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- PDB-3vkf: Crystal Structure of Neurexin 1beta/Neuroligin 1 complex -

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Basic information

Entry
Database: PDB / ID: 3vkf
TitleCrystal Structure of Neurexin 1beta/Neuroligin 1 complex
Components
  • Neurexin-1-beta
  • Neuroligin-1
KeywordsCELL ADHESION / Alpha/Beta Hydrolase / Beta-sandwich / Synapse Matulation / Calcium Binding / N-glycosylation / Membrane
Function / homology
Function and homology information


neurexin clustering involved in presynaptic membrane assembly / regulation of presynapse organization / 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 / protein complex involved in cell-cell adhesion / positive regulation of neuromuscular synaptic transmission / terminal button organization ...neurexin clustering involved in presynaptic membrane assembly / regulation of presynapse organization / 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 / protein complex involved in cell-cell adhesion / positive regulation of neuromuscular synaptic transmission / terminal button organization / neuron to neuron synapse / positive regulation of synaptic vesicle exocytosis / postsynaptic density protein 95 clustering / excitatory synapse assembly / postsynaptic specialization assembly / negative regulation of dendritic spine morphogenesis / postsynaptic membrane assembly / neuronal ion channel clustering / positive regulation of synaptic vesicle clustering / presynaptic membrane assembly / synapse maturation / NMDA glutamate receptor clustering / maintenance of synapse structure / Neurexins and neuroligins / synaptic vesicle targeting / 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 / 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 / postsynaptic specialization membrane / positive regulation of synapse assembly / positive regulation of ruffle assembly / positive regulation of dendritic spine development / positive regulation of protein localization to synapse / positive regulation of intracellular signal transduction / positive regulation of filopodium assembly / heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules / synaptic vesicle transport / regulation of neuron differentiation / regulation of NMDA receptor activity / positive regulation of excitatory postsynaptic potential / excitatory synapse / synaptic vesicle endocytosis / GABA-ergic synapse / protein targeting / synaptic cleft / synapse assembly / cellular response to calcium ion / cell adhesion molecule binding / positive regulation of synaptic transmission, glutamatergic / neuron projection morphogenesis / dendritic shaft / long-term synaptic potentiation / cell projection / PDZ domain binding / positive regulation of synaptic transmission, GABAergic / synapse organization / modulation of chemical synaptic transmission / neuromuscular junction / establishment of protein localization / positive regulation of neuron projection development / neuron projection development / rhythmic process / presynapse / signaling receptor activity / presynaptic membrane / nervous system development / chemical synaptic transmission / scaffold protein binding / angiogenesis / dendritic spine / postsynaptic density / membrane => GO:0016020 / receptor complex / cell adhesion / external side of plasma membrane / dendrite / glutamatergic synapse / synapse / protein-containing complex binding / Golgi apparatus / cell surface / identical protein binding / metal ion binding / plasma membrane
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 / Laminin G domain / Carboxylesterase type B, conserved site ...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
Neurexin-1-beta / Neuroligin-1
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
Bos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 Å
AuthorsTanaka, H. / Miyazaki, N. / Nogi, T. / Iwasaki, K. / Takagi, J.
CitationJournal: Cell Rep / Year: 2012
Title: Higher-order architecture of cell adhesion mediated by polymorphic synaptic adhesion molecules neurexin and neuroligin.
Authors: Tanaka, H. / Miyazaki, N. / Matoba, K. / Nogi, T. / Iwasaki, K. / Takagi, J.
History
DepositionNov 15, 2011Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 1, 2012Provider: repository / Type: Initial release
Revision 1.1Jun 26, 2013Group: Database references
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / 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 / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.type_symbol / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _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_auth_asym_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.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_comp_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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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: Neurexin-1-beta
D: Neurexin-1-beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)170,9349
Polymers169,8254
Non-polymers1,1095
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Neuroligin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,1593
Polymers65,3521
Non-polymers8082
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
B: Neuroligin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,5732
Polymers65,3521
Non-polymers2211
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
C: Neurexin-1-beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,6012
Polymers19,5611
Non-polymers401
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
D: Neurexin-1-beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,6012
Polymers19,5611
Non-polymers401
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)81.261, 95.186, 120.396
Angle α, β, γ (deg.)90.00, 108.62, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Neuroligin-1 / / Neuroligin I


