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- EMDB-29811: Cryo-EM structure of full length Neuroligin-2 from Mouse -

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Basic information

Entry
Database: EMDB / ID: EMD-29811
TitleCryo-EM structure of full length Neuroligin-2 from Mouse
Map data
Sample
  • Complex: Neuroligin-2 Dimer
    • Protein or peptide: Neuroligin-1,Neuroligin-2
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsNeuroligin-2 / Membrane protein
Function / homology
Function and homology information


regulation of presynapse organization / neurexin clustering involved in presynaptic membrane assembly / cell-cell adhesion involved in synapse maturation / positive regulation of presynaptic active zone assembly / cytoskeletal matrix organization at active zone / positive regulation of circadian sleep/wake cycle, wakefulness / positive regulation of neuromuscular synaptic transmission / Neurexins and neuroligins / jump response / neurotransmitter-gated ion channel clustering ...regulation of presynapse organization / neurexin clustering involved in presynaptic membrane assembly / cell-cell adhesion involved in synapse maturation / positive regulation of presynaptic active zone assembly / cytoskeletal matrix organization at active zone / positive regulation of circadian sleep/wake cycle, wakefulness / positive regulation of neuromuscular synaptic transmission / Neurexins and neuroligins / jump response / neurotransmitter-gated ion channel clustering / positive regulation of t-SNARE clustering / neuron to neuron synapse / postsynaptic specialization assembly / positive regulation of synaptic vesicle exocytosis / negative regulation of dendritic spine morphogenesis / terminal button organization / gephyrin clustering involved in postsynaptic density assembly / postsynaptic density protein 95 clustering / regulation of respiratory gaseous exchange by nervous system process / synapse maturation / postsynaptic membrane assembly / excitatory synapse assembly / positive regulation of synaptic vesicle clustering / presynaptic membrane assembly / neurexin family protein binding / maintenance of synapse structure / : / synaptic vesicle clustering / thigmotaxis / synaptic membrane adhesion / presynapse assembly / receptor localization to synapse / insulin metabolic process / NMDA glutamate receptor clustering / filopodium tip / cell adhesion mediator activity / ribbon synapse / calcium-dependent cell-cell adhesion / positive regulation of synaptic transmission, GABAergic / positive regulation of synaptic vesicle endocytosis / regulation of postsynaptic density assembly / inhibitory synapse / neuron cell-cell adhesion / neuron projection arborization / protein localization to synapse / dopaminergic synapse / neuromuscular process controlling balance / positive regulation of synapse assembly / protein localization to cell surface / glycinergic synapse / AMPA selective glutamate receptor signaling pathway / positive regulation of filopodium assembly / inhibitory synapse assembly / heterophilic cell-cell adhesion / positive regulation of inhibitory postsynaptic potential / positive regulation of ruffle assembly / NMDA selective glutamate receptor signaling pathway / regulation of NMDA receptor activity / regulation of neuron differentiation / synaptic transmission, GABAergic / postsynaptic specialization membrane / positive regulation of protein localization to synapse / positive regulation of dendritic spine development / synaptic vesicle transport / AMPA glutamate receptor clustering / locomotory exploration behavior / positive regulation of intracellular signal transduction / social behavior / protein targeting / regulation of presynapse assembly / synaptic cleft / neuron projection morphogenesis / positive regulation of synaptic transmission, glutamatergic / sensory perception of pain / synapse assembly / cell adhesion molecule binding / cellular response to calcium ion / excitatory synapse / positive regulation of excitatory postsynaptic potential / dendritic shaft / PDZ domain binding / establishment of protein localization / neuromuscular junction / positive regulation of neuron projection development / positive regulation of insulin secretion / synapse organization / modulation of chemical synaptic transmission / long-term synaptic potentiation / GABA-ergic synapse / neuron projection development / rhythmic process / nervous system development / presynapse / signaling receptor activity / presynaptic membrane / scaffold protein binding / dendritic spine / signaling receptor complex / postsynaptic membrane / postsynaptic density
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)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.28 Å
AuthorsBoyd R / Wang W
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)1R25Gm146860 United States
McKnight Foundation2022 Scholar Award United States
CitationJournal: Sci Adv / Year: 2026
Title: Weaker neuroligin 2-neurexin β1 interaction tethers membranes and recruits gephyrin at membrane junctions through clustering.
Authors: Robbie Boyd / Khuloud Jaqaman / Weiwei Wang /
Abstract: Single-pass transmembrane proteins neuroligin (NL) and neurexin (NRX) constitute a pair of synaptic adhesion molecules that are essential for the formation of functional synapses. Binding affinities ...Single-pass transmembrane proteins neuroligin (NL) and neurexin (NRX) constitute a pair of synaptic adhesion molecules that are essential for the formation of functional synapses. Binding affinities vary by ~1000-fold between combinations of NL and NRX subtypes, which contribute to chemical and spatial specificities. Among major NL-NRX subtypes, NL2 and NRXβ1 have the lowest affinity. Here, we report structures of NL2 in complex with NRXβ1 in several conformations, along with NL2 alone. We identify mechanisms underlying the modulation of NL-NRX affinities and how the weaker NL2-NRXβ1 interaction alone is capable of tethering lipid membranes. We further show that NL2 and NRXβ1 cluster at intercellular junctions and recruit the master postsynaptic scaffolding protein gephyrin, which further clusters neurotransmitter receptors. These findings suggest a dual role of the NL2-NRXβ1 interaction-both as mechanical tether and as signaling receptor-to ensure correct spatial and chemical coordination between two cells to generate functional synapses.
History
DepositionFeb 16, 2023-
Header (metadata) releaseMay 14, 2025-
Map releaseMay 14, 2025-
UpdateApr 8, 2026-
Current statusApr 8, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_29811.png

