[English] 日本語
Yorodumi
- PDB-8g7d: Cryo-EM structure of full length Neuroligin-2 from Mouse -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8g7d
TitleCryo-EM structure of full length Neuroligin-2 from Mouse
ComponentsNeuroligin-1,Neuroligin-2
KeywordsMEMBRANE PROTEIN / Neuroligin-2
Function / homology
Function and homology information


regulation of presynapse organization / neurexin clustering involved in presynaptic membrane assembly / cell-cell adhesion involved in synapse maturation / positive regulation of presynaptic active zone assembly / cytoskeletal matrix organization at active zone / positive regulation of circadian sleep/wake cycle, wakefulness / protein complex involved in cell-cell adhesion / Neurexins and neuroligins / positive regulation of neuromuscular synaptic transmission / jump response ...regulation of presynapse organization / neurexin clustering involved in presynaptic membrane assembly / cell-cell adhesion involved in synapse maturation / positive regulation of presynaptic active zone assembly / cytoskeletal matrix organization at active zone / positive regulation of circadian sleep/wake cycle, wakefulness / protein complex involved in cell-cell adhesion / Neurexins and neuroligins / positive regulation of neuromuscular synaptic transmission / jump response / neurotransmitter-gated ion channel clustering / positive regulation of t-SNARE clustering / neuron to neuron synapse / postsynaptic specialization assembly / gephyrin clustering involved in postsynaptic density assembly / positive regulation of synaptic vesicle exocytosis / terminal button organization / negative regulation of dendritic spine morphogenesis / postsynaptic density protein 95 clustering / postsynaptic membrane assembly / synapse maturation / excitatory synapse assembly / positive regulation of synaptic vesicle clustering / presynaptic membrane assembly / neurexin family protein binding / maintenance of synapse structure / : / synaptic vesicle clustering / thigmotaxis / synaptic membrane adhesion / presynapse assembly / receptor localization to synapse / cell adhesion mediator activity / neuron cell-cell adhesion / regulation of respiratory gaseous exchange by nervous system process / insulin metabolic process / NMDA glutamate receptor clustering / filopodium tip / ribbon synapse / calcium-dependent cell-cell adhesion / inhibitory synapse / regulation of postsynaptic density assembly / positive regulation of synaptic vesicle endocytosis / protein localization to synapse / neuron projection arborization / dopaminergic synapse / glycinergic synapse / AMPA selective glutamate receptor signaling pathway / protein localization to cell surface / inhibitory synapse assembly / positive regulation of synapse assembly / positive regulation of inhibitory postsynaptic potential / NMDA selective glutamate receptor signaling pathway / heterophilic cell-cell adhesion / positive regulation of filopodium assembly / regulation of neuron differentiation / neuromuscular process controlling balance / postsynaptic specialization membrane / positive regulation of ruffle assembly / positive regulation of protein localization to synapse / synaptic transmission, GABAergic / positive regulation of dendritic spine development / synaptic vesicle transport / AMPA glutamate receptor clustering / positive regulation of intracellular signal transduction / locomotory exploration behavior / social behavior / regulation of presynapse assembly / protein targeting / synaptic cleft / positive regulation of synaptic transmission, glutamatergic / neuron projection morphogenesis / synapse assembly / cell adhesion molecule binding / excitatory synapse / sensory perception of pain / cellular response to calcium ion / positive regulation of excitatory postsynaptic potential / dendritic shaft / positive regulation of synaptic transmission, GABAergic / PDZ domain binding / neuromuscular junction / establishment of protein localization / positive regulation of neuron projection development / synapse organization / modulation of chemical synaptic transmission / GABA-ergic synapse / neuron projection development / positive regulation of insulin secretion / long-term synaptic potentiation / rhythmic process / nervous system development / presynapse / signaling receptor activity / scaffold protein binding / presynaptic membrane / dendritic spine / postsynaptic membrane / signaling receptor complex / postsynaptic density
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)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.28 Å
AuthorsBoyd, R. / Wang, W.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)1R25Gm146860 United States
McKnight Foundation2022 Scholar Award United States
CitationJournal: Sci Adv / Year: 2026
Title: Weaker neuroligin 2-neurexin β1 interaction tethers membranes and recruits gephyrin at membrane junctions through clustering.
Authors: Robbie Boyd / Khuloud Jaqaman / Weiwei Wang /
Abstract: Single-pass transmembrane proteins neuroligin (NL) and neurexin (NRX) constitute a pair of synaptic adhesion molecules that are essential for the formation of functional synapses. Binding affinities ...Single-pass transmembrane proteins neuroligin (NL) and neurexin (NRX) constitute a pair of synaptic adhesion molecules that are essential for the formation of functional synapses. Binding affinities vary by ~1000-fold between combinations of NL and NRX subtypes, which contribute to chemical and spatial specificities. Among major NL-NRX subtypes, NL2 and NRXβ1 have the lowest affinity. Here, we report structures of NL2 in complex with NRXβ1 in several conformations, along with NL2 alone. We identify mechanisms underlying the modulation of NL-NRX affinities and how the weaker NL2-NRXβ1 interaction alone is capable of tethering lipid membranes. We further show that NL2 and NRXβ1 cluster at intercellular junctions and recruit the master postsynaptic scaffolding protein gephyrin, which further clusters neurotransmitter receptors. These findings suggest a dual role of the NL2-NRXβ1 interaction-both as mechanical tether and as signaling receptor-to ensure correct spatial and chemical coordination between two cells to generate functional synapses.
History
DepositionFeb 16, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 14, 2025Provider: repository / Type: Initial release
Revision 1.0May 14, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0May 14, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0May 14, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0May 14, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0May 14, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1Apr 8, 2026Group: Data collection / Database references / Category: citation / citation_author / em_admin
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _em_admin.last_update
Revision 1.1Apr 8, 2026Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Database references / Experimental summary / Data content type: EM metadata / EM metadata / EM metadata / Category: citation / citation_author / em_admin
Data content type: EM metadata / EM metadata ...EM metadata / EM metadata / EM metadata / EM metadata / EM metadata / EM metadata / EM metadata / EM metadata / EM metadata / EM metadata / EM metadata / EM metadata
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _em_admin.last_update

