[English] 日本語
Yorodumi
- PDB-3biw: Crystal structure of the Neuroligin-1/Neurexin-1beta synaptic adh... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3biw
TitleCrystal structure of the Neuroligin-1/Neurexin-1beta synaptic adhesion complex
Components
  • Neurexin-1-beta
  • Neuroligin-1
KeywordsCell adhesion/Cell adhesion / protein-protein complex / esterase domain / LNS domain / alpha-beta hydrolase / Cell adhesion / Cell junction / Glycoprotein / Membrane / Postsynaptic cell membrane / Synapse / Transmembrane / Alternative promoter usage / Cell adhesion-Cell adhesion COMPLEX
Function / homology
Function and homology information


regulation of presynapse organization / protein-containing complex assembly involved in synapse maturation / neurexin clustering involved in presynaptic membrane assembly / positive regulation of cAMP-mediated signaling / positive regulation of presynaptic active zone assembly / cell-cell adhesion involved in synapse maturation / cytoskeletal matrix organization at active zone / positive regulation of synaptic vesicle exocytosis / positive regulation of circadian sleep/wake cycle, wakefulness / negative regulation of dendritic spine morphogenesis ...regulation of presynapse organization / protein-containing complex assembly involved in synapse maturation / neurexin clustering involved in presynaptic membrane assembly / positive regulation of cAMP-mediated signaling / positive regulation of presynaptic active zone assembly / cell-cell adhesion involved in synapse maturation / cytoskeletal matrix organization at active zone / positive regulation of synaptic vesicle exocytosis / positive regulation of circadian sleep/wake cycle, wakefulness / negative regulation of dendritic spine morphogenesis / type 1 fibroblast growth factor receptor binding / guanylate kinase-associated protein clustering / protein complex involved in cell-cell adhesion / positive regulation of neuromuscular synaptic transmission / neuron to neuron synapse / trans-synaptic protein complex / neuroligin clustering involved in postsynaptic membrane assembly / cerebellar granule cell differentiation / regulation of trans-synaptic signaling by endocannabinoid, modulating synaptic transmission / trans-synaptic signaling, modulating synaptic transmission / postsynaptic specialization assembly / negative regulation of filopodium assembly / neuronal ion channel clustering / gephyrin clustering involved in postsynaptic density assembly / excitatory synapse assembly / slit diaphragm / terminal button organization / postsynaptic density protein 95 clustering / positive regulation of synaptic vesicle clustering / postsynaptic membrane assembly / synapse maturation / vocal learning / gamma-aminobutyric acid receptor clustering / Neurexins and neuroligins / maintenance of synapse structure / presynaptic membrane assembly / neuroligin family protein binding / positive regulation of synapse maturation / regulation of grooming behavior / synaptic vesicle targeting / synaptic vesicle clustering / positive regulation of fibroblast growth factor receptor signaling pathway / synaptic membrane adhesion / regulation of postsynaptic specialization assembly / receptor localization to synapse / filopodium tip / neuron cell-cell adhesion / regulation of respiratory gaseous exchange by nervous system process / neurexin family protein binding / NMDA glutamate receptor clustering / inhibitory synapse / presynapse assembly / positive regulation of synaptic vesicle endocytosis / calcium-dependent cell-cell adhesion via plasma membrane cell adhesion molecules / vocalization behavior / regulation of postsynaptic density assembly / neuron projection arborization / AMPA glutamate receptor clustering / protein localization to synapse / regulation of AMPA receptor activity / neurotransmitter secretion / acetylcholine receptor binding / regulation of NMDA receptor activity / regulation of synaptic vesicle cycle / vesicle docking involved in exocytosis / AMPA selective glutamate receptor signaling pathway / positive regulation of synapse assembly / NMDA selective glutamate receptor signaling pathway / heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules / positive regulation of ruffle assembly / positive regulation of filopodium assembly / regulation of neuron differentiation / postsynaptic specialization membrane / positive regulation of protein localization to synapse / synaptic vesicle transport / positive regulation of phospholipase C-activating G protein-coupled receptor signaling pathway / positive regulation of dendritic spine development / adult behavior / positive regulation of intracellular signal transduction / neuromuscular process controlling balance / excitatory synapse / social behavior / positive regulation of excitatory postsynaptic potential / endocytic vesicle / regulation of presynapse assembly / synaptic cleft / axonal growth cone / prepulse inhibition / protein targeting / synapse assembly / cell adhesion molecule binding / presynaptic active zone membrane / calcium channel regulator activity / positive regulation of synaptic transmission, glutamatergic / cellular response to calcium ion / dendritic shaft / neuron projection morphogenesis / cell projection / PDZ domain binding / positive regulation of synaptic transmission, GABAergic
Similarity search - Function
Syndecan/Neurexin domain / Syndecan domain / Neuroligin / : / Neurexin/syndecan/glycophorin C / putative band 4.1 homologues' binding motif / : / Laminin G domain / Laminin G domain profile. / Laminin G domain ...Syndecan/Neurexin domain / Syndecan domain / Neuroligin / : / 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 / EGF-like domain / EGF-type aspartate/asparagine hydroxylation site / Aspartic acid and asparagine hydroxylation site. / Epidermal growth factor-like domain. / Jelly Rolls - #200 / EGF-like domain profile. / EGF-like domain / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Concanavalin A-like lectin/glucanase domain superfamily / Jelly Rolls / Sandwich / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Neuroligin-1 / Neurexin-1 / Neurexin-1-beta
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.5 Å
AuthorsArac, D. / Boucard, A.A. / Ozkan, E. / Strop, P. / Newell, E. / Sudhof, T.C. / Brunger, A.T.
CitationJournal: Neuron / Year: 2007
Title: Structures of Neuroligin-1 and the Neuroligin-1/Neurexin-1beta Complex Reveal Specific Protein-Protein and Protein-Ca(2+) Interactions.
Authors: Arac, D. / Boucard, A.A. / Ozkan, E. / Strop, P. / Newell, E. / Sudhof, T.C. / Brunger, A.T.
History
DepositionDec 1, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 18, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Aug 23, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 1.3Oct 25, 2017Group: Refinement description / Category: software
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / struct_asym / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_entity_nonpoly.entity_id / _pdbx_entity_nonpoly.name / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 16, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Neuroligin-1
B: Neuroligin-1
C: Neuroligin-1
D: Neuroligin-1
E: Neurexin-1-beta
F: Neurexin-1-beta
G: Neurexin-1-beta
H: Neurexin-1-beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)365,20429
Polymers361,0368
Non-polymers4,16821
Water00
1
A: Neuroligin-1
D: Neuroligin-1
E: Neurexin-1-beta
H: Neurexin-1-beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)182,35013
Polymers180,5184
Non-polymers1,8329
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Neuroligin-1
C: Neuroligin-1
F: Neurexin-1-beta
G: Neurexin-1-beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)182,85416
Polymers180,5184
Non-polymers2,33612
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)229.830, 148.796, 123.602
Angle α, β, γ (deg.)90.000, 90.380, 90.000
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A,B,C, using restrain
22chain E,F,G, using restrain
33chain A,B,C,D, using restrain
44chain E,F,G,H, using restrain

