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- EMDB-34219: Cryo-EM structure of human Neuroligin 3 -

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Basic information

Entry
Database: EMDB / ID: EMD-34219
TitleCryo-EM structure of human Neuroligin 3
Map data
Sample
  • Complex: homodimer of Neuroligin 3
    • Protein or peptide: Neuroligin-3NLGN3
KeywordsNeuroligin / synapse protein / plasma membrane / MEMBRANE PROTEIN
Function / homology
Function and homology information


asymmetric, glutamatergic, excitatory synapse / symmetric, GABA-ergic, inhibitory synapse / rhythmic synaptic transmission / postsynaptic membrane assembly / presynaptic membrane assembly / neuron cell-cell adhesion / regulation of respiratory gaseous exchange by nervous system process / neurexin family protein binding / presynapse assembly / vocalization behavior ...asymmetric, glutamatergic, excitatory synapse / symmetric, GABA-ergic, inhibitory synapse / rhythmic synaptic transmission / postsynaptic membrane assembly / presynaptic membrane assembly / neuron cell-cell adhesion / regulation of respiratory gaseous exchange by nervous system process / neurexin family protein binding / presynapse assembly / vocalization behavior / inhibitory postsynaptic potential / axon extension / Neurexins and neuroligins / positive regulation of synapse assembly / positive regulation of AMPA receptor activity / adult behavior / social behavior / positive regulation of excitatory postsynaptic potential / excitatory synapse / synaptic vesicle endocytosis / endocytic vesicle / synapse assembly / cell adhesion molecule binding / positive regulation of synaptic transmission, glutamatergic / receptor-mediated endocytosis / learning / synapse organization / modulation of chemical synaptic transmission / presynapse / signaling receptor activity / chemical synaptic transmission / scaffold protein binding / postsynaptic membrane / molecular adaptor activity / synapse / cell surface / membrane / 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: 3.9 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) releaseSep 20, 2023-
Map releaseSep 20, 2023-
UpdateApr 3, 2024-
Current statusApr 3, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_34219.png

Downloads & links

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Map

FileDownload / File: emd_34219.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 0.842 Å
Density
Contour LevelBy AUTHOR: 0.01
Minimum - Maximum-0.022966964 - 0.04936592
Average (Standard dev.)0.00022718747 (±0.0018015665)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 215.552 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_34219_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_34219_half_map_1.map
Projections & Slices
AxesZYX

Projections

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Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_34219_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
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Histogram

Histogram (log scale)

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Sample components

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Entire : homodimer of Neuroligin 3

EntireName: homodimer of Neuroligin 3
Components
  • Complex: homodimer of Neuroligin 3
    • Protein or peptide: Neuroligin-3NLGN3

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Supramolecule #1: homodimer of Neuroligin 3

SupramoleculeName: homodimer of Neuroligin 3 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Neuroligin-3

MacromoleculeName: Neuroligin-3 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 93.999062 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MWLRLGPPSL SLSPKPTVGR SLCLTLWFLS LALRASTQAP APTVNTHFGK LRGARVPLPS EILGPVDQYL GVPYAAPPIG EKRFLPPEP PPSWSGIRNA THFPPVCPQN IHTAVPEVML PVWFTANLDI VATYIQEPNE DCLYLNVYVP TEDVKRISKE C ARKPNKKI ...String:
MWLRLGPPSL SLSPKPTVGR SLCLTLWFLS LALRASTQAP APTVNTHFGK LRGARVPLPS EILGPVDQYL GVPYAAPPIG EKRFLPPEP PPSWSGIRNA THFPPVCPQN IHTAVPEVML PVWFTANLDI VATYIQEPNE DCLYLNVYVP TEDVKRISKE C ARKPNKKI CRKGGSGAKK QGEDLADNDG DEDEDIRDSG AKPVMVYIHG GSYMEGTGNM IDGSILASYG NVIVITLNYR VG VLGFLST GDQAAKGNYG LLDQIQALRW VSENIAFFGG DPRRITVFGS GIGASCVSLL TLSHHSEGLF QRAIIQSGSA LSS WAVNYQ PVKYTSLLAD KVGCNVLDTV DMVDCLRQKS AKELVEQDIQ PARYHVAFGP VIDGDVIPDD PEILMEQGEF LNYD IMLGV NQGEGLKFVE GVVDPEDGVS GTDFDYSVSN FVDNLYGYPE GKDTLRETIK FMYTDWADRD NPETRRKTLV ALFTD HQWV EPSVVTADLH ARYGSPTYFY AFYHHCQSLM KPAWSDAAHG DEVPYVFGVP MVGPTDLFPC NFSKNDVMLS AVVMTY WTN FAKTGDPNKP VPQDTKFIHT KANRFEEVAW SKYNPRDQLY LHIGLKPRVR DHYRATKVAF WKHLVPHLYN LHDMFHY TS TTTKVPPPDT THSSHITRRP NGKTWSTKRP AISPAYSNEN AQGSWNGDQD AGPLLVENPR DYSTELSVTI AVGASLLF L NVLAFAALYY RKDKRRQEPL RQPSPQRGAG APELGAAPEE ELAALQLGPT HHECEAGPPH DTLRLTALPD YTLTLRRSP DDIPLMTPNT ITMIPNSLVG LQTLHPYNTF AAGFNSTGLP HSHSTTRV

UniProtKB: Neuroligin-3

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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 K2 SUMMIT (4k 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: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 255939
FSC plot (resolution estimation)

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