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- PDB-8g7d: Cryo-EM structure of full length Neuroligin-2 from Mouse -

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Basic information

Entry
Database: PDB / ID: 8g7d
TitleCryo-EM structure of full length Neuroligin-2 from Mouse
ComponentsNeuroligin-1,Neuroligin-2
KeywordsMEMBRANE PROTEIN / Neuroligin-2
Function / homology
Function and homology information


neurexin clustering involved in presynaptic membrane assembly / cell-cell adhesion involved in synapse maturation / cytoskeletal matrix organization at active zone / positive regulation of synaptic vesicle exocytosis / positive regulation of circadian sleep/wake cycle, wakefulness / negative regulation of dendritic spine morphogenesis / Neurexins and neuroligins / protein complex involved in cell-cell adhesion / positive regulation of neuromuscular synaptic transmission / neuron to neuron synapse ...neurexin clustering involved in presynaptic membrane assembly / cell-cell adhesion involved in synapse maturation / cytoskeletal matrix organization at active zone / positive regulation of synaptic vesicle exocytosis / positive regulation of circadian sleep/wake cycle, wakefulness / negative regulation of dendritic spine morphogenesis / Neurexins and neuroligins / protein complex involved in cell-cell adhesion / positive regulation of neuromuscular synaptic transmission / neuron to neuron synapse / jump response / neurotransmitter-gated ion channel clustering / positive regulation of t-SNARE clustering / postsynaptic specialization assembly / gephyrin clustering involved in postsynaptic density assembly / terminal button organization / postsynaptic density protein 95 clustering / positive regulation of synaptic vesicle clustering / postsynaptic membrane assembly / excitatory synapse assembly / synapse maturation / presynaptic membrane assembly / neurexin family protein binding / maintenance of synapse structure / synaptic vesicle targeting / synaptic vesicle clustering / presynapse assembly / synaptic membrane adhesion / thigmotaxis / receptor localization to synapse / filopodium tip / neuron cell-cell adhesion / insulin metabolic process / regulation of respiratory gaseous exchange by nervous system process / NMDA glutamate receptor clustering / inhibitory synapse / ribbon synapse / positive regulation of synaptic vesicle endocytosis / calcium-dependent cell-cell adhesion / regulation of postsynaptic density assembly / AMPA glutamate receptor clustering / protein localization to synapse / dopaminergic synapse / positive regulation of inhibitory postsynaptic potential / glycinergic synapse / inhibitory synapse assembly / AMPA selective glutamate receptor signaling pathway / protein localization to cell surface / positive regulation of synapse assembly / NMDA selective glutamate receptor signaling pathway / heterophilic cell-cell adhesion / regulation of neuron differentiation / positive regulation of filopodium assembly / postsynaptic specialization membrane / neuromuscular process controlling balance / positive regulation of protein localization to synapse / synaptic transmission, GABAergic / positive regulation of dendritic spine development / locomotory exploration behavior / excitatory synapse / social behavior / positive regulation of excitatory postsynaptic potential / regulation of presynapse assembly / synaptic cleft / positive regulation of synaptic transmission, glutamatergic / synapse assembly / cell adhesion molecule binding / neuron projection morphogenesis / sensory perception of pain / dendritic shaft / positive regulation of synaptic transmission, GABAergic / neuromuscular junction / establishment of protein localization / positive regulation of neuron projection development / synapse organization / positive regulation of insulin secretion / modulation of chemical synaptic transmission / GABA-ergic synapse / rhythmic process / nervous system development / presynapse / presynaptic membrane / dendritic spine / postsynaptic membrane / receptor complex / postsynaptic density / axon / external side of plasma membrane / positive regulation of cell population proliferation / dendrite / synapse / glutamatergic synapse / cell surface / Golgi apparatus / 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
Similarity search - Domain/homology
Neuroligin-2 / Neuroligin-1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.28 Å
AuthorsBoyd, R. / Wang, W.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)1R25Gm146860 United States
McKnight Foundation2022 Scholar Award United States
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 16, 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-1,Neuroligin-2
B: Neuroligin-1,Neuroligin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)191,3386
Polymers190,4542
Non-polymers8854
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-1,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: Nlgn1, Kiaa1070, Nlgn2, Kiaa1366 / Production host: Homo sapiens (human) / References: UniProt: Q99K10, UniProt: Q69ZK9
#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.: 4 / 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
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 / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
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.: 5.2 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: 3000 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: 4989
Image scansWidth: 5760 / Height: 4092

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Processing

EM software
IDNameVersionCategory
1RELION3.1particle selection
2SerialEMimage acquisition
4CTFFIND4CTF correction
7UCSF Chimera1.16model fitting
9RELION3.1initial Euler assignment
10cryoSPARC3final Euler assignment
11cryoSPARC3classification
12cryoSPARC33D reconstruction
13PHENIX1model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 674761
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.28 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 77577 / 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_d0.0038577
ELECTRON MICROSCOPYf_angle_d0.50111706
ELECTRON MICROSCOPYf_dihedral_angle_d4.1921189
ELECTRON MICROSCOPYf_chiral_restr0.041286
ELECTRON MICROSCOPYf_plane_restr0.0041528

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