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- PDB-3mw2: Crystal structure of beta-neurexin 1 with the splice insert 4 -

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Basic information

Entry
Database: PDB / ID: 3mw2
TitleCrystal structure of beta-neurexin 1 with the splice insert 4
ComponentsNeurexin-1-alpha
KeywordsCELL ADHESION / NEUREXIN / LNS domain / CALCIUM-binding / GLYCOPROTEIN
Function / homology
Function and homology information


regulation of postsynaptic specialization assembly / gephyrin clustering involved in postsynaptic density assembly / Neurexins and neuroligins / 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 / postsynaptic membrane assembly / neuroligin family protein binding / positive regulation of synapse maturation ...regulation of postsynaptic specialization assembly / gephyrin clustering involved in postsynaptic density assembly / Neurexins and neuroligins / 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 / postsynaptic membrane assembly / neuroligin family protein binding / positive regulation of synapse maturation / regulation of postsynaptic density assembly / synaptic membrane adhesion / regulation of grooming behavior / presynapse assembly / regulation of synaptic vesicle cycle / neurotransmitter secretion / acetylcholine receptor binding / positive regulation of synapse assembly / adult behavior / neuromuscular process controlling balance / endocytic vesicle / positive regulation of excitatory postsynaptic potential / regulation of presynapse assembly / calcium channel regulator activity / prepulse inhibition / GABA-ergic synapse / presynaptic active zone membrane / cell adhesion molecule binding / synapse assembly / cellular response to calcium ion / positive regulation of synaptic transmission, glutamatergic / learning / cell projection / Schaffer collateral - CA1 synapse / transmembrane signaling receptor activity / presynaptic membrane / chemical synaptic transmission / nuclear membrane / vesicle / signaling receptor binding / neuronal cell body / glutamatergic synapse / calcium ion binding / protein-containing complex binding / nucleolus / cell surface / signal transduction / endoplasmic reticulum / protein-containing complex / plasma membrane
Similarity search - Function
Neurexin/syndecan/glycophorin C / putative band 4.1 homologues' binding motif / : / Laminin G domain / Laminin G domain profile. / Laminin G domain / Laminin G domain / EGF-like domain / EGF-type aspartate/asparagine hydroxylation site / Aspartic acid and asparagine hydroxylation site. ...Neurexin/syndecan/glycophorin C / putative band 4.1 homologues' binding motif / : / Laminin G domain / Laminin G domain profile. / Laminin G domain / Laminin G domain / EGF-like domain / EGF-type aspartate/asparagine hydroxylation site / Aspartic acid and asparagine hydroxylation site. / Epidermal growth factor-like domain. / Jelly Rolls - #200 / EGF-like domain profile. / EGF-like domain / Concanavalin A-like lectin/glucanase domain superfamily / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
PHOSPHATE ION / Neurexin-1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.69 Å
AuthorsJin, X. / Shapiro, L.
CitationJournal: Neuron / Year: 2010
Title: Splice Form Dependence of beta-Neurexin/Neuroligin Binding Interactions.
Authors: Koehnke, J. / Katsamba, P.S. / Ahlsen, G. / Bahna, F. / Vendome, J. / Honig, B. / Shapiro, L. / Jin, X.
History
DepositionMay 5, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 28, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / 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 / 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 / _pdbx_struct_assembly_gen.asym_id_list / _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
Revision 2.1Sep 6, 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
Revision 2.2Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)46,7755
Polymers45,5072
Non-polymers1,2683
Water2,666148
1
A: Neurexin-1-alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,4353
Polymers22,7541
Non-polymers6822
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Neurexin-1-alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,3402
Polymers22,7541
Non-polymers5871
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)85.890, 59.819, 105.697
Angle α, β, γ (deg.)90.00, 103.86, 90.00
Int Tables number5
Space group name H-MC121
DetailsThe biological unit is a monomer.

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Components

#1: Protein Neurexin-1-alpha / Neurexin I-alpha


Mass: 22753.578 Da / Num. of mol.: 2 / Fragment: UNP residues 1132 to 1334
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Nrxn1, Kiaa0578 / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: Q9CS84
#2: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[beta-D-mannopyranose-(1-6)]2-acetamido-2-deoxy-beta- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[beta-D-mannopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4[DManpb1-6]DGlcpNAcb1-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_a6-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}[(6+1)][b-D-Manp]{}}}LINUCSPDB-CARE
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 148 / 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: 2.9 Å3/Da / Density % sol: 57.53 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.9
Details: 26% PEG1000, 0.2M lithium sulfate, 0.1M phosphate-citrate, pH 4.9, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4C / Wavelength: 0.9795 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jun 12, 2009
Details: Si (111) crystal monochromator with vertical focusing mirror
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. all: 18319 / Num. obs: 14339 / % possible obs: 78.3 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.6 % / Rmerge(I) obs: 0.09 / Rsym value: 0.09 / Net I/σ(I): 19.7

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Processing

Software
NameVersionClassification
MAR345data collection
PHASERphasing
REFMAC5.2.0019refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ID 3BOD

3bod


Resolution: 2.69→20 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.84 / SU B: 26.824 / SU ML: 0.3 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R Free: 0.386 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28724 739 5.1 %RANDOM
Rwork0.2058 ---
all0.21 14286 --
obs0.21016 13752 99.02 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 35.836 Å2
Baniso -1Baniso -2Baniso -3
1-0.64 Å20 Å2-0.91 Å2
2--0.97 Å20 Å2
3----2.05 Å2
Refinement stepCycle: LAST / Resolution: 2.69→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3041 0 83 148 3272
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0223209
X-RAY DIFFRACTIONr_angle_refined_deg1.2341.9754357
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6615397
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.20423.867150
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.00715524
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.5921526
X-RAY DIFFRACTIONr_chiral_restr0.0760.2495
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.022414
X-RAY DIFFRACTIONr_nbd_refined0.20.21235
X-RAY DIFFRACTIONr_nbtor_refined0.3060.22105
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1540.2166
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2020.254
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1960.25
X-RAY DIFFRACTIONr_mcbond_it0.4071.51994
X-RAY DIFFRACTIONr_mcangle_it0.73623115
X-RAY DIFFRACTIONr_scbond_it1.03131365
X-RAY DIFFRACTIONr_scangle_it1.8324.51238
LS refinement shellResolution: 2.69→2.759 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.461 50 -
Rwork0.348 946 -
obs--90.79 %
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)
12.76081.24060.2853.02470.04324.91240.1038-0.1793-0.03610.0586-0.23360.0515-0.12040.1480.1299-0.2254-0.0022-0.0412-0.25460.0424-0.091425.8861-0.244713.8177
25.7741.53891.26413.46220.79166.0680.0785-0.65690.27140.234-0.27590.1607-0.1429-0.33770.1973-0.0725-0.18570.00810.003-0.0083-0.078410.9478-7.819640.0964
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A84 - 288
2X-RAY DIFFRACTION2B84 - 288

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