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- PDB-3bl8: Crystal structure of the extracellular domain of neuroligin 2A fr... -

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Basic information

Entry
Database: PDB / ID: 3bl8
TitleCrystal structure of the extracellular domain of neuroligin 2A from mouse
ComponentsNeuroligin-2
KeywordsCELL ADHESION / neuroligin 2A / Glycoprotein / Membrane / Phosphoprotein / Transmembrane
Function / homology
Function and homology information


Neurexins and neuroligins / jump response / neurotransmitter-gated ion channel clustering / positive regulation of t-SNARE clustering / postsynaptic specialization assembly / gephyrin clustering involved in postsynaptic density assembly / terminal button organization / postsynaptic density protein 95 clustering / postsynaptic membrane assembly / positive regulation of synaptic vesicle clustering ...Neurexins and neuroligins / jump response / neurotransmitter-gated ion channel clustering / positive regulation of t-SNARE clustering / postsynaptic specialization assembly / gephyrin clustering involved in postsynaptic density assembly / terminal button organization / postsynaptic density protein 95 clustering / postsynaptic membrane assembly / positive regulation of synaptic vesicle clustering / presynaptic membrane assembly / neurexin family protein binding / thigmotaxis / presynapse assembly / cell adhesion mediator activity / neuron cell-cell adhesion / regulation of respiratory gaseous exchange by nervous system process / insulin metabolic process / ribbon synapse / inhibitory synapse / protein localization to synapse / dopaminergic synapse / glycinergic synapse / positive regulation of synapse assembly / protein localization to cell surface / inhibitory synapse assembly / positive regulation of inhibitory postsynaptic potential / neuromuscular process controlling balance / postsynaptic specialization membrane / positive regulation of protein localization to synapse / positive regulation of dendritic spine development / synaptic transmission, GABAergic / locomotory exploration behavior / social behavior / regulation of presynapse assembly / positive regulation of synaptic transmission, glutamatergic / synapse assembly / cell adhesion molecule binding / excitatory synapse / sensory perception of pain / positive regulation of excitatory postsynaptic potential / dendritic shaft / positive regulation of synaptic transmission, GABAergic / synapse organization / modulation of chemical synaptic transmission / GABA-ergic synapse / positive regulation of insulin secretion / presynaptic membrane / dendritic spine / postsynaptic membrane / axon / positive regulation of cell population proliferation / synapse / dendrite / cell surface / identical protein binding / 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
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.3 Å
AuthorsJin, X. / Koehnke, J. / Shapiro, L.
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2008
Title: Crystal structure of the extracellular cholinesterase-like domain from neuroligin-2.
Authors: Koehnke, J. / Jin, X. / Budreck, E.C. / Posy, S. / Scheiffele, P. / Honig, B. / Shapiro, L.
History
DepositionDec 10, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 19, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 25, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software / Item: _pdbx_unobs_or_zero_occ_atoms.label_asym_id
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 / database_PDB_caveat / 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_unobs_or_zero_occ_atoms / pdbx_validate_chiral / pdbx_validate_close_contact / 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 / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.src_method / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_unobs_or_zero_occ_atoms.label_asym_id / _pdbx_validate_chiral.auth_asym_id / _pdbx_validate_chiral.auth_seq_id / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Mar 31, 2021Group: Source and taxonomy / Structure summary / Category: chem_comp / entity_src_gen
Item: _chem_comp.pdbx_synonyms / _entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_strain
Revision 2.2Oct 30, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _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-2
B: Neuroligin-2
C: Neuroligin-2
D: Neuroligin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)261,6678
Polymers259,4034
Non-polymers2,2644
Water93752
1
A: Neuroligin-2
C: Neuroligin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)130,5094
Polymers129,7022
Non-polymers8082
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2560 Å2
MethodPISA
2
B: Neuroligin-2
D: Neuroligin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)131,1584
Polymers129,7022
Non-polymers1,4562
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)214.723, 92.567, 188.408
Angle α, β, γ (deg.)90.000, 98.360, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
Neuroligin-2


