[English] 日本語
Yorodumi
- PDB-1c4r: THE STRUCTURE OF THE LIGAND-BINDING DOMAIN OF NEUREXIN 1BETA: REG... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1c4r
TitleTHE STRUCTURE OF THE LIGAND-BINDING DOMAIN OF NEUREXIN 1BETA: REGULATION OF LNS DOMAIN FUNCTION BY ALTERNATIVE SPLICING
ComponentsNEUREXIN-I BETA
KeywordsMEMBRANE PROTEIN / LECTIN-LIKE / NEUROBIOLOGY / CELL-CELL ADHESION / CELL-CELL RECOGNITION / ALTERNATIVE SPLICING
Function / homology
Function and homology information


protein-containing complex assembly involved in synapse maturation / : / positive regulation of presynaptic active zone assembly / cell-cell adhesion involved in synapse maturation / guanylate kinase-associated protein clustering / protein complex involved in cell-cell adhesion / positive regulation of neuromuscular synaptic transmission / neuron to neuron synapse / neuroligin clustering involved in postsynaptic membrane assembly / regulation of trans-synaptic signaling by endocannabinoid, modulating synaptic transmission ...protein-containing complex assembly involved in synapse maturation / : / positive regulation of presynaptic active zone assembly / cell-cell adhesion involved in synapse maturation / guanylate kinase-associated protein clustering / protein complex involved in cell-cell adhesion / positive regulation of neuromuscular synaptic transmission / neuron to neuron synapse / neuroligin clustering involved in postsynaptic membrane assembly / regulation of trans-synaptic signaling by endocannabinoid, modulating synaptic transmission / type 1 fibroblast growth factor receptor binding / trans-synaptic signaling, modulating synaptic transmission / trans-synaptic protein complex / negative regulation of filopodium assembly / gephyrin clustering involved in postsynaptic density assembly / cerebellar granule cell differentiation / slit diaphragm / postsynaptic density protein 95 clustering / postsynaptic membrane assembly / synapse maturation / gamma-aminobutyric acid receptor clustering / vocal learning / presynaptic membrane assembly / neuroligin family protein binding / positive regulation of synapse maturation / maintenance of synapse structure / regulation of grooming behavior / synaptic vesicle clustering / presynapse assembly / synaptic membrane adhesion / regulation of postsynaptic specialization assembly / positive regulation of fibroblast growth factor receptor signaling pathway / receptor localization to synapse / neuron cell-cell adhesion / NMDA glutamate receptor clustering / inhibitory synapse / calcium-dependent cell-cell adhesion / vocalization behavior / regulation of postsynaptic density assembly / protein localization to synapse / acetylcholine receptor binding / neurotransmitter secretion / regulation of synaptic vesicle cycle / AMPA selective glutamate receptor signaling pathway / positive regulation of synapse assembly / NMDA selective glutamate receptor signaling pathway / heterophilic cell-cell adhesion / neuromuscular process controlling balance / positive regulation of phospholipase C-activating G protein-coupled receptor signaling pathway / adult behavior / excitatory synapse / endocytic vesicle / social behavior / positive regulation of excitatory postsynaptic potential / regulation of presynapse assembly / prepulse inhibition / positive regulation of synaptic transmission, glutamatergic / axonal growth cone / synapse assembly / cell adhesion molecule binding / neuron projection morphogenesis / presynaptic active zone membrane / cellular response to calcium ion / positive regulation of synaptic transmission, GABAergic / learning / positive regulation of protein localization to plasma membrane / calcium channel regulator activity / neuromuscular junction / establishment of protein localization / circadian rhythm / positive regulation of neuron projection development / GABA-ergic synapse / Schaffer collateral - CA1 synapse / neuron projection development / calcium-dependent protein binding / transmembrane signaling receptor activity / presynaptic membrane / angiogenesis / nuclear membrane / chemical synaptic transmission / vesicle / positive regulation of ERK1 and ERK2 cascade / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / signaling receptor binding / negative regulation of gene expression / neuronal cell body / calcium ion binding / positive regulation of gene expression / protein-containing complex binding / glutamatergic synapse / cell surface / endoplasmic reticulum / signal transduction / 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 / Resolution: 2.6 Å
AuthorsRudenko, G. / Nguyen, T. / Chelliah, Y. / Sudhof, T.C. / Deisenhofer, J.
CitationJournal: Cell(Cambridge,Mass.) / Year: 1999
Title: The structure of the ligand-binding domain of neurexin Ibeta: regulation of LNS domain function by alternative splicing.
Authors: Rudenko, G. / Nguyen, T. / Chelliah, Y. / Sudhof, T.C. / Deisenhofer, J.
History
DepositionSep 28, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 4, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: NEUREXIN-I BETA
B: NEUREXIN-I BETA
C: NEUREXIN-I BETA
D: NEUREXIN-I BETA
E: NEUREXIN-I BETA
F: NEUREXIN-I BETA
G: NEUREXIN-I BETA
H: NEUREXIN-I BETA