NCS ensembles :
ID
1
2
3
4
DetailsThe biological assembly is a heterotetramer of two Neurexin-1beta molecules bound to a Neuroligin-1 dimer.

-
Components

#1: Protein
Neuroligin-1 / Neuroligin I


Mass: 64228.961 Da / Num. of mol.: 4 / Fragment: extracellular esterase domain of Neuroligin-1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Nlgn1 / Plasmid: pAcGP67A / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q62765
#2: Protein
Neurexin-1-beta / Neurexin I-beta


Mass: 26030.043 Da / Num. of mol.: 4 / Fragment: extracellular LNS domain of Neurexin-1beta
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Nrxn1 / Plasmid: pAcGP67A / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q63373, UniProt: Q63372*PLUS
#3: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#4: 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.: 12
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
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
#5: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Ca
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.93 Å3/Da / Density % sol: 57.98 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 8% PEG6000, 0.1 M MgCl2, 0.1 M MES, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 130 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 15, 2007
RadiationMonochromator: Double crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.41→50 Å / Num. obs: 53484 / % possible obs: 92.5 % / Redundancy: 3 % / Rmerge(I) obs: 0.093 / Χ2: 1.042 / Net I/σ(I): 9.8
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
3.41-3.5320.68840830.97171.2
3.53-3.672.50.4951680.998189.7
3.67-3.842.90.3453360.953193
3.84-4.0430.26854211.024193.4
4.04-4.330.18453311.057192.9
4.3-4.6330.12453731.12193.2
4.63-5.0930.10154511.103194.7
5.09-5.833.10.09356381.05197.4
5.83-7.343.40.07757921.083199.6
7.34-503.40.04858910.9971100

-
Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation3.39 Å45.9 Å
Translation3.39 Å45.9 Å

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
CNS1.2refinement
PDB_EXTRACT3.004data extraction
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.5→45.9 Å / Rfactor Rfree error: 0.005 / FOM work R set: 0.785 / Data cutoff high absF: 3736422 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.276 2539 5.1 %RANDOM
Rwork0.246 ---
obs-49818 94.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 67.015 Å2 / ksol: 0.3 e/Å3
Displacement parametersBiso mean: 133.3 Å2
Baniso -1Baniso -2Baniso -3
1--8.24 Å20 Å2-4.49 Å2
2--12.52 Å20 Å2
3----4.27 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.53 Å0.48 Å
Luzzati d res low-5 Å
Luzzati sigma a0.69 Å0.7 Å
Refinement stepCycle: LAST / Resolution: 3.5→45.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms22180 0 258 0 22438
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d23.9
X-RAY DIFFRACTIONc_improper_angle_d0.85
X-RAY DIFFRACTIONc_mcbond_it26.821.5
X-RAY DIFFRACTIONc_mcangle_it41.622
X-RAY DIFFRACTIONc_scbond_it27.932
X-RAY DIFFRACTIONc_scangle_it40.992.5
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDRmsTypeWeight
11BX-RAY DIFFRACTION0.067restrain300
11CX-RAY DIFFRACTION0.076restrain300
22FX-RAY DIFFRACTION0.021restrain300
22GX-RAY DIFFRACTION0.02restrain300
33BX-RAY DIFFRACTION0.067restrain300
33CX-RAY DIFFRACTION0.076restrain300
33DX-RAY DIFFRACTION0.086restrain300
44FX-RAY DIFFRACTION0.021restrain300
44GX-RAY DIFFRACTION0.02restrain300
44HX-RAY DIFFRACTION0.021restrain300
LS refinement shellResolution: 3.5→3.72 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.35 392 5 %
Rwork0.34 7480 -
all-7872 -
obs--90.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2dna-rna_rep.paramdna-rna.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4ion.paramion.top
X-RAY DIFFRACTION5carbohydrate.param

+
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