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- PDB-8g7z: Cryo-EM structure of full length Neuroligin-2 from Mouse bound to... -

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Basic information

Entry
Database: PDB / ID: 8g7z
TitleCryo-EM structure of full length Neuroligin-2 from Mouse bound to two Neurexin-1 Beta conformation one
Components
  • Neurexin-1
  • Neuroligin-2
KeywordsMEMBRANE PROTEIN / Neuroligin-2 / Neurexin-1 beta
Function / homology
Function and homology information


jump response / neurotransmitter-gated ion channel clustering / positive regulation of t-SNARE clustering / regulation of biological quality / gephyrin clustering involved in postsynaptic density assembly / terminal button organization / postsynaptic density protein 95 clustering / postsynaptic specialization assembly / positive regulation of synaptic vesicle clustering / postsynaptic membrane assembly ...jump response / neurotransmitter-gated ion channel clustering / positive regulation of t-SNARE clustering / regulation of biological quality / gephyrin clustering involved in postsynaptic density assembly / terminal button organization / postsynaptic density protein 95 clustering / postsynaptic specialization assembly / positive regulation of synaptic vesicle clustering / postsynaptic membrane assembly / presynaptic membrane assembly / Neurexins and neuroligins / thigmotaxis / ribbon synapse / neuron cell-cell adhesion / insulin metabolic process / regulation of respiratory gaseous exchange by nervous system process / neurexin family protein binding / inhibitory synapse / presynapse assembly / protein localization to synapse / dopaminergic synapse / cell junction assembly / glycinergic synapse / regulation of AMPA receptor activity / positive regulation of inhibitory postsynaptic potential / inhibitory synapse assembly / protein localization to cell surface / positive regulation of synapse assembly / positive regulation of dendritic spine development / positive regulation of protein localization to synapse / postsynaptic specialization membrane / synaptic transmission, GABAergic / social behavior / locomotory exploration behavior / neuromuscular process controlling balance / excitatory synapse / positive regulation of excitatory postsynaptic potential / regulation of presynapse assembly / synapse assembly / cell adhesion molecule binding / sensory perception of pain / positive regulation of synaptic transmission, glutamatergic / dendritic shaft / positive regulation of synaptic transmission, GABAergic / GABA-ergic synapse / modulation of chemical synaptic transmission / synapse organization / positive regulation of insulin secretion / nervous system development / presynaptic membrane / postsynaptic membrane / cell adhesion / axon / positive regulation of cell population proliferation / synapse / dendrite / glutamatergic synapse / cell surface / identical protein binding / plasma membrane
Similarity search - Function
Neuroligin / Syndecan/Neurexin domain / Syndecan domain / : / Neurexin/syndecan/glycophorin C / putative band 4.1 homologues' binding motif / : / Laminin G domain / Laminin G domain profile. / Laminin G domain ...Neuroligin / Syndecan/Neurexin domain / Syndecan domain / : / Neurexin/syndecan/glycophorin C / putative band 4.1 homologues' binding motif / : / Laminin G domain / Laminin G domain profile. / Laminin G domain / Laminin G domain / Carboxylesterase type B, conserved site / Carboxylesterases type-B signature 2. / Carboxylesterase, type B / Carboxylesterase family / Alpha/Beta hydrolase fold / Concanavalin A-like lectin/glucanase domain superfamily
Similarity search - Domain/homology
Neurexin I / Neuroligin-2
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.22 Å
AuthorsBoyd, R. / Wang, W.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)1R35Gm146860 United States
Other private2022 Scholar Award
CitationJournal: To Be Published
Title: Cryo-EM structure of full length mouse Neuroligin-2 at 3.28 Angstroms resolution
Authors: Boyd, R. / Wang, W.
History
DepositionFeb 17, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 14, 2025Provider: repository / Type: Initial release
Revision 1.0May 14, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0May 14, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0May 14, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0May 14, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0May 14, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Neuroligin-2
B: Neuroligin-2
C: Neurexin-1
D: Neurexin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)292,73212
Polymers291,3244
Non-polymers1,4078
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein Neuroligin-2


Mass: 95226.797 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Nlgn2 / Production host: Homo sapiens (human) / References: UniProt: Q62888
#2: Protein Neurexin-1


Mass: 50435.332 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Nrxn1 / Production host: Homo sapiens (human) / References: UniProt: E0CZA5
#3: 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.: 6 / Source method: obtained synthetically / 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
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Neuroligin 2 Dimer with 2 Neurexin-1 Beta confirmation one
Type: COMPLEX / Entity ID: #1-#2 / Source: RECOMBINANT
Molecular weightValue: 0.18 MDa / Experimental value: NO
Source (natural)Organism: Mus musculus (house mouse)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 7.4
Buffer component
IDConc.NameFormulaBuffer-ID
120 mMHEPESC8H18N2O4S1
2150 mMSodium ChlorideNaCl1
31 mMMagnesium ChlorideMgCl21
40.5 mMCalcium ChlorideCaCl21
50.05 %LMNG1
SpecimenConc.: 6.2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid mesh size: 400 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 298 K / Details: Blot force 20, blot time 5s, single blot

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Electron microscopy imaging

MicroscopyModel: FEI TITAN
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 105000 X / Calibrated magnification: 105000 X / Nominal defocus max: 2500 nm / Nominal defocus min: 1000 nm / Calibrated defocus max: 3600 nm / Cs: 0 mm / C2 aperture diameter: 70 µm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 90 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 6615
Image scansWidth: 5760 / Height: 4092

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Processing

EM softwareName: PHENIX / Version: 1.20.1_4487: / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 2964465
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.22 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 51041 / Algorithm: BACK PROJECTION / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL
Atomic model buildingPDB-ID: 3BL8

3bl8


Accession code: 3BL8 / Source name: PDB / Type: experimental model
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00411371
ELECTRON MICROSCOPYf_angle_d0.56915486
ELECTRON MICROSCOPYf_dihedral_angle_d4.5761585
ELECTRON MICROSCOPYf_chiral_restr0.0471706
ELECTRON MICROSCOPYf_plane_restr0.0042027

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