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- PDB-3be8: Crystal structure of the synaptic protein neuroligin 4 -

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Basic information

Entry
Database: PDB / ID: 3be8
TitleCrystal structure of the synaptic protein neuroligin 4
ComponentsNeuroligin-4, X-linked
KeywordsCELL ADHESION / Neuroligin / cell adhesion protein / synaptic protein / a/b-hydrolase fold / four-helix bundle / Glycoprotein / Membrane / Transmembrane
Function / homology
Function and homology information


asymmetric, glutamatergic, excitatory synapse / symmetric, GABA-ergic, inhibitory synapse / postsynaptic membrane assembly / presynaptic membrane assembly / brainstem development / neuron cell-cell adhesion / neurexin family protein binding / negative regulation of excitatory postsynaptic potential / presynapse assembly / vocalization behavior ...asymmetric, glutamatergic, excitatory synapse / symmetric, GABA-ergic, inhibitory synapse / postsynaptic membrane assembly / presynaptic membrane assembly / brainstem development / neuron cell-cell adhesion / neurexin family protein binding / negative regulation of excitatory postsynaptic potential / presynapse assembly / vocalization behavior / cell-cell junction organization / Neurexins and neuroligins / chloride ion binding / organ growth / adult behavior / social behavior / excitatory synapse / synaptic vesicle endocytosis / cell adhesion molecule binding / cerebellum development / learning / postsynaptic density membrane / synapse organization / modulation of chemical synaptic transmission / neuron differentiation / presynapse / signaling receptor activity / scaffold protein binding / chemical synaptic transmission / synapse / dendrite / cell surface / protein homodimerization activity / membrane / plasma membrane
Similarity search - Function
Neuroligin / Carboxylesterase type B, conserved site / Carboxylesterases type-B signature 2. / Carboxylesterase, type B / Carboxylesterase family / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
CITRATE ANION / PHOSPHATE ION / Neuroligin-4, X-linked
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsFabrichny, I.P. / Leone, P. / Sulzenbacher, G. / Comoletti, D. / Miller, M.T. / Taylor, P. / Bourne, Y. / Marchot, P.
CitationJournal: Neuron / Year: 2007
Title: Structural Analysis of the Synaptic Protein Neuroligin and Its beta-Neurexin Complex: Determinants for Folding and Cell Adhesion
Authors: Fabrichny, I.P. / Leone, P. / Sulzenbacher, G. / Comoletti, D. / Miller, M.T. / Taylor, P. / Bourne, Y. / Marchot, P.
History
DepositionNov 16, 2007Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 29, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Jul 29, 2020Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / database_PDB_caveat ...chem_comp / database_PDB_caveat / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_conn_type / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_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_type.id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Nov 1, 2023Group: Data collection / Database references ...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
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-4, X-linked
B: Neuroligin-4, X-linked
hetero molecules


Theoretical massNumber of molelcules
Total (without water)134,33319
Polymers132,4602
Non-polymers1,87317
Water10,665592
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)139.730, 154.050, 81.300
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

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Protein / Sugars , 2 types, 6 molecules AB

#1: Protein Neuroligin-4, X-linked / / Neuroligin X / HNLX


Mass: 66230.203 Da / Num. of mol.: 2 / Fragment: extracellular cholinesterase-like domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NLGN4X / Cell (production host): HUMAN EMBRYONIC KIDNEY CELLS (HEK) / Cell line (production host): HEK 293 / Production host: Homo sapiens (human) / References: UniProt: Q8N0W4
#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 / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 4
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 , 6 types, 605 molecules

#3: Chemical ChemComp-FLC / CITRATE ANION / Citric acid


Mass: 189.100 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H5O7
#4: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#5: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#7: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 592 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsTHIS IS SPONTANEOUS MUTAGENESIS OF CDNA CLONES.

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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: 3.33 Å3/Da / Density % sol: 63.02 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 4.2
Details: 10% PEG-3000, 0.1M sodium phosphate-citrate, 0.3M sodium chloride, 0.01M calcium chloride, pH 4.2, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Mar 26, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 2.2→30 Å / Num. obs: 89603 / % possible obs: 99.9 % / Redundancy: 6.6 % / Rsym value: 0.065 / Net I/σ(I): 21.6
Reflection shellResolution: 2.2→2.25 Å / Redundancy: 6.6 % / Mean I/σ(I) obs: 4.5 / Rsym value: 0.47

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MxCuBEdata collection
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1J06

