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- PDB-6pnp: Crystal structure of the splice insert-free neurexin-1 LNS2 domai... -

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Basic information

Entry
Database: PDB / ID: 6pnp
TitleCrystal structure of the splice insert-free 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


Neurexins and neuroligins / neuroligin clustering involved in postsynaptic membrane assembly / regulation of trans-synaptic signaling by endocannabinoid, modulating synaptic transmission / trans-synaptic signaling, modulating synaptic transmission / trans-synaptic protein complex / gephyrin clustering involved in postsynaptic density assembly / postsynaptic density protein 95 clustering / postsynaptic membrane assembly / neuroligin family protein binding / positive regulation of synapse maturation ...Neurexins and neuroligins / neuroligin clustering involved in postsynaptic membrane assembly / regulation of trans-synaptic signaling by endocannabinoid, modulating synaptic transmission / trans-synaptic signaling, modulating synaptic transmission / trans-synaptic protein complex / gephyrin clustering involved in postsynaptic density assembly / postsynaptic density protein 95 clustering / postsynaptic membrane assembly / neuroligin family protein binding / positive regulation of synapse maturation / regulation of grooming behavior / presynapse assembly / synaptic membrane adhesion / regulation of postsynaptic specialization assembly / regulation of insulin secretion involved in cellular response to glucose stimulus / regulation of postsynaptic density assembly / acetylcholine receptor binding / neurotransmitter secretion / regulation of synaptic vesicle cycle / positive regulation of synapse assembly / vesicle docking involved in exocytosis / neuromuscular process controlling balance / adult behavior / positive regulation of excitatory postsynaptic potential / regulation of presynapse assembly / synaptic cleft / prepulse inhibition / positive regulation of synaptic transmission, glutamatergic / synapse assembly / cell adhesion molecule binding / presynaptic active zone membrane / learning / cell projection / calcium channel regulator activity / modulation of chemical synaptic transmission / GABA-ergic synapse / Schaffer collateral - CA1 synapse / presynaptic membrane / nuclear membrane / vesicle / chemical synaptic transmission / signaling receptor binding / neuronal cell body / calcium ion binding / glutamatergic synapse / cell surface / endoplasmic reticulum / protein-containing complex / 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 ...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: 1.94 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
Revision 1.5Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)40,2152
Polymers40,2152
Non-polymers00
Water1,20767
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2450 Å2
ΔGint-10 kcal/mol
Surface area15480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.705, 60.983, 79.619
Angle α, β, γ (deg.)90.000, 106.740, 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-335-

HOH

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Components

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


Mass: 21133.787 Da / Num. of mol.: 1 / Mutation: C293A
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.: 67 / 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: 2.07 Å3/Da / Density % sol: 40.65 %
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: APS / Beamline: 24-ID-C / Wavelength: 0.9791 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Mar 21, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 1.94→45.6 Å / Num. obs: 24370 / % possible obs: 94.99 % / Redundancy: 13 % / Biso Wilson estimate: 39.5 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.1 / Rpim(I) all: 0.02859 / Rrim(I) all: 0.1045 / Net I/σ(I): 14.05
Reflection shellResolution: 1.94→2.01 Å / Redundancy: 9.1 % / Rmerge(I) obs: 1.214 / Mean I/σ(I) obs: 1.29 / Num. unique obs: 1662 / CC1/2: 0.796 / Rpim(I) all: 0.4089 / % possible all: 68.58

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2h0b

2h0b


Resolution: 1.94→45.6 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 28.02
RfactorNum. reflection% reflection
Rfree0.2466 1992 8.56 %
Rwork0.1982 --
obs0.2025 23258 95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 315.29 Å2 / Biso mean: 76.06 Å2 / Biso min: 23.78 Å2
Refinement stepCycle: final / Resolution: 1.94→45.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2545 0 0 67 2612
Biso mean---59.94 -
Num. residues----325
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.9401-1.98860.3458930.296299663
1.9886-2.04230.3371250.2719134784
2.0423-2.10240.30231380.2585146993
2.1024-2.17030.28471440.2489153797
2.1703-2.24790.27721490.234158199
2.2479-2.33790.31041460.2399156098
2.3379-2.44430.27661490.22221588100
2.4443-2.57310.2871480.23611582100
2.5731-2.73430.28271490.23951590100
2.7343-2.94540.28421490.2405159299
2.9454-3.24170.27291490.21741581100
3.2417-3.71060.27321500.1887159299
3.7106-4.67430.19291510.15551618100
4.6743-45.60.20471520.1702163399
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)
12.43640.4909-0.9923.515-2.16865.20240.1604-0.15460.00520.58440.19330.4414-0.2009-0.6483-0.21480.4229-0.06370.03180.33890.05580.31989.403934.567925.2338
21.3269-0.29280.50482.8446-2.16074.20580.1488-0.0877-0.0286-0.0066-0.06080.1662-0.05350.1965-0.10750.2793-0.026-0.03180.2067-0.01790.267421.592145.81545.1103
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain 'A' and resid 295 through 487)A295 - 487
2X-RAY DIFFRACTION2(chain 'B' and resid 118 through 263)B118 - 263

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