+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-34220 | |||||||||
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Title | Cryo-EM structure of human Neuroligin 2 | |||||||||
Map data | ||||||||||
Sample |
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Keywords | synapse 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 / regulation of presynapse assembly / excitatory synapse / 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 | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.5 Å | |||||||||
Authors | Zhang H / Zhang Z / Hou M | |||||||||
Funding support | China, 1 items
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Citation | Journal: 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 |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_34220.map.gz | 59.7 MB | EMDB map data format | |
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Header (meta data) | emd-34220-v30.xml emd-34220.xml | 13.5 KB 13.5 KB | Display Display | EMDB header |
Images | emd_34220.png | 113.1 KB | ||
Filedesc metadata | emd-34220.cif.gz | 5.4 KB | ||
Others | emd_34220_half_map_1.map.gz emd_34220_half_map_2.map.gz | 59.2 MB 59.2 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-34220 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-34220 | HTTPS FTP |
-Related structure data
Related structure data | 8gs4MC 8gs3C M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_34220.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Voxel size | X=Y=Z: 0.92 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #2
File | emd_34220_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_34220_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : homodimer of Neuroligin 2
Entire | Name: homodimer of Neuroligin 2 |
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Components |
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-Supramolecule #1: homodimer of Neuroligin 2
Supramolecule | Name: homodimer of Neuroligin 2 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Homo sapiens (human) |
-Macromolecule #1: Neuroligin-2
Macromolecule | Name: Neuroligin-2 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 90.913781 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: 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 |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.4 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Calibrated 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 recording | Film 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 |
-Image processing
Startup model | Type of model: NONE |
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Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 192341 |