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- PDB-7cee: Crystal structure of mouse neuroligin-3 -

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Basic information

Entry
Database: PDB / ID: 7cee
TitleCrystal structure of mouse neuroligin-3
ComponentsNeuroligin-3NLGN3
KeywordsCELL ADHESION / synapse organization / trans-synaptic complex / esterase domain
Function / homology
Function and homology information


rhythmic synaptic transmission / Neurexins and neuroligins / postsynaptic specialization assembly / negative regulation of dendritic spine morphogenesis / postsynaptic membrane assembly / regulation of terminal button organization / positive regulation of synaptic vesicle clustering / circadian sleep/wake cycle / presynaptic membrane assembly / positive regulation of inhibitory postsynaptic potential ...rhythmic synaptic transmission / Neurexins and neuroligins / postsynaptic specialization assembly / negative regulation of dendritic spine morphogenesis / postsynaptic membrane assembly / regulation of terminal button organization / positive regulation of synaptic vesicle clustering / circadian sleep/wake cycle / presynaptic membrane assembly / positive regulation of inhibitory postsynaptic potential / inhibitory synapse / neuron cell-cell adhesion / regulation of respiratory gaseous exchange by nervous system process / neurexin family protein binding / negative regulation of excitatory postsynaptic potential / vocalization behavior / regulation of dendritic spine morphogenesis / regulation of AMPA receptor activity / postsynaptic specialization membrane / inhibitory postsynaptic potential / axon extension / positive regulation of synapse assembly / regulation of long-term synaptic potentiation / positive regulation of AMPA receptor activity / positive regulation of protein localization to synapse / adult behavior / positive regulation of dendritic spine development / oligodendrocyte differentiation / regulation of NMDA receptor activity / social behavior / positive regulation of excitatory postsynaptic potential / excitatory synapse / synaptic vesicle endocytosis / endocytic vesicle / GABA-ergic synapse / prepulse inhibition / regulation of synaptic transmission, glutamatergic / synapse assembly / excitatory postsynaptic potential / cell adhesion molecule binding / positive regulation of synaptic transmission, glutamatergic / receptor-mediated endocytosis / learning / long-term synaptic potentiation / synapse organization / modulation of chemical synaptic transmission / visual learning / presynapse / signaling receptor activity / chemical synaptic transmission / scaffold protein binding / postsynaptic membrane / molecular adaptor activity / neuronal cell body / dendrite / synapse / glutamatergic synapse / cell surface / plasma membrane
Similarity search - Function
Neuroligin-3 / Neuroligin / Carboxylesterase type B, conserved site / Carboxylesterases type-B signature 2. / Carboxylesterase, type B / Carboxylesterase family / Alpha/Beta hydrolase fold
Similarity search - Domain/homology
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.763 Å
AuthorsYamagata, A. / Yoshida, T. / Shiroshima, T. / Maeda, A. / Fukai, S.
Funding support Japan, 4items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)JP16H04749 Japan
Japan Society for the Promotion of Science (JSPS)JP25293057 Japan
Japan Society for the Promotion of Science (JSPS)JP24247014 Japan
Japan Science and TechnologyJPMJCR12M5 Japan
CitationJournal: Nat Commun / Year: 2021
Title: Canonical versus non-canonical transsynaptic signaling of neuroligin 3 tunes development of sociality in mice.
Authors: Yoshida, T. / Yamagata, A. / Imai, A. / Kim, J. / Izumi, H. / Nakashima, S. / Shiroshima, T. / Maeda, A. / Iwasawa-Okamoto, S. / Azechi, K. / Osaka, F. / Saitoh, T. / Maenaka, K. / Shimada, ...Authors: Yoshida, T. / Yamagata, A. / Imai, A. / Kim, J. / Izumi, H. / Nakashima, S. / Shiroshima, T. / Maeda, A. / Iwasawa-Okamoto, S. / Azechi, K. / Osaka, F. / Saitoh, T. / Maenaka, K. / Shimada, T. / Fukata, Y. / Fukata, M. / Matsumoto, J. / Nishijo, H. / Takao, K. / Tanaka, S. / Okabe, S. / Tabuchi, K. / Uemura, T. / Mishina, M. / Mori, H. / Fukai, S.
History
DepositionJun 23, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 24, 2021Provider: repository / Type: Initial release
Revision 1.1Apr 7, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 29, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _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-3
B: Neuroligin-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)146,8706
Polymers145,9852
Non-polymers8854
Water1,06359
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2570 Å2
ΔGint-4 kcal/mol
Surface area40630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.842, 167.142, 177.950
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A and segid A
21chain B and segid B

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111chain A and segid AA0
211chain B and segid BB0

