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- PDB-5ojk: Crystal structure of the human neuroligin 1 cholinesterase domain... -

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Basic information

Entry
Database: PDB / ID: 5ojk
TitleCrystal structure of the human neuroligin 1 cholinesterase domain containing spliced sequence B (SSB) (NL1(-A+B))
ComponentsNeuroligin-1,Neuroligin-1
KeywordsCELL ADHESION / neuroligin-neurexin / synaptic organizer protein / spliced sequence B
Function / homology
Function and homology information


asymmetric, glutamatergic, excitatory synapse / neurexin clustering involved in presynaptic membrane assembly / cytoskeletal matrix organization at active zone / positive regulation of circadian sleep/wake cycle, wakefulness / protein complex involved in cell-cell adhesion / positive regulation of neuromuscular synaptic transmission / neuronal signal transduction / positive regulation of synaptic vesicle exocytosis / negative regulation of dendritic spine morphogenesis / terminal button organization ...asymmetric, glutamatergic, excitatory synapse / neurexin clustering involved in presynaptic membrane assembly / cytoskeletal matrix organization at active zone / positive regulation of circadian sleep/wake cycle, wakefulness / protein complex involved in cell-cell adhesion / positive regulation of neuromuscular synaptic transmission / neuronal signal transduction / positive regulation of synaptic vesicle exocytosis / negative regulation of dendritic spine morphogenesis / terminal button organization / postsynaptic density protein 95 clustering / postsynaptic membrane assembly / excitatory synapse assembly / presynaptic membrane assembly / neurexin family protein binding / : / synaptic vesicle clustering / presynapse assembly / receptor localization to synapse / cell adhesion mediator activity / neuron cell-cell adhesion / NMDA glutamate receptor clustering / filopodium tip / calcium-dependent cell-cell adhesion / positive regulation of synaptic vesicle endocytosis / protein localization to synapse / neuron projection arborization / AMPA selective glutamate receptor signaling pathway / positive regulation of synapse assembly / NMDA selective glutamate receptor signaling pathway / heterophilic cell-cell adhesion / positive regulation of filopodium assembly / regulation of neuron differentiation / Neurexins and neuroligins / postsynaptic specialization membrane / positive regulation of ruffle assembly / positive regulation of dendritic spine development / AMPA glutamate receptor clustering / positive regulation of intracellular signal transduction / protein targeting / synaptic cleft / neuron projection morphogenesis / positive regulation of synaptic transmission, glutamatergic / synapse assembly / cell adhesion molecule binding / excitatory synapse / cellular response to calcium ion / positive regulation of synaptic transmission, GABAergic / positive regulation of excitatory postsynaptic potential / PDZ domain binding / neuromuscular junction / establishment of protein localization / modulation of chemical synaptic transmission / GABA-ergic synapse / neuron projection development / rhythmic process / nervous system development / amyloid-beta binding / presynapse / signaling receptor activity / scaffold protein binding / dendritic spine / postsynaptic membrane / signaling receptor complex / postsynaptic density / postsynapse / synapse / dendrite / glutamatergic synapse / cell surface / Golgi apparatus / membrane / identical protein binding / plasma membrane
Similarity search - Function
Neuroligin / : / Carboxylesterase type B, conserved site / Carboxylesterases type-B signature 2. / Carboxylesterase, type B / Carboxylesterase family / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
TRIETHYLENE GLYCOL / Neuroligin-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.55 Å
AuthorsElegheert, 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 21, 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 1.2Jan 31, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Jan 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
Revision 1.5Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Neuroligin-1,Neuroligin-1
B: Neuroligin-1,Neuroligin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)132,1628
Polymers131,1192
Non-polymers1,0436
Water1,964109
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3300 Å2
ΔGint13 kcal/mol
Surface area40680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.570, 118.050, 214.340
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121
Components on special symmetry positions
IDModelComponents
11B-852-

HOH

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Components

#1: Protein Neuroligin-1,Neuroligin-1


Mass: 65559.469 Da / Num. of mol.: 2
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: 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.: 2
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
#3: Chemical
ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H14O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 109 / Source method: isolated from a natural source / Formula: H2O
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: 2.39 Å3/Da / Density % sol: 48.57 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2M KSCN, 0.1M Bis-tris propane pH 8.5, 20% w/v PEG3350

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9686 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 26, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9686 Å / Relative weight: 1
ReflectionResolution: 2.55→51.7 Å / Num. obs: 40826 / % possible obs: 97.3 % / Redundancy: 7.5 % / CC1/2: 0.999 / Rpim(I) all: 0.068 / Net I/σ(I): 8.4
Reflection shellResolution: 2.55→2.62 Å / Redundancy: 7.3 % / Mean I/σ(I) obs: 1.5 / Num. unique obs: 3077 / CC1/2: 0.541 / Rpim(I) all: 0.484 / % possible all: 98.8

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Processing

Software
NameVersionClassification
PHENIX(dev_2044)refinement
xia2data reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3BIX

3bix


Resolution: 2.55→51.7 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 31.46
RfactorNum. reflection% reflection
Rfree0.278 2005 4.92 %
Rwork0.236 --
obs0.2381 40739 96.71 %
Solvent computationShrinkage radii: 0.7 Å / VDW probe radii: 0.9 Å
Refinement stepCycle: LAST / Resolution: 2.55→51.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8387 0 68 109 8564
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0038714
X-RAY DIFFRACTIONf_angle_d0.78211891
X-RAY DIFFRACTIONf_dihedral_angle_d10.5095109
X-RAY DIFFRACTIONf_chiral_restr0.0361296
X-RAY DIFFRACTIONf_plane_restr0.0031549
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5501-2.61380.36581400.33312820X-RAY DIFFRACTION98
2.6138-2.68450.34381470.32092712X-RAY DIFFRACTION98
2.6845-2.76350.34361440.29392762X-RAY DIFFRACTION98
2.7635-2.85270.31331480.27942735X-RAY DIFFRACTION98
2.8527-2.95460.33561390.25732773X-RAY DIFFRACTION97
2.9546-3.07290.29651460.25552767X-RAY DIFFRACTION98
3.0729-3.21270.31511410.25482749X-RAY DIFFRACTION97
3.2127-3.38210.29431350.24372765X-RAY DIFFRACTION97
3.3821-3.59390.25921520.24252746X-RAY DIFFRACTION97
3.5939-3.87130.28561360.21832779X-RAY DIFFRACTION97
3.8713-4.26080.26051350.20572745X-RAY DIFFRACTION96
4.2608-4.87690.21521400.19212767X-RAY DIFFRACTION95
4.8769-6.14280.24731440.21282788X-RAY DIFFRACTION95
6.1428-51.71260.27181580.23662826X-RAY DIFFRACTION92

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