Mass: 64850.801 Da / Num. of mol.: 4 / Fragment: esterase-like domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Nlgn2, Kiaa1366 / Plasmid: pCEP4-NL2A / Cell line (production host): HEK293-GNTI / Production host: Homo sapiens (human) / References: UniProt: Q69ZK9
#2: Polysaccharide alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...alpha-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: obtained synthetically
DescriptorTypeProgram
DManpa1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1a_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
#3: Polysaccharide alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-3)-[alpha-D- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1235.105 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3[DManpa1-6]DManpa1-3[DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,7,6/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3-3-3/a4-b1_b4-c1_c3-d1_c6-g1_d3-e1_d6-f1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}[(6+1)][a-D-Manp]{}}}}}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.: 2 / Source method: obtained synthetically / 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 52 / Source method: isolated from a natural source / Formula: H2O
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: 3.57 Å3/Da / Density % sol: 65.55 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.8
Details: 3.5% PEG 6000, 0.1M Bicine, pH 8.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4C / Wavelength: 0.9793 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jun 7, 2007
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 3.3→30 Å / Num. all: 57279 / Num. obs: 54385 / % possible obs: 98.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.1 % / Rmerge(I) obs: 0.101 / Χ2: 1.003 / Net I/σ(I): 7.9
Reflection shellResolution: 3.3→3.42 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.503 / Mean I/σ(I) obs: 1.4 / Num. unique all: 5279 / Rsym value: 0.503 / Χ2: 1.015 / % possible all: 96.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
DMphasing
REFMAC5.2.0019refinement
PDB_EXTRACT3.004data extraction
ADSCQuantumdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.3→20 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.918 / SU B: 61.915 / SU ML: 0.467 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.513 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.262 2714 5 %RANDOM
Rwork0.219 ---
obs0.221 54190 98.51 %-
all-54279 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 126.202 Å2
Baniso -1Baniso -2Baniso -3
1-1.45 Å20 Å2-9.25 Å2
2---2.62 Å20 Å2
3----1.52 Å2
Refinement stepCycle: LAST / Resolution: 3.3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17172 0 150 52 17374
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.02217826
X-RAY DIFFRACTIONr_angle_refined_deg1.2131.95724315
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0552179
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.63924.101851
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.917152691
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.00115100
X-RAY DIFFRACTIONr_chiral_restr0.0860.22632
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0213892
X-RAY DIFFRACTIONr_nbd_refined0.2090.28863
X-RAY DIFFRACTIONr_nbtor_refined0.3090.212039
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1370.2522
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2130.244
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1060.25
X-RAY DIFFRACTIONr_mcbond_it0.2781.511096
X-RAY DIFFRACTIONr_mcangle_it0.51217560
X-RAY DIFFRACTIONr_scbond_it0.52837612
X-RAY DIFFRACTIONr_scangle_it0.9374.56754
LS refinement shellResolution: 3.3→3.385 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.325 190 -
Rwork0.332 3578 -
all-3768 -
obs--96.69 %
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)
13.22250.0194-0.58633.7692-0.7022.1452-0.0827-0.46790.01740.43230.1417-0.21590.01630.0725-0.059-0.6722-0.03230.046-0.8698-0.0829-0.626548.498946.658110.9178
23.1231-0.19732.90542.2111-0.46587.2258-0.3199-0.78610.33090.4620.078-0.3425-0.93310.36890.2419-0.22110.082-0.0656-0.0598-0.1192-0.3587-16.839951.03540.7273
32.87650.75130.01172.4094-1.23793.88420.2119-0.4134-0.4720.3166-0.0303-0.08640.2677-0.2045-0.1816-0.1688-0.09890.0131-0.17070.1926-0.17719.319711.522552.7535
45.13570.17733.23541.64490.13634.76560.27060.0768-0.40140.0210.2845-0.07060.3305-0.5432-0.55510.2362-0.0784-0.24340.7312-0.5033-0.220416.40647.478392.7006
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA42 - 6053 - 566
2X-RAY DIFFRACTION2BB42 - 6053 - 566
3X-RAY DIFFRACTION3CC42 - 6053 - 566
4X-RAY DIFFRACTION4DD42 - 6053 - 566

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