositol anchor protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)337,79522
Polymers333,0824
Non-polymers4,71218
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_675-x+1,-y+2,z1
Buried area14960 Å2
ΔGint37 kcal/mol
Surface area111120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)109.420, 184.140, 96.470
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Neuroligin-1 /


Mass: 64397.254 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NLGN1, KIAA1070 / Plasmid: pHLsec / Cell line (production host): HEK293S GnTI-/- / Production host: Homo sapiens (human) / References: UniProt: Q8N2Q7
#2: Protein MAM domain-containing glycosylphosphatidylinositol anchor protein 1


Mass: 102143.867 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Gene: MDGA1 / Plasmid: pHLsec / Cell line (production host): HEK293S GnTI-/- / Production host: Homo sapiens (human) / References: UniProt: Q0WYX8
#3: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-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.: 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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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.92 Å3/Da / Density % sol: 57.84 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1M Na.HEPES pH 7.0, 7.5% w/v PEG8000

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 15, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 3.3→92.07 Å / Num. obs: 29576 / % possible obs: 98.7 % / Redundancy: 4.5 % / CC1/2: 0.999 / Net I/σ(I): 15.6
Reflection shellResolution: 3.3→3.39 Å / Redundancy: 4.6 % / Mean I/σ(I) obs: 1.6 / Num. unique obs: 2080 / CC1/2: 0.638 / Rrim(I) all: 1.063 / % possible all: 95.4

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Processing

Software
NameVersionClassification
PHENIX(dev_2044:)refinement
xia2data reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5OJ2

5oj2


Resolution: 3.3→72.362 Å / SU ML: 0.47 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.59
RfactorNum. reflection% reflection
Rfree0.2771 1474 4.98 %
Rwork0.2269 --
obs0.2294 29572 98.41 %
Solvent computationShrinkage radii: 0.8 Å / VDW probe radii: 1 Å
Refinement stepCycle: LAST / Resolution: 3.3→72.362 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9659 0 151 0 9810
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00310061
X-RAY DIFFRACTIONf_angle_d0.93913737
X-RAY DIFFRACTIONf_dihedral_angle_d11.4876051
X-RAY DIFFRACTIONf_chiral_restr0.0411569
X-RAY DIFFRACTIONf_plane_restr0.0041774
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.3001-3.40660.38381180.31812473X-RAY DIFFRACTION96
3.4066-3.52840.36571380.29062527X-RAY DIFFRACTION100
3.5284-3.66960.34261350.26632535X-RAY DIFFRACTION99
3.6696-3.83660.29061470.25462519X-RAY DIFFRACTION99
3.8366-4.03890.30151510.22412534X-RAY DIFFRACTION99
4.0389-4.29190.26161210.19942545X-RAY DIFFRACTION99
4.2919-4.62330.20841190.1892515X-RAY DIFFRACTION97
4.6233-5.08840.25461300.18372557X-RAY DIFFRACTION98
5.0884-5.82440.29721420.20352595X-RAY DIFFRACTION100
5.8244-7.33710.25791420.24482620X-RAY DIFFRACTION99
7.3371-72.37950.26211310.23522678X-RAY DIFFRACTION97

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