[English] 日本語
Yorodumi
- PDB-6pnp: Crystal structure of the splice insert-free neurexin-1 LNS2 domai... -

+
Open data


ID or keywords:

Loading...

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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more