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Neuroligin-1,Neuroligin-2
B: Neuroligin-1,Neuroligin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)191,3386
Polymers190,4542
Non-polymers8854
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551

-
Components

#1: Protein Neuroligin-1,Neuroligin-2


Mass: 95226.797 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Nlgn1, Kiaa1070, Nlgn2, Kiaa1366 / Production host: Homo sapiens (human) / References: UniProt: Q99K10, UniProt: Q69ZK9
#2: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H15NO6 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

-
Sample preparation

ComponentName: Neuroligin-2 Dimer / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Source (natural)Organism: Mus musculus (house mouse)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 7.4
Buffer component
IDConc.NameFormulaBuffer-ID
120 mMHEPESC8H18N2O4S1
2150 mMSodium ChlorideNaCl1
31 mMMagnesium chlorideMgCl21
40.5 mMCalcium chlorideCaCl21
50.05 %LMNG1
SpecimenConc.: 5.2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid mesh size: 400 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 298 K / Details: Blot force 20, blot time 5s, single blot

-
Electron microscopy imaging

MicroscopyModel: FEI TITAN
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 105000 X / Calibrated magnification: 105000 X / Nominal defocus max: 2500 nm / Nominal defocus min: 1000 nm / Calibrated defocus max: 3000 nm / Cs: 0 mm / C2 aperture diameter: 70 µm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 90 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 4989
Image scansWidth: 5760 / Height: 4092

-
Processing

EM software
IDNameVersionCategory
1RELION3.1particle selection
2SerialEMimage acquisition
4CTFFIND4CTF correction
7UCSF Chimera1.16model fitting
9RELION3.1initial Euler assignment
10cryoSPARC3final Euler assignment
11cryoSPARC3classification
12cryoSPARC33D reconstruction
13PHENIX1model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 674761
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.28 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 77577 / Algorithm: BACK PROJECTION / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL
Atomic model buildingPDB-ID: 3BL8

3bl8


Accession code: 3BL8 / Source name: PDB / Type: experimental model
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0038577
ELECTRON MICROSCOPYf_angle_d0.50111706
ELECTRON MICROSCOPYf_dihedral_angle_d4.1921189
ELECTRON MICROSCOPYf_chiral_restr0.041286
ELECTRON MICROSCOPYf_plane_restr0.0041528

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more