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Components

#1: Protein Neuroligin-3 / NLGN3 / Gliotactin homolog


Mass: 72992.523 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Nlgn3 / Cell line (production host): HEK293F / Production host: Homo sapiens (human) / References: UniProt: Q8BYM5
#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 / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6 / Feature type: SUBJECT OF INVESTIGATION
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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 59 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 3.35 Å3/Da / Density % sol: 63.32 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 15% PEG 3350, 0.2 M ammonium chloride, 0.1 M MES-Na

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jun 23, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.76→50 Å / Num. obs: 50446 / % possible obs: 99.1 % / Redundancy: 7.7 % / Biso Wilson estimate: 55.71 Å2 / Rmerge(I) obs: 0.111 / Rpim(I) all: 0.037 / Rrim(I) all: 0.117 / Χ2: 0.777 / Net I/σ(I): 4.8 / Num. measured all: 388970
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.76-2.814.80.39824430.5180.190.4440.34298.7
2.81-2.864.70.38124890.6360.1790.4240.36997.6
2.86-2.9150.35624290.7350.1630.3940.37298.3
2.91-2.975.10.34324700.7530.1540.3790.39898.1
2.97-3.045.30.31724500.8270.140.3490.39898
3.04-3.115.20.29524870.8620.130.3250.41798.3
3.11-3.195.60.27124590.9170.1140.2950.42998.3
3.19-3.276.50.24224850.9580.0930.2610.50299.2
3.27-3.376.90.21925000.9750.0810.2340.5699.1
3.37-3.487.20.19825210.9790.0730.2120.56799.4
3.48-3.67.70.17624900.9850.0610.1870.70299.2
3.6-3.757.90.15925090.9890.0540.1690.899.5
3.75-3.927.90.14325320.990.050.1520.84599.3
3.92-4.129.60.13325610.9930.0420.140.94999.9
4.12-4.3810.20.11525330.9960.0350.121.03499.7
4.38-4.7210.50.10225550.9960.0310.1071.16699.9
4.72-5.199.80.09825470.9960.0310.1031.04899.7
5.19-5.94110.09226010.9970.0280.0960.93299.9
5.94-7.4810.70.07826130.9970.0240.0820.88199.7
7.48-5011.40.05427720.9980.0160.0560.96199.7

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.9_1692refinement
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3BIX

3bix


Resolution: 2.763→49.664 Å / SU ML: 0.42 / Cross valid method: THROUGHOUT / σ(F): 1.43 / Phase error: 28.76 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2514 2501 4.96 %
Rwork0.2175 47875 -
obs0.2192 50376 98.28 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 189.63 Å2 / Biso mean: 70.8628 Å2 / Biso min: 41.76 Å2
Refinement stepCycle: final / Resolution: 2.763→49.664 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8374 0 56 59 8489
Biso mean--128.24 59.42 -
Num. residues----1067
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0038692
X-RAY DIFFRACTIONf_angle_d0.87111878
X-RAY DIFFRACTIONf_chiral_restr0.0451297
X-RAY DIFFRACTIONf_plane_restr0.0041547
X-RAY DIFFRACTIONf_dihedral_angle_d13.7923106
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A5038X-RAY DIFFRACTION4.55TORSIONAL
12B5038X-RAY DIFFRACTION4.55TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.763-2.8160.38771170.379220184
2.816-2.87350.40441510.3663264598
2.8735-2.93590.38821320.3496258198
2.9359-3.00420.391450.3299262198
3.0042-3.07930.36081420.3174261298
3.0793-3.16260.32421450.2927262098
3.1626-3.25560.29021220.2699265099
3.2556-3.36070.29991100.2415268599
3.3607-3.48080.25651180.2356269999
3.4808-3.62010.25961110.2317269199
3.6201-3.78480.28851340.2167267399
3.7848-3.98430.26811700.2042265299
3.9843-4.23380.22191530.18232685100
4.2338-4.56040.21341500.16642708100
4.5604-5.0190.19311340.16092735100
5.019-5.74430.21751330.16992756100
5.7443-7.23370.18391720.18882762100
7.2337-49.6640.20361620.18372899100
Refinement TLS params.Method: refined / Origin x: 41.5403 Å / Origin y: 13.8112 Å / Origin z: -10.5651 Å
111213212223313233
T0.56 Å20.0115 Å2-0.048 Å2-0.5819 Å2-0.0504 Å2--0.5394 Å2
L1.5988 °2-0.0363 °2-1.2903 °2-0.0812 °20.1352 °2--1.1163 °2
S0.0287 Å °0.1898 Å °0.0452 Å °-0.063 Å °-0.0066 Å °0.0001 Å °-0.0314 Å °-0.0852 Å °-0.0001 Å °
Refinement TLS groupSelection details: all

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