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- EMDB-34220: Cryo-EM structure of human Neuroligin 2 -

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Basic information

Entry
Database: EMDB / ID: EMD-34220
TitleCryo-EM structure of human Neuroligin 2
Map data
Sample
  • Complex: homodimer of Neuroligin 2
    • Protein or peptide: Neuroligin-2
Keywordssynapse protein / plasma membrane / MEMBRANE PROTEIN
Function / homology
Function and homology information


neurotransmitter-gated ion channel clustering / jump response / positive regulation of t-SNARE clustering / symmetric, GABA-ergic, inhibitory synapse / gephyrin clustering involved in postsynaptic density assembly / terminal button organization / postsynaptic density protein 95 clustering / cell-cell junction maintenance / postsynaptic membrane assembly / positive regulation of synaptic vesicle clustering ...neurotransmitter-gated ion channel clustering / jump response / positive regulation of t-SNARE clustering / symmetric, GABA-ergic, inhibitory synapse / gephyrin clustering involved in postsynaptic density assembly / terminal button organization / postsynaptic density protein 95 clustering / cell-cell junction maintenance / postsynaptic membrane assembly / positive regulation of synaptic vesicle clustering / presynaptic membrane assembly / thigmotaxis / ribbon synapse / inhibitory synapse / regulation of respiratory gaseous exchange by nervous system process / insulin metabolic process / neuron cell-cell adhesion / presynapse assembly / neurexin family protein binding / dopaminergic synapse / protein localization to synapse / inhibitory synapse assembly / regulation of AMPA receptor activity / positive regulation of inhibitory postsynaptic potential / glycinergic synapse / synaptic transmission, GABAergic / postsynaptic specialization membrane / protein localization to cell surface / Neurexins and neuroligins / positive regulation of synapse assembly / positive regulation of protein localization to synapse / positive regulation of dendritic spine development / locomotory exploration behavior / social behavior / positive regulation of excitatory postsynaptic potential / neuromuscular process controlling balance / synaptic vesicle endocytosis / excitatory synapse / regulation of presynapse assembly / sensory perception of pain / cell adhesion molecule binding / synapse assembly / positive regulation of synaptic transmission, glutamatergic / dendritic shaft / positive regulation of synaptic transmission, GABAergic / synapse organization / modulation of chemical synaptic transmission / positive regulation of insulin secretion / cell-cell adhesion / presynaptic membrane / signaling receptor activity / chemical synaptic transmission / postsynaptic membrane / synapse / positive regulation of cell population proliferation / cell surface / membrane / 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
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsZhang H / Zhang Z / Hou M
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Front Endocrinol (Lausanne) / Year: 2022
Title: Expression and structural analysis of human neuroligin 2 and neuroligin 3 implicated in autism spectrum disorders.
Authors: Zhenzhen Zhang / Mengzhuo Hou / Huaxing Ou / Daping Wang / Zhifang Li / Huawei Zhang / Jianping Lu /
Abstract: The development of autism spectrum disorders (ASDs) involves both environmental factors such as maternal diabetes and genetic factors such as neuroligins (NLGNs). NLGN2 and NLGN3 are two members of ...The development of autism spectrum disorders (ASDs) involves both environmental factors such as maternal diabetes and genetic factors such as neuroligins (NLGNs). NLGN2 and NLGN3 are two members of NLGNs with distinct distributions and functions in synapse development and plasticity. The relationship between maternal diabetes and NLGNs, and the distinct working mechanisms of different NLGNs currently remain unclear. Here, we first analyzed the expression levels of NLGN2 and NLGN3 in a streptozotocin-induced ASD mouse model and different brain regions to reveal their differences and similarities. Then, cryogenic electron microscopy (cryo-EM) structures of human NLGN2 and NLGN3 were determined. The overall structures are similar to their homologs in previous reports. However, structural comparisons revealed the relative rotations of two protomers in the homodimers of NLGN2 and NLGN3. Taken together with the previously reported NLGN2-MDGA1 complex, we speculate that the distinct assembly adopted by NLGN2 and NLGN3 may affect their interactions with MDGAs. Our results provide structural insights into the potential distinct mechanisms of NLGN2 and NLGN3 implicated in the development of ASD.
History
DepositionSep 4, 2022-
Header (metadata) releaseMar 1, 2023-
Map releaseMar 1, 2023-
UpdateApr 3, 2024-
Current statusApr 3, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_34220.png

Downloads & links

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Map

FileDownload / File: emd_34220.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 0.92 Å
Density
Contour LevelBy AUTHOR: 0.38
Minimum - Maximum-2.581008 - 4.059253
Average (Standard dev.)0.0005898646 (±0.08533712)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 235.52 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_34220_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_34220_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 : homodimer of Neuroligin 2

EntireName: homodimer of Neuroligin 2
Components
  • Complex: homodimer of Neuroligin 2
    • Protein or peptide: Neuroligin-2

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Supramolecule #1: homodimer of Neuroligin 2

SupramoleculeName: homodimer of Neuroligin 2 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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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: Homo sapiens (human)
Molecular weightTheoretical: 90.913781 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MWLLALCLVG LAGAQRGGGG PGGGAPGGPG LGLGSLGEER FPVVNTAYGR VRGVRRELNN EILGPVVQFL GVPYATPPLG ARRFQPPEA PASWPGVRNA TTLPPACPQN LHGALPAIML PVWFTDNLEA AATYVQNQSE DCLYLNLYVP TEDGPLTKKR D EATLNPPD ...String:
MWLLALCLVG LAGAQRGGGG PGGGAPGGPG LGLGSLGEER FPVVNTAYGR VRGVRRELNN EILGPVVQFL GVPYATPPLG ARRFQPPEA PASWPGVRNA TTLPPACPQN LHGALPAIML PVWFTDNLEA AATYVQNQSE DCLYLNLYVP TEDGPLTKKR D EATLNPPD TDIRDPGKKP VMLFLHGGSY MEGTGNMFDG SVLAAYGNVI VATLNYRLGV LGFLSTGDQA AKGNYGLLDQ IQ ALRWLSE NIAHFGGDPE RITIFGSGAG ASCVNLLILS HHSEGLFQKA IAQSGTAISS WSVNYQPLKY TRLLAAKVGC DRE DSAEAV ECLRRKPSRE LVDQDVQPAR YHIAFGPVVD GDVVPDDPEI LMQQGEFLNY DMLIGVNQGE GLKFVEDSAE SEDG VSASA FDFTVSNFVD NLYGYPEGKD VLRETIKFMY TDWADRDNGE MRRKTLLALF TDHQWVAPAV ATAKLHADYQ SPVYF YTFY HHCQAEGRPE WADAAHGDEL PYVFGVPMVG ATDLFPCNFS KNDVMLSAVV MTYWTNFAKT GDPNQPVPQD TKFIHT KPN RFEEVVWSKF NSKEKQYLHI GLKPRVRDNY RANKVAFWLE LVPHLHNLHT ELFTTTTRLP PYATRWPPRP PAGAPGT RR PPPPATLPPE PEPEPGPRAY DRFPGDSRDY STELSVTVAV GASLLFLNIL AFAALYYKRD RRQELRCRRL SPPGGSGS G VPGGGPLLPA AGRELPPEEE LVSLQLKRGG GVGADPAEAL RPACPPDYTL ALRRAPDDVP LLAPGALTLL PSGLGPPPP PPPPSLHPFG PFPPPPPTAT SHNNTLPHPH STTRV

UniProtKB: Neuroligin-2

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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

BufferpH: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated defocus min: 1.5 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.5 µm
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 50.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 192341

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