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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


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 / jump response / neurotransmitter-gated ion channel clustering / positive regulation of t-SNARE clustering / Neurexins and neuroligins / protein complex involved in cell-cell adhesion ...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 / jump response / neurotransmitter-gated ion channel clustering / positive regulation of t-SNARE clustering / Neurexins and neuroligins / protein complex involved in cell-cell adhesion / positive regulation of neuromuscular synaptic transmission / neuron to neuron synapse / gephyrin clustering involved in postsynaptic density assembly / excitatory synapse assembly / terminal button organization / postsynaptic density protein 95 clustering / postsynaptic specialization assembly / negative regulation of dendritic spine morphogenesis / positive regulation of synaptic vesicle clustering / postsynaptic membrane assembly / presynaptic membrane assembly / synapse maturation / maintenance of synapse structure / thigmotaxis / ribbon synapse / synaptic vesicle targeting / synaptic vesicle clustering / neuron cell-cell adhesion / insulin metabolic process / synaptic membrane adhesion / regulation of respiratory gaseous exchange by nervous system process / neurexin family protein binding / inhibitory synapse / receptor localization to synapse / filopodium tip / presynapse assembly / NMDA glutamate receptor clustering / positive regulation of synaptic vesicle endocytosis / calcium-dependent cell-cell adhesion via plasma membrane cell adhesion molecules / protein localization to synapse / regulation of postsynaptic density assembly / dopaminergic synapse / AMPA glutamate receptor clustering / glycinergic synapse / regulation of AMPA receptor activity / positive regulation of inhibitory postsynaptic potential / regulation of NMDA receptor activity / inhibitory synapse assembly / protein localization to cell surface / positive regulation of synapse assembly / heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules / positive regulation of filopodium assembly / regulation of neuron differentiation / 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 / synaptic cleft / synapse assembly / cell adhesion molecule binding / sensory perception of pain / positive regulation of synaptic transmission, glutamatergic / neuron projection morphogenesis / dendritic shaft / positive regulation of synaptic transmission, GABAergic / GABA-ergic synapse / establishment of protein localization / modulation of chemical synaptic transmission / synapse organization / neuromuscular junction / positive regulation of insulin secretion / positive regulation of neuron projection development / 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 / synapse / dendrite / 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)
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: 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, 2023-
Header (metadata) releaseMay 14, 2025-
Map releaseMay 14, 2025-
UpdateMay 14, 2025-
Current statusMay 14, 2025Processing 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
AxesZYX

Projections

Slices (1/2)
Density Histograms

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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