Mass: 65351.578 Da / Num. of mol.: 2
Fragment: Acetylcholinesterase-like domain (UNP RESIDUES 45-638)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Nlgn1 / Plasmid: pSGHV0 / Cell line (production host): CHO / Production host: Cricetulus griseus (Chinese hamster) / Strain (production host): Lec 3.2.8.1 / References: UniProt: Q62765
#2: Protein Neurexin-1-beta / Neurexin I-beta


Mass: 19560.889 Da / Num. of mol.: 2 / Fragment: LNS domain (UNP RESIDUES 83-290)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (cattle) / Gene: NRXN1 / Plasmid: pGEX-3T / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q28142
#3: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}}LINUCSPDB-CARE
#4: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2
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.: 2 / Source method: obtained synthetically / Formula: Ca
Sequence detailsSEQUENCE OF THE CHAIN A/B WAS BASED ON ISOFORM 3 OF DATABASE Q62765 (NLGN1_RAT). SEQUENCE OF THE ...SEQUENCE OF THE CHAIN A/B WAS BASED ON ISOFORM 3 OF DATABASE Q62765 (NLGN1_RAT). SEQUENCE OF THE CHAIN C/D WAS BASED ON ISOFORM 3B OF DATABASE Q28142 (NRX1B_BOVIN).

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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: 2.6 Å3/Da / Density % sol: 52.66 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.1M sodium chloride, 0.005M calcium chloride, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Feb 26, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.3→48.91 Å / Num. obs: 25519 / % possible obs: 97.3 % / Observed criterion σ(I): -3 / Redundancy: 3.7 % / Biso Wilson estimate: 58.4 Å2
Reflection shellResolution: 3.3→3.48 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.311 / Mean I/σ(I) obs: 4.3 / Num. unique all: 3541 / % possible all: 93.7

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
MOLREPphasing
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.3→48.91 Å / Cor.coef. Fo:Fc: 0.915 / Cor.coef. Fo:Fc free: 0.842 / SU B: 72.166 / SU ML: 0.534 / Cross valid method: THROUGHOUT / ESU R Free: 0.697 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2869 2586 10.1 %RANDOM
Rwork0.20524 ---
obs0.21365 22921 96.78 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 66.469 Å2
Baniso -1Baniso -2Baniso -3
1--1.22 Å20 Å2-1.32 Å2
2--0.02 Å20 Å2
3---0.36 Å2
Refinement stepCycle: LAST / Resolution: 3.3→48.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11251 0 69 0 11320
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.02211623
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.0461.95615843
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.32351435
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.12324.49539
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.007151801
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.6091556
X-RAY DIFFRACTIONr_chiral_restr0.0710.21740
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.028978
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1960.25474
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3050.27816
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1220.2370
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.1650.25
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1570.293
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0550.24
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.2251.57314
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.41211574
X-RAY DIFFRACTIONr_scbond_it0.38834903
X-RAY DIFFRACTIONr_scangle_it0.6564.54269
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.3→3.385 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.344 179 -
Rwork0.259 1591 -
obs--91.47 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
17.8904-1.9851-2.35284.71441.05542.2680.08790.0029-0.13830.0762-0.09610.30740.0011-0.02060.0082-0.2104-0.0204-0.0118-0.41540.0072-0.1857-49.457-7.10249.912
210.8740.9156-2.34343.68561.84633.44740.1303-0.28860.57250.03640.0506-0.15180.00140.0844-0.1809-0.11530.0454-0.0477-0.10620.0822-0.170424.865-2.006-15.517
32.0882-0.10520.0421.38370.11392.35280.0107-0.01250.0242-0.1276-0.0211-0.1185-0.11220.08910.0104-0.2943-0.0230.023-0.37110.0349-0.1999-8.35-1.151148.7848
41.8259-0.13210.2580.9964-0.68974.29440.03170.0825-0.0786-0.0202-0.06370.087-0.146-0.13150.032-0.1337-0.043-0.0201-0.1156-0.034-0.1722-16.62571.8414-12.2669
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1C82 - 288
2X-RAY DIFFRACTION1C2001
3X-RAY DIFFRACTION2D82 - 288
4X-RAY DIFFRACTION2D2001
5X-RAY DIFFRACTION3A52 - 634
6X-RAY DIFFRACTION3A2001 - 2004
7X-RAY DIFFRACTION4B52 - 634
8X-RAY DIFFRACTION4B2001

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