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- PDB-3biw: Crystal structure of the Neuroligin-1/Neurexin-1beta synaptic adh... -

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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 / neurexin clustering involved in presynaptic membrane assembly / protein-containing complex assembly involved in synapse maturation / 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 / regulation of postsynaptic specialization assembly / gephyrin clustering involved in postsynaptic density assembly / protein complex involved in cell-cell adhesion ...regulation of presynapse organization / neurexin clustering involved in presynaptic membrane assembly / protein-containing complex assembly involved in synapse maturation / 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 / regulation of postsynaptic specialization assembly / gephyrin clustering involved in postsynaptic density assembly / protein complex involved in cell-cell adhesion / retrograde trans-synaptic signaling by trans-synaptic protein complex / type 1 fibroblast growth factor receptor binding / positive regulation of neuromuscular synaptic transmission / guanylate kinase-associated protein clustering / neuron to neuron synapse / trans-synaptic signaling, modulating synaptic transmission / terminal button organization / positive regulation of synaptic vesicle exocytosis / neuroligin clustering involved in postsynaptic membrane assembly / excitatory synapse assembly / postsynaptic density protein 95 clustering / regulation of trans-synaptic signaling by endocannabinoid, modulating synaptic transmission / cerebellar granule cell differentiation / postsynaptic specialization assembly / negative regulation of dendritic spine morphogenesis / postsynaptic membrane assembly / gamma-aminobutyric acid receptor clustering / neuronal ion channel clustering / positive regulation of synaptic vesicle clustering / presynaptic membrane assembly / synapse maturation / Neurexins and neuroligins / maintenance of synapse structure / negative regulation of filopodium assembly / vocal learning / slit diaphragm / neuroligin family protein binding / positive regulation of synapse maturation / synaptic vesicle targeting / positive regulation of fibroblast growth factor receptor signaling pathway / regulation of postsynaptic density assembly / synaptic vesicle clustering / neuron cell-cell adhesion / inhibitory synapse / regulation of respiratory gaseous exchange by nervous system process / synaptic membrane adhesion / neurexin family protein binding / regulation of grooming behavior / presynapse assembly / receptor localization to synapse / filopodium tip / protein localization to synapse / NMDA glutamate receptor clustering / vocalization behavior / neuron projection arborization / regulation of synaptic vesicle cycle / positive regulation of synaptic vesicle endocytosis / calcium-dependent cell-cell adhesion via plasma membrane cell adhesion molecules / regulation of AMPA receptor activity / AMPA glutamate receptor clustering / neurotransmitter secretion / filopodium assembly / neuron maturation / acetylcholine receptor binding / vesicle docking involved in exocytosis / positive regulation of ruffle assembly / positive regulation of synapse assembly / regulation of NMDA receptor activity / postsynaptic specialization membrane / positive regulation of filopodium assembly / positive regulation of intracellular signal transduction / regulation of neuron differentiation / heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules / positive regulation of protein localization to synapse / synaptic vesicle transport / positive regulation of dendritic spine development / adult behavior / positive regulation of protein kinase A signaling / social behavior / neuromuscular process controlling balance / endocytic vesicle / positive regulation of excitatory postsynaptic potential / synaptic vesicle endocytosis / excitatory synapse / regulation of presynapse assembly / calcium channel regulator activity / protein targeting / prepulse inhibition / axonal growth cone / synaptic cleft / GABA-ergic synapse / presynaptic active zone membrane / cell adhesion molecule binding / synapse assembly / cellular response to calcium ion / positive regulation of synaptic transmission, glutamatergic / neuron projection morphogenesis / dendritic shaft / learning / positive regulation of synaptic transmission, GABAergic
Similarity search - Function
Neuroligin / Syndecan/Neurexin domain / Syndecan domain / : / Neurexin/syndecan/glycophorin C / putative band 4.1 homologues' binding motif / : / Laminin G domain / Laminin G domain profile. / Laminin G domain ...Neuroligin / Syndecan/Neurexin domain / Syndecan domain / : / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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.

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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

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Experimental details

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Experiment

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

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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

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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

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Phasing

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

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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

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