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- PDB-6pnq: Crystal structure of the SS2A splice insert-containing neurexin-1... -

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Basic information

Entry
Database: PDB / ID: 6pnq
TitleCrystal structure of the SS2A splice insert-containing neurexin-1 LNS2 domain in complex with neurexophilin-1
Components
  • Neurexin-1
  • Neurexophilin-1
KeywordsCELL ADHESION / Synapse / complex / splice-variant
Function / homology
Function and homology information


regulation of trans-synaptic signaling by endocannabinoid, modulating synaptic transmission / regulation of postsynaptic specialization assembly / gephyrin clustering involved in postsynaptic density assembly / Neurexins and neuroligins / neuroligin clustering involved in postsynaptic membrane assembly / postsynaptic density protein 95 clustering / postsynaptic membrane assembly / neuroligin family protein binding / positive regulation of synapse maturation / regulation of postsynaptic density assembly ...regulation of trans-synaptic signaling by endocannabinoid, modulating synaptic transmission / regulation of postsynaptic specialization assembly / gephyrin clustering involved in postsynaptic density assembly / Neurexins and neuroligins / neuroligin clustering involved in postsynaptic membrane assembly / postsynaptic density protein 95 clustering / 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 / positive regulation of excitatory postsynaptic potential / neuromuscular process controlling balance / regulation of presynapse assembly / calcium channel regulator activity / endocytic vesicle / GABA-ergic synapse / prepulse inhibition / 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 / endoplasmic reticulum / signal transduction / protein-containing complex / extracellular region / plasma membrane
Similarity search - Function
Neurexophilin / Neurexophilin/NXPE / Neurexophilin / 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 ...Neurexophilin / Neurexophilin/NXPE / Neurexophilin / 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
Neurexophilin-1 / Neurexin-1
Similarity search - Component
Biological speciesMus musculus (house mouse)
Rattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.947 Å
AuthorsWilson, S.C. / White, K.I. / Zhou, Q. / Brunger, A.T.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Mental Health (NIH/NIMH)R37MH63105 United States
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: Embo J. / Year: 2019
Title: Structures of neurexophilin-neurexin complexes reveal a regulatory mechanism of alternative splicing.
Authors: Wilson, S.C. / White, K.I. / Zhou, Q. / Pfuetzner, R.A. / Choi, U.B. / Sudhof, T.C. / Brunger, A.T.
History
DepositionJul 2, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 9, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Nov 20, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Nov 27, 2019Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.4Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Neurexin-1
B: Neurexophilin-1


Theoretical massNumber of molelcules
Total (without water)41,0402
Polymers41,0402
Non-polymers00
Water3,243180
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS, gel filtration, light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2420 Å2
ΔGint-12 kcal/mol
Surface area15330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.962, 61.443, 79.392
Angle α, β, γ (deg.)90.000, 106.220, 90.000
Int Tables number5
Space group name H-MC121
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Components on special symmetry positions
IDModelComponents
11B-368-

HOH

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Components

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


Mass: 21958.762 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Nrxn1, Kiaa0578 / Production host: Homo sapiens (human) / References: UniProt: Q9CS84
#2: Protein Neurexophilin-1 / Neurophilin


Mass: 19081.398 Da / Num. of mol.: 1 / Mutation: N146D, N156D, N162D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Nxph1, Nph1 / Production host: Homo sapiens (human) / References: UniProt: Q63366
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 180 / 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: 2.05 Å3/Da / Density % sol: 40.1 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 16% PEG 3350, 2% Tacsimate, and 0.1 M sodium citrate tribasic

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.97946 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 22, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 1.947→45.92 Å / Num. obs: 23404 / % possible obs: 83.17 % / Redundancy: 12 % / Biso Wilson estimate: 20.68 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.108 / Rpim(I) all: 0.03071 / Net I/σ(I): 11.4
Reflection shellResolution: 1.95→2.02 Å / Redundancy: 6.3 % / Rmerge(I) obs: 1.421 / Mean I/σ(I) obs: 0.78 / Num. unique obs: 583 / CC1/2: 0.559 / Rpim(I) all: 0.5289 / % possible all: 24.18

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6PNP

6pnp


Resolution: 1.947→45.92 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 25.82
RfactorNum. reflection% reflection
Rfree0.24 1997 9.81 %
Rwork0.1963 --
obs0.2007 20360 83.17 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 152.62 Å2 / Biso mean: 35.86 Å2 / Biso min: 5.84 Å2
Refinement stepCycle: final / Resolution: 1.947→45.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2553 0 0 180 2733
Biso mean---36.28 -
Num. residues----327
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.9473-1.9960.3393370.314334722
1.996-2.050.2772580.283153233
2.05-2.11030.3042960.25288157
2.1103-2.17840.28791330.2437122278
2.1784-2.25630.29241560.222144591
2.2563-2.34660.281640.2164150297
2.3466-2.45340.2661660.2073152897
2.4534-2.58280.24461650.2082151697
2.5828-2.74460.24571700.2054156499
2.7446-2.95640.29011710.2106157799
2.9564-3.25390.23011670.1951151997
3.2539-3.72450.19731700.1765156699
3.7245-4.69180.19511710.1553157298
4.6918-45.920.23611730.1904159298
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)
12.09830.3511-0.2362.8837-1.12222.97960.1865-0.3732-0.01560.46280.01620.3604-0.0213-0.36940.00540.1697-0.1060.06430.22010.04560.1267-26.38774.367425.5397
21.0260.1429-0.4232.2226-1.00383.28690.2283-0.0365-0.0571-0.0694-0.17450.04960.0730.2254-0.0039-0.0343-0.04870.0020.03350.00620.1469-13.287516.03345.4063
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain 'A' and resid 295 through 492)A295 - 492
2X-RAY DIFFRACTION2(chain 'B' and resid 119 through 261)B119 - 261

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