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- PDB-2r1b: Crystal Structure of rat neurexin 1beta with a splice insert at SS#4 -

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Basic information

Entry
Database: PDB / ID: 2r1b
TitleCrystal Structure of rat neurexin 1beta with a splice insert at SS#4
ComponentsNeurexin-1-beta
KeywordsCELL ADHESION / SPLICING / beta-sandwich
Function / homology
Function and homology information


protein-containing complex assembly involved in synapse maturation / cell-cell adhesion involved in synapse maturation / positive regulation of presynaptic active zone assembly / regulation of postsynaptic specialization assembly / gephyrin clustering involved in postsynaptic density assembly / protein complex involved in cell-cell adhesion / type 1 fibroblast growth factor receptor binding / positive regulation of neuromuscular synaptic transmission / guanylate kinase-associated protein clustering / neuron to neuron synapse ...protein-containing complex assembly involved in synapse maturation / cell-cell adhesion involved in synapse maturation / positive regulation of presynaptic active zone assembly / regulation of postsynaptic specialization assembly / gephyrin clustering involved in postsynaptic density assembly / protein complex involved in cell-cell adhesion / type 1 fibroblast growth factor receptor binding / positive regulation of neuromuscular synaptic transmission / guanylate kinase-associated protein clustering / neuron to neuron synapse / trans-synaptic signaling, modulating synaptic transmission / neuroligin clustering involved in postsynaptic membrane assembly / postsynaptic density protein 95 clustering / regulation of trans-synaptic signaling by endocannabinoid, modulating synaptic transmission / cerebellar granule cell differentiation / postsynaptic membrane assembly / gamma-aminobutyric acid receptor clustering / presynaptic membrane assembly / synapse maturation / maintenance of synapse structure / negative regulation of filopodium assembly / vocal learning / slit diaphragm / neuroligin family protein binding / positive regulation of synapse maturation / positive regulation of fibroblast growth factor receptor signaling pathway / regulation of postsynaptic density assembly / synaptic vesicle clustering / neuron cell-cell adhesion / inhibitory synapse / synaptic membrane adhesion / regulation of grooming behavior / presynapse assembly / receptor localization to synapse / protein localization to synapse / NMDA glutamate receptor clustering / vocalization behavior / regulation of synaptic vesicle cycle / calcium-dependent cell-cell adhesion via plasma membrane cell adhesion molecules / regulation of AMPA receptor activity / neurotransmitter secretion / filopodium assembly / neuron maturation / acetylcholine receptor binding / positive regulation of synapse assembly / regulation of NMDA receptor activity / heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules / adult behavior / positive regulation of protein kinase A signaling / social behavior / neuromuscular process controlling balance / endocytic vesicle / positive regulation of excitatory postsynaptic potential / excitatory synapse / regulation of presynapse assembly / calcium channel regulator activity / prepulse inhibition / axonal growth cone / GABA-ergic synapse / presynaptic active zone membrane / cell adhesion molecule binding / synapse assembly / cellular response to calcium ion / positive regulation of synaptic transmission, glutamatergic / neuron projection morphogenesis / learning / positive regulation of synaptic transmission, GABAergic / positive regulation of protein localization to plasma membrane / establishment of protein localization / neuromuscular junction / Schaffer collateral - CA1 synapse / positive regulation of neuron projection development / circadian rhythm / calcium-dependent protein binding / neuron projection development / transmembrane signaling receptor activity / positive regulation of peptidyl-serine phosphorylation / presynaptic membrane / chemical synaptic transmission / nuclear membrane / angiogenesis / vesicle / positive regulation of ERK1 and ERK2 cascade / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / negative regulation of gene expression / signaling receptor binding / neuronal cell body / glutamatergic synapse / calcium ion binding / positive regulation of gene expression / protein-containing complex binding / cell surface / signal transduction / endoplasmic reticulum / protein-containing complex / plasma membrane
Similarity search - Function
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 / Jelly Rolls - #200 ...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 / Jelly Rolls - #200 / Concanavalin A-like lectin/glucanase domain superfamily / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.72 Å
AuthorsRudenko, G.
CitationJournal: Structure / Year: 2008
Title: Regulation of Neurexin 1beta Tertiary Structure and Ligand Binding through Alternative Splicing
Authors: Shen, K.C. / Kuczynska, D.A. / Wu, I.J. / Murray, B.H. / Sheckler, L.R. / Rudenko, G.
History
DepositionAug 22, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 25, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Jul 24, 2019Group: Data collection / Refinement description / Category: software
Item: _software.classification / _software.name / _software.version
Revision 1.4Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ncs_dom_lim / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Neurexin-1-beta
B: Neurexin-1-beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,0704
Polymers47,9902
Non-polymers802
Water6,359353
1
A: Neurexin-1-beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,0352
Polymers23,9951
Non-polymers401
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Neurexin-1-beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,0352
Polymers23,9951
Non-polymers401
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)84.122, 39.260, 85.410
Angle α, β, γ (deg.)90.00, 115.47, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31A
41B
51A
61B
71A
81B
91A
101B
111A
121B
131A
141B

NCS domain segments:

