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- EMDB-29829: Cryo-EM structure of full length Neuroligin-2 from Mouse bound to... -

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Basic information

Entry
Database: EMDB / ID: EMD-29829
TitleCryo-EM structure of full length Neuroligin-2 from Mouse bound to two Neurexin-1 Beta conformation one
Map data
Sample
  • Complex: Neuroligin 2 Dimer with 2 Neurexin-1 Beta confirmation one
    • Protein or peptide: Neuroligin-2
    • Protein or peptide: Neurexin-1
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: CALCIUM ION
KeywordsNeuroligin-2 / membrane protein / 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 / inhibitory synapse assembly / cell junction assembly / regulation of AMPA receptor activity / glycinergic synapse / positive regulation of inhibitory postsynaptic potential / protein localization to cell surface / positive regulation of synapse assembly / postsynaptic specialization membrane / synaptic transmission, GABAergic / positive regulation of protein localization to synapse / positive regulation of dendritic spine development / 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 / GABA-ergic synapse / positive regulation of synaptic transmission, GABAergic / modulation of chemical synaptic transmission / synapse organization / positive regulation of insulin secretion / presynaptic membrane / nervous system development / 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)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.22 Å
AuthorsBoyd R / Wang W
Funding support United States, 2 items
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, 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_29829.png

Downloads & links

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Map

FileDownload / File: emd_29829.map.gz / Format: CCP4 / Size: 91.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 288 pix.
= 239.04 Å		0.83 Å/pix.
x 288 pix.
= 239.04 Å		0.83 Å/pix.
x 288 pix.
= 239.04 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.83 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.35
Minimum - Maximum-3.2559164 - 4.784611
Average (Standard dev.)0.00136841 (±0.12700766)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions288288288
Spacing288288288
CellA=B=C: 239.04 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_29829_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_29829_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 with 2 Neurexin-1 Beta confirmation one

EntireName: Neuroligin 2 Dimer with 2 Neurexin-1 Beta confirmation one
Components
  • Complex: Neuroligin 2 Dimer with 2 Neurexin-1 Beta confirmation one
    • Protein or peptide: Neuroligin-2
    • Protein or peptide: Neurexin-1
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: CALCIUM ION

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Supramolecule #1: Neuroligin 2 Dimer with 2 Neurexin-1 Beta confirmation one

SupramoleculeName: Neuroligin 2 Dimer with 2 Neurexin-1 Beta confirmation one
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 180 KDa

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Macromolecule #1: Neuroligin-2

MacromoleculeName: 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-2

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Macromolecule #2: Neurexin-1

MacromoleculeName: Neurexin-1 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 50.435332 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MYQRMLRCGA DLGSPGGGSG GGAGGRLALI WIVPLTLGGL LGVAWGASSL GAHHIHHFHG SSKEFEQKLI SEEDLGFEID KVWHDFPAT SPIAIYRSPA SLRGGHAGTT YIFSKGGGQI TYKWPPNDRP STRADRLAIG FSTVQKEAVL VRVDSSSGLG D YLELHIHQ ...String:
MYQRMLRCGA DLGSPGGGSG GGAGGRLALI WIVPLTLGGL LGVAWGASSL GAHHIHHFHG SSKEFEQKLI SEEDLGFEID KVWHDFPAT SPIAIYRSPA SLRGGHAGTT YIFSKGGGQI TYKWPPNDRP STRADRLAIG FSTVQKEAVL VRVDSSSGLG D YLELHIHQ GKIGVKFNVG TDDIAIEESN AIINDGKYHV VRFTRSGGNA TLQVDSWPVI ERYPAGRQLT IFNSQATIII GG KEQGQPF QGQLSGLYYN GLKVLNMAAE NDANIAIVGN VRLVGEVPSS MTTESTATAM QSEMSTSIME TTTTLATSTA RRG KPPTKE PISQTTDDIL VASAECPSDD EDIDPCEPSS GGLANPTRVG GREPYPGSAE VIRESSSTTG MVVGIVAAAA LCIL ILLYA MYKYRNRDEG SYHVDESRNY ISNSAQSNGA VVKEKQPSSA KSANKNKKNK DKEYYVSNSL EVLFQ

UniProtKB: Neurexin I, Neurexin I

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Macromolecule #3: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 3 / Number of copies: 6 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

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

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Macromolecule #4: CALCIUM ION

MacromoleculeName: CALCIUM ION / type: ligand / ID: 4 / Number of copies: 2 / Formula: CA
Molecular weightTheoretical: 40.078 Da

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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

Concentration6.2 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: 6615 / 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: 3.6 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: 2964465
CTF correctionType: 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: 3.22 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 51041
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final 3D classificationNumber classes: 3 / Avg.num./class: 40000

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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-8g7z:
Cryo-EM structure of full length Neuroligin-2 from Mouse bound to two Neurexin-1 Beta conformation one

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