1j06


Resolution: 2.2→29.68 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.943 / SU B: 7.116 / SU ML: 0.095 / TLS residual ADP flag: UNVERIFIED / Cross valid method: THROUGHOUT / ESU R: 0.165 / ESU R Free: 0.149 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20075 4474 5 %RANDOM
Rwork0.1669 ---
obs0.16858 85129 99.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 33.923 Å2
Baniso -1Baniso -2Baniso -3
1--0.38 Å20 Å20 Å2
2--0.21 Å20 Å2
3---0.17 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.149 Å0.165 Å
Refinement stepCycle: LAST / Resolution: 2.2→29.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8504 0 111 592 9207
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0228966
X-RAY DIFFRACTIONr_bond_other_d0.0020.027829
X-RAY DIFFRACTIONr_angle_refined_deg1.3891.96212250
X-RAY DIFFRACTIONr_angle_other_deg0.865318291
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.16951104
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.65224.61423
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.795151392
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.7841538
X-RAY DIFFRACTIONr_chiral_restr0.0870.21331
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0210011
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021787
X-RAY DIFFRACTIONr_nbd_refined0.2080.21675
X-RAY DIFFRACTIONr_nbd_other0.1780.27683
X-RAY DIFFRACTIONr_nbtor_refined0.1770.24296
X-RAY DIFFRACTIONr_nbtor_other0.0860.24552
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1520.2541
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2330.221
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2940.262
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1970.213
X-RAY DIFFRACTIONr_mcbond_it0.7581.55555
X-RAY DIFFRACTIONr_mcbond_other0.1491.52192
X-RAY DIFFRACTIONr_mcangle_it1.26828812
X-RAY DIFFRACTIONr_scbond_it1.90633931
X-RAY DIFFRACTIONr_scangle_it2.8374.53421
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.239 350 -
Rwork0.19 6218 -
obs--99.98 %
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)
12.1190.6349-0.06941.193-0.0321.1698-0.031-0.1157-0.1473-0.0338-0.0146-0.1763-0.02980.29630.0456-0.1122-0.02190.0092-0.07390.0234-0.1488116.590134.687555.3565
28.78695.0372-2.38889.8741-1.997411.11360.3396-0.6729-0.62040.8152-0.18780.94790.7276-0.2378-0.15180.24550.0513-0.08360.28270.03320.1055114.213833.971975.6563
33.13451.2458-0.37811.9380.31052.6985-0.04-0.62050.58090.17550.1017-0.0217-0.48390.2532-0.06170.123-0.0506-0.02770.1556-0.1984-0.0031113.114855.31872.61
44.61641.0598-0.01672.5205-0.64632.62830.0839-0.62750.25650.2933-0.06310.3001-0.1531-0.2305-0.0208-0.0767-0.00940.02920.0354-0.0428-0.085986.890733.091469.6751
53.22950.0838-0.04662.3815-0.55891.62380.051-0.4279-0.4090.30760.0161-0.22140.09420.1789-0.0671-0.0396-0.0016-0.0057-0.12150.050.0121110.066218.199161.1115
61.3923-0.05650.07681.5118-0.13650.76050.035-0.0291-0.11260.1089-0.06430.03910.0092-0.02470.0293-0.10370.03820.0115-0.1594-0.0309-0.167342.573818.661864.4688
75.543-1.4862-3.26012.2792-0.38532.76070.00891.07080.0359-0.48960.0165-0.29510.05680.1808-0.02530.21520.0604-0.0410.2898-0.05250.068843.697123.711145.4671
84.7532-1.59761.04872.5007-0.44531.941-0.03770.24020.29480.0269-0.089-0.0476-0.27940.01340.1267-0.01290.05480.0194-0.09680.0406-0.145837.810242.689752.1192
95.59070.1939-0.89852.25570.01122.18340.00470.48020.4089-0.3437-0.00840.018-0.30270.03840.0037-0.04750.0114-0.0495-0.02730.05010.001970.267232.141652.272
103.35360.5018-0.1272.4527-0.03982.8264-0.02540.5832-0.3-0.42750.0476-0.21960.10570.199-0.0222-0.02360.06510.0357-0.0704-0.08410.014754.81967.660855.357
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA-2 - 11011 - 79
2X-RAY DIFFRACTION1AA142 - 291111 - 260
3X-RAY DIFFRACTION1AA340 - 373309 - 342
4X-RAY DIFFRACTION1AA449 - 472418 - 441
5X-RAY DIFFRACTION1AA561 - 582530 - 551
6X-RAY DIFFRACTION2AA111 - 14180 - 110
7X-RAY DIFFRACTION3AA292 - 339261 - 308
8X-RAY DIFFRACTION4AA374 - 448343 - 417
9X-RAY DIFFRACTION4AA583 - 597552 - 566
10X-RAY DIFFRACTION5AA473 - 560442 - 529
11X-RAY DIFFRACTION6BB-2 - 11011 - 79
12X-RAY DIFFRACTION6BB142 - 291111 - 260
13X-RAY DIFFRACTION6BB340 - 373309 - 342
14X-RAY DIFFRACTION6BB449 - 472418 - 441
15X-RAY DIFFRACTION6BB561 - 582530 - 551
16X-RAY DIFFRACTION7BB111 - 14180 - 110
17X-RAY DIFFRACTION8BB292 - 339261 - 308
18X-RAY DIFFRACTION9BB374 - 448343 - 417
19X-RAY DIFFRACTION9BB583 - 597552 - 566
20X-RAY DIFFRACTION10BB473 - 560442 - 529

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