Ens-ID: 1 / Refine code: 2

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLYGLYILEILEAA80 - 1156 - 41
21GLYGLYILEILEBB80 - 1156 - 41
32VALVALLEULEUAA120 - 12646 - 52
42VALVALLEULEUBB120 - 12646 - 52
53GLYGLYTYRTYRAA134 - 13860 - 64
63GLYGLYTYRTYRBB134 - 13860 - 64
74GLYGLYASPASPAA146 - 17072 - 96
84GLYGLYASPASPBB146 - 17072 - 96
95THRTHRGLUGLUAA179 - 196105 - 122
105THRTHRGLUGLUBB179 - 196105 - 122
116LEULEUGLNGLNAA219 - 233145 - 159
126LEULEUGLNGLNBB219 - 233145 - 159
137SERSERPROPROAA239 - 292165 - 218
147SERSERPROPROBB239 - 292165 - 218

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Components

#1: Protein Neurexin-1-beta / neurexin I-beta


Mass: 23994.895 Da / Num. of mol.: 2 / Fragment: LNS/LG domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Nrxn1 / Plasmid: pGEX-KG / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q63373
#2: Chemical ChemComp-CA / CALCIUM ION


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


Mass: 18.015 Da / Num. of mol.: 353 / 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: 2.65 Å3/Da / Density % sol: 53.64 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 17% Peg 8000, 0.1 M Tris pH 8.5, 0.2 M MgCl2, 5 mM CaCl2, 0.5% beta-octyl-glucoside, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 103 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 32-ID / Wavelength: 1 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jan 1, 2005
RadiationMonochromator: see beam-line specifications / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.72→19.9 Å / Num. all: 49680 / Num. obs: 49680 / % possible obs: 92.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.2 % / Biso Wilson estimate: 22.5 Å2 / Rmerge(I) obs: 0.054 / Net I/σ(I): 25.9
Reflection shellResolution: 1.72→1.76 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.355 / Mean I/σ(I) obs: 3.1 / Num. unique all: 2877 / Rsym value: 0.355 / % possible all: 73.1

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Processing

Software
NameVersionClassification
REFMAC5.2refinement
CNSrefinement
MAR345softwaredata collection
MOSFLMdata reduction
SCALAdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1C4R

1c4r


Resolution: 1.72→19.9 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.937 / SU B: 4.487 / SU ML: 0.076 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.113 / ESU R Free: 0.108 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.22474 3770 7.6 %RANDOM
Rwork0.19745 ---
all0.19956 49679 --
obs0.19956 45909 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 26.719 Å2
Baniso -1Baniso -2Baniso -3
1--1.48 Å20 Å2-0.91 Å2
2---0.17 Å20 Å2
3---0.86 Å2
Refinement stepCycle: LAST / Resolution: 1.72→19.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2980 0 2 353 3335
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0223075
X-RAY DIFFRACTIONr_angle_refined_deg1.7081.934168
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.265390
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.39724.286140
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.34515511
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.4411521
X-RAY DIFFRACTIONr_chiral_restr0.1570.2475
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022325
X-RAY DIFFRACTIONr_nbd_refined0.2230.21116
X-RAY DIFFRACTIONr_nbtor_refined0.2950.22046
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1660.2170
X-RAY DIFFRACTIONr_metal_ion_refined0.0550.26
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2530.267
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.4430.228
X-RAY DIFFRACTIONr_mcbond_it1.241.52032
X-RAY DIFFRACTIONr_mcangle_it1.72523112
X-RAY DIFFRACTIONr_scbond_it2.7631242
X-RAY DIFFRACTIONr_scangle_it4.1584.51056
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

NumberTypeRms dev position (Å)Weight position
632tight positional0.090.05
540medium positional0.330.5
632tight thermal0.260.5
540medium thermal0.852
LS refinement shellResolution: 1.72→1.765 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.415 209 -
Rwork0.356 2539 -
obs-2748 100 %
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)
12.5290.02931.0271.92690.5342.9277-0.0356-0.22850.1760.27770.0687-0.0557-0.1447-0.0386-0.033-0.09670.0122-0.0134-0.1759-0.0198-0.1995-9.928436.16262.6089
228.45558.278427.70892.40848.061326.9820.60380.1881-0.91550.19860.2012-0.05921.23140.4388-0.80490.21290.0581-0.1929-0.0162-0.09160.008215.603740.387481.1426
33.53820.6220.54161.64830.17311.4277-0.0404-0.1531-0.13530.08060.02530.10290.0729-0.0650.0151-0.1998-0.00330.0413-0.20630.0163-0.161343.8979-10.031844.7897
423.99743.91967.86380.95920.9133.0094-0.420.29730.6954-0.09610.18230.2529-0.3509-0.0190.2377-0.1083-0.0260.0001-0.13090.03380.021715.2238-14.533931.6886
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA80 - 1986 - 124
2X-RAY DIFFRACTION1AA238 - 294164 - 220
3X-RAY DIFFRACTION2AA216 - 237142 - 163
4X-RAY DIFFRACTION3BB80 - 1986 - 124
5X-RAY DIFFRACTION3BB238 - 292164 - 218
6X-RAY DIFFRACTION4BB216 - 237142 - 163

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