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- PDB-3bix: Crystal structure of the extracellular esterase domain of Neuroligin-1 -

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Basic information

Entry
Database: PDB / ID: 3bix
TitleCrystal structure of the extracellular esterase domain of Neuroligin-1
ComponentsNeuroligin-1
KeywordsCELL ADHESION / esterase domain / alpha-beta hydrolase / Cell junction / Glycoprotein / Membrane / Postsynaptic cell membrane / Synapse / Transmembrane
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 / excitatory synapse assembly / postsynaptic density protein 95 clustering / 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 / maintenance of synapse structure / Neurexins and neuroligins / synaptic vesicle targeting / synaptic membrane adhesion / synaptic vesicle clustering / inhibitory synapse / receptor localization to synapse / neuron cell-cell adhesion / regulation of respiratory gaseous exchange by nervous system process / neurexin family protein binding / filopodium tip / protein localization to synapse / NMDA glutamate receptor clustering / 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 / AMPA glutamate receptor clustering / postsynaptic specialization membrane / positive regulation of synapse assembly / positive regulation of ruffle assembly / positive regulation of filopodium assembly / positive regulation of protein localization to synapse / positive regulation of intracellular signal transduction / heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules / synaptic vesicle transport / regulation of neuron differentiation / positive regulation of dendritic spine development / regulation of NMDA receptor activity / positive regulation of excitatory postsynaptic potential / excitatory synapse / synaptic vesicle endocytosis / protein targeting / GABA-ergic synapse / 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 / 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 / nervous system development / chemical synaptic transmission / scaffold protein binding / dendritic spine / postsynaptic density / receptor complex / external side of plasma membrane / dendrite / synapse / glutamatergic synapse / protein-containing complex binding / Golgi apparatus / 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
NICKEL (II) ION / Neuroligin-1
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.8 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 1.4Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / 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 / _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

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)259,67228
Polymers256,9164
Non-polymers2,75624
Water35,3991965
1
A: Neuroligin-1
hetero molecules

C: Neuroligin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)129,83614
Polymers128,4582
Non-polymers1,37812
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_554-y,x-y,z-1/31
Buried area4440 Å2
MethodPISA
2
B: Neuroligin-1
D: Neuroligin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)129,83614
Polymers128,4582
Non-polymers1,37812
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)173.744, 173.744, 108.045
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number145
Space group name H-MP32

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Components

#1: Protein
Neuroligin-1 / / Neuroligin I


Mass: 64228.961 Da / Num. of mol.: 4 / Fragment: extracellular esterase domain
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: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 8
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
#3: Chemical ChemComp-NI / NICKEL (II) ION / Nickel


Mass: 58.693 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ni
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1965 / 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: 3.66 Å3/Da / Density % sol: 66.44 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.7
Details: 1.2 M tri-Sodium citrate, 0.1 M Tris, pH 8.7, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 130 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 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: 1.75→50 Å / Num. obs: 360486 / % possible obs: 98.3 % / Redundancy: 2.7 % / Rmerge(I) obs: 0.077 / Χ2: 0.992 / Net I/σ(I): 10.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.75-1.8120.601337370.65191.9
1.81-1.892.30.516357390.898197.3
1.89-1.972.40.401359041.057198
1.97-2.072.50.237361031.06198.5
2.07-2.22.60.155362660.907198.9
2.2-2.382.70.135362641.083199
2.38-2.612.90.096365991.026199.7
2.61-2.9930.092366271.0671100
2.99-3.7730.07366240.993199.9
3.77-503.10.035366230.998199.9

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Phasing

PhasingMethod: molecular replacement

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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: 1.8→45.88 Å / Rfactor Rfree error: 0.002 / FOM work R set: 0.866 / Data cutoff high absF: 1687471.75 / 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
Rfree0.205 16809 5 %RANDOM
Rwork0.185 ---
obs-334460 98.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 54.314 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso mean: 25.1 Å2
Baniso -1Baniso -2Baniso -3
1-2.13 Å20 Å20 Å2
2--2.13 Å20 Å2
3----4.26 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.22 Å0.19 Å
Luzzati d res low-5 Å
Luzzati sigma a0.22 Å0.2 Å
Refinement stepCycle: LAST / Resolution: 1.8→45.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17540 0 170 1965 19675
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d22.8
X-RAY DIFFRACTIONc_improper_angle_d0.81
X-RAY DIFFRACTIONc_mcbond_it1.171.5
X-RAY DIFFRACTIONc_mcangle_it1.782
X-RAY DIFFRACTIONc_scbond_it2.022
X-RAY DIFFRACTIONc_scangle_it3.152.5
LS refinement shellResolution: 1.8→1.91 Å / Rfactor Rfree error: 0.006 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.297 2813 5.1 %
Rwork0.269 52025 -
all-54838 -
obs--97.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2edo.pardna-rna.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4ion.paramion.top
X-RAY DIFFRACTION5carbohydrate.param

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