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- PDB-3b3q: Crystal structure of a synaptic adhesion complex -

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Basic information

Entry
Database: PDB / ID: 3b3q
TitleCrystal structure of a synaptic adhesion complex
Components
  • NRXN1 protein
  • Nlgn1 protein
KeywordsCELL ADHESION / synaptic formation / adhesion / heterophilic / protein-protein complex / calcium binding / Membrane / Transmembrane
Function / homology
Function and homology information


neurexin clustering involved in presynaptic membrane assembly / regulation of presynapse organization / : / protein-containing complex assembly involved in synapse maturation / positive regulation of presynaptic active zone assembly / cytoskeletal matrix organization at active zone / cell-cell adhesion involved in synapse maturation / positive regulation of circadian sleep/wake cycle, wakefulness / retrograde trans-synaptic signaling by trans-synaptic protein complex / gephyrin clustering involved in postsynaptic density assembly ...neurexin clustering involved in presynaptic membrane assembly / regulation of presynapse organization / : / protein-containing complex assembly involved in synapse maturation / positive regulation of presynaptic active zone assembly / cytoskeletal matrix organization at active zone / cell-cell adhesion involved in synapse maturation / positive regulation of circadian sleep/wake cycle, wakefulness / retrograde trans-synaptic signaling by trans-synaptic protein complex / gephyrin clustering involved in postsynaptic density assembly / Neurexins and neuroligins / protein complex involved in cell-cell adhesion / positive regulation of neuromuscular synaptic transmission / guanylate kinase-associated protein clustering / type 1 fibroblast growth factor receptor binding / neuronal signal transduction / terminal button organization / neuron to neuron synapse / positive regulation of synaptic vesicle exocytosis / neuroligin clustering involved in postsynaptic membrane assembly / postsynaptic density protein 95 clustering / excitatory synapse assembly / cerebellar granule cell differentiation / negative regulation of dendritic spine morphogenesis / postsynaptic membrane assembly / gamma-aminobutyric acid receptor clustering / positive regulation of synaptic vesicle clustering / presynaptic membrane assembly / synapse maturation / NMDA glutamate receptor clustering / maintenance of synapse structure / negative regulation of filopodium assembly / neuroligin family protein binding / synaptic vesicle targeting / positive regulation of fibroblast growth factor receptor signaling pathway / synaptic membrane adhesion / synaptic vesicle clustering / receptor localization to synapse / inhibitory synapse / neuron cell-cell adhesion / regulation of respiratory gaseous exchange by nervous system process / neurexin family protein binding / AMPA glutamate receptor clustering / filopodium tip / protein localization to synapse / vocalization behavior / neuron projection arborization / positive regulation of synaptic vesicle endocytosis / calcium-dependent cell-cell adhesion via plasma membrane cell adhesion molecules / regulation of AMPA receptor activity / Neurexins and neuroligins / positive regulation of synapse assembly / NMDA selective glutamate receptor complex / positive regulation of ruffle assembly / positive regulation of protein kinase C activity / positive regulation of intracellular signal transduction / positive regulation of dendritic spine development / positive regulation of protein localization to synapse / positive regulation of filopodium assembly / heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules / synaptic vesicle transport / regulation of neuron differentiation / adult behavior / positive regulation of protein kinase A signaling / plasma membrane => GO:0005886 / regulation of NMDA receptor activity / social behavior / positive regulation of excitatory postsynaptic potential / excitatory synapse / synaptic vesicle endocytosis / endocytic vesicle / GABA-ergic synapse / protein targeting / synaptic cleft / axonal growth cone / synapse assembly / cellular response to calcium ion / cell adhesion molecule binding / positive regulation of synaptic transmission, glutamatergic / neuron projection morphogenesis / dendritic shaft / learning / long-term synaptic potentiation / PDZ domain binding / positive regulation of synaptic transmission, GABAergic / synapse organization / positive regulation of protein localization to plasma membrane / modulation of chemical synaptic transmission / neuromuscular junction / establishment of protein localization / positive regulation of neuron projection development / neuron projection development / calcium-dependent protein binding / rhythmic process / transmembrane signaling receptor activity / presynapse / signaling receptor activity / presynaptic membrane / positive regulation of peptidyl-serine phosphorylation / nervous system development
Similarity search - Function
Neuroligin-1 / 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 ...Neuroligin-1 / 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 / Jelly Rolls - #200 / Alpha/Beta hydrolase fold, catalytic domain / Concanavalin A-like lectin/glucanase domain superfamily / Alpha/Beta hydrolase fold / Jelly Rolls / Sandwich / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
NRXN1 protein / Neurexin-1-beta / Nlgn1 protein / Neuroligin-1
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsChen, X. / Liu, H. / Shim, A. / Focia, P. / He, X.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2008
Title: Structural basis for synaptic adhesion mediated by neuroligin-neurexin interactions.
Authors: Chen, X. / Liu, H. / Shim, A.H. / Focia, P.J. / He, X.
History
DepositionOct 22, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 15, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2May 15, 2013Group: Structure summary
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms / 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_seq_id / _atom_site.label_asym_id / _atom_site.label_entity_id / _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.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _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_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Aug 30, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms
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: Nlgn1 protein
B: Nlgn1 protein
E: NRXN1 protein
F: NRXN1 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)173,73710
Polymers172,1634
Non-polymers1,5756
Water27,9591552
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)116.590, 125.400, 131.860
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 2 types, 4 molecules ABEF

#1: Protein Nlgn1 protein


Mass: 64623.363 Da / Num. of mol.: 2 / Fragment: cholinesterase-like domain / Mutation: N343Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Nlgn1 / Plasmid: pAcGP67A / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q4KMN5, UniProt: Q99K10*PLUS
#2: Protein NRXN1 protein


Mass: 21457.939 Da / Num. of mol.: 2 / Fragment: LNS domain or LG domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NRXN1 / Plasmid: pAcGP67A / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: A4FVB9, UniProt: P58400*PLUS

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Sugars , 2 types, 4 molecules

#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 / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1
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

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Non-polymers , 2 types, 1554 molecules

#5: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1552 / Source method: isolated from a natural source / Formula: H2O

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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: 2.8 Å3/Da / Density % sol: 56.06 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 1M sodium citrate, 0.1M sodium cacodylate, 0.2M sodium chloride, 0.01M calcium chloride, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.9787 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Feb 20, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9787 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 76375 / % possible obs: 97.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.5 % / Biso Wilson estimate: 27.5 Å2 / Rmerge(I) obs: 0.062 / Net I/σ(I): 19.3
Reflection shellResolution: 2.4→2.5 Å / Redundancy: 4 % / Rmerge(I) obs: 0.463 / Mean I/σ(I) obs: 3.2 / % possible all: 96.9

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entries 1N5M and 1C4R

1n5m

1c4r


Resolution: 2.4→24.64 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.261 3783 -random
Rwork0.242 ---
all0.243 ---
obs0.243 74475 97.5 %-
Displacement parametersBiso mean: 62.9 Å2
Baniso -1Baniso -2Baniso -3
1--1.56 Å2-1.34 Å22.9 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.4 Å0.36 Å
Luzzati d res low-5 Å
Luzzati sigma a0.6 Å0.54 Å
Refinement stepCycle: LAST / Resolution: 2.4→24.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11300 0 100 1552 12952
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_dihedral_angle_d26.5
X-RAY DIFFRACTIONc_improper_angle_d1.2
LS refinement shellResolution: 2.4→2.55 Å / Rfactor Rfree error: 0.015
RfactorNum. reflection% reflection
Rfree0.382 618 -
Rwork0.364 --
obs-11549 97 %

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