Downloads & links

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Map

FileDownload / File: emd_29811.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.84 Å/pix.
x 320 pix.
= 269.44 Å		0.84 Å/pix.
x 320 pix.
= 269.44 Å		0.84 Å/pix.
x 320 pix.
= 269.44 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.842 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.25
Minimum - Maximum-1.9932051 - 3.6054566
Average (Standard dev.)0.0054802955 (±0.07772256)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 269.44 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_29811_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_29811_half_map_2.map
Projections & Slices
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Histogram

Histogram (log scale)

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Sample components

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Entire : Neuroligin-2 Dimer

EntireName: Neuroligin-2 Dimer
Components
  • Complex: Neuroligin-2 Dimer
    • Protein or peptide: Neuroligin-1,Neuroligin-2
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: Neuroligin-2 Dimer

SupramoleculeName: Neuroligin-2 Dimer / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Mus musculus (house mouse)

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Macromolecule #1: Neuroligin-1,Neuroligin-2

MacromoleculeName: Neuroligin-1,Neuroligin-2 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 95.226797 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MALPRCMWPN YVWRAMMACV VHRGSGAPLT LCLLGCLLQT FHVLSQKYPY DVPDYAQRGG GGPGGGAPGG PGLGLGSLGE ERFPVVNTA YGRVRGVRRE LNNEILGPVV QFLGVPYATP PLGARRFQPP EAPASWPGVR NATTLPPACP QNLHGALPAI M LPVWFTDN ...String:
MALPRCMWPN YVWRAMMACV VHRGSGAPLT LCLLGCLLQT FHVLSQKYPY DVPDYAQRGG GGPGGGAPGG PGLGLGSLGE ERFPVVNTA YGRVRGVRRE LNNEILGPVV QFLGVPYATP PLGARRFQPP EAPASWPGVR NATTLPPACP QNLHGALPAI M LPVWFTDN LEAAATYVQN QSEDCLYLNL YVPTEDDIRD SGKKPVMLFL HGGSYMEGTG NMFDGSVLAA YGNVIVVTLN YR LGVLGFL STGDQAAKGN YGLLDQIQAL RWLSENIAHF GGDPERITIF GSGAGASCVN LLILSHHSEG LFQKAIAQSG TAI SSWSVN YQPLKYTRLL AAKVGCDRED STEAVECLRR KSSRELVDQD VQPARYHIAF GPVVDGDVVP DDPEILMQQG EFLN YDMLI GVNQGEGLKF VEDSAESEDG VSASAFDFTV SNFVDNLYGY PEGKDVLRET IKFMYTDWAD RDNGEMRRKT LLALF TDHQ WVAPAVATAK LHADYQSPVY FYTFYHHCQA EGRPEWADAA HGDELPYVFG VPMVGATDLF PCNFSKNDVM LSAVVM TYW TNFAKTGDPN QPVPQDTKFI HTKPNRFEEV VWSKFNSKEK QYLHIGLKPR VRDNYRANKV AFWLELVPHL HNLHTEL FT TTTRLPPYAT RWPPRTPGPG TSGTRRPPPP ATLPPESDID LGPRAYDRFP GDSRDYSTEL SVTVAVGASL LFLNILAF A ALYYKRDRRQ ELRCRRLSPP GGSGSGVPGG GPLLPTAGRE LPPEEELVSL QLKRGGGVGA DPAEALRPAC PPDYTLALR RAPDDVPLLA PGALTLLPSG LGPPPPPPPP SLHPFGPFPP PPPTATSHNN TLPHPHSTTR VSNSLEVLFQ

UniProtKB: Neuroligin-1, Neuroligin-2

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Macromolecule #2: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 2 / Number of copies: 4 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration5.2 mg/mL
BufferpH: 7.4
Component:
ConcentrationFormulaName
20.0 mMC8H18N2O4SHEPES
150.0 mMNaClSodium Chloride
1.0 mMMgCl2Magnesium chloride
0.5 mMCaCl2Calcium chloride
0.05 %LMNG
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 400 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 38.0 kPa
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 298 K / Instrument: FEI VITROBOT MARK IV / Details: Blot force 20, blot time 5s, single blot.

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Electron microscopy

MicroscopeFEI TITAN
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Digitization - Dimensions - Width: 5760 pixel / Digitization - Dimensions - Height: 4092 pixel / Number grids imaged: 1 / Number real images: 4989 / Average electron dose: 90.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Calibrated defocus max: 3.0 µm / Calibrated magnification: 105000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 0.0 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 105000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN

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Image processing

Particle selectionNumber selected: 674761
CTF correctionSoftware - Name: CTFFIND (ver. 4) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

3bl8

Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 3.28 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 3) / Number images used: 77577
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3)
Final 3D classificationNumber classes: 3 / Avg.num./class: 40000 / Software - Name: cryoSPARC (ver. 3)

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Atomic model buiding 1

Initial modelPDB ID:

3bl8


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

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

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