Theoretical massNumber of molelcules
Total (without water)157,5458
Polymers157,5458
Non-polymers00
Water1,946108
1
A: NEUREXIN-I BETA


Theoretical massNumber of molelcules
Total (without water)19,6931
Polymers19,6931
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: NEUREXIN-I BETA


Theoretical massNumber of molelcules
Total (without water)19,6931
Polymers19,6931
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: NEUREXIN-I BETA


Theoretical massNumber of molelcules
Total (without water)19,6931
Polymers19,6931
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: NEUREXIN-I BETA


Theoretical massNumber of molelcules
Total (without water)19,6931
Polymers19,6931
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: NEUREXIN-I BETA


Theoretical massNumber of molelcules
Total (without water)19,6931
Polymers19,6931
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: NEUREXIN-I BETA


Theoretical massNumber of molelcules
Total (without water)19,6931
Polymers19,6931
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
G: NEUREXIN-I BETA


Theoretical massNumber of molelcules
Total (without water)19,6931
Polymers19,6931
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
8
H: NEUREXIN-I BETA


Theoretical massNumber of molelcules
Total (without water)19,6931
Polymers19,6931
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)116.600, 195.900, 103.610
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.424815, 0.840268, -0.33687), (-0.390713, 0.505855, 0.76906), (0.816624, -0.195089, 0.543199)-16.3289, 27.93887, -56.88909
2given(-0.999994, -0.002871, -0.002148), (0.002873, -0.999996, -0.000619), (-0.002147, -0.000626, 0.999997)56.89447, 114.06898, -51.76969
3given(-0.452665, 0.67133, -0.586865), (-0.393556, 0.440163, 0.807075), (0.80013, 0.596299, 0.06496)44.31973, 16.31723, -20.75792
4given(-0.547045, -0.046415, -0.835815), (0.019452, -0.998897, 0.042741), (-0.836877, 0.007123, 0.547344)86.74764, 98.46935, 45.61501
5given(-0.422769, -0.829235, 0.365561), (0.381053, -0.528652), (0.822231, -0.181373, 0.539481)70.67656, 87.05943, -5.62592
6given(0.457336, -0.633189, 0.624433), (0.416336, -0.468016, -0.779503), (0.785817, 0.616468, 0.049579)8.57387, 96.52338, 31.55213
7given(0.457336, -0.633189, 0.624433), (0.416336, -0.468016, -0.779503), (0.785817, 0.616468, 0.049579)8.57387, 96.52338, 31.55213

-
Components

#1: Protein
NEUREXIN-I BETA


Mass: 19693.072 Da / Num. of mol.: 8 / Fragment: EXTRACELLULAR DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Plasmid: PGEX-KG / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q63373
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 108 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

-
Sample preparation

CrystalDensity Matthews: 3.75 Å3/Da / Density % sol: 67.24 %
Crystal growpH: 6.5 / Details: pH 6.50
Crystal grow
*PLUS
Temperature: 21 ℃ / pH: 7.5 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110 mg/mlprotein1drop
220 mMHEPES1drop
3150 mM1dropNaCl
41 mMEDTA1drop
515 %1,2,3-heptanetriol1drop
621 %(w/v)mPEG50001reservoir
7100 mMsodium cacodylate1reservoir
8200 mMammonium sulfate1reservoir

-
Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL1-5 / Wavelength: 1.0712, 0.9791, 0.9793, 0.9221
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.07121
20.97911
30.97931
40.92211
ReflectionBiso Wilson estimate: 29.3 Å2
Reflection
*PLUS
Highest resolution: 2.6 Å / Lowest resolution: 20 Å / Num. obs: 73128 / % possible obs: 98.1 % / Num. measured all: 351083 / Rmerge(I) obs: 0.095
Reflection shell
*PLUS
Highest resolution: 2.6 Å / Lowest resolution: 2.64 Å / % possible obs: 82.7 % / Rmerge(I) obs: 0.495 / Mean I/σ(I) obs: 3.1

-
Processing

Software
NameClassification
CNSrefinement
CNSphasing
RefinementResolution: 2.6→20 Å / Rfactor Rfree error: 0.005 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.279 3841 5.3 %SHELLS
Rwork0.249 ---
obs0.249 72682 98.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 38.87 Å2 / ksol: 0.37 e/Å3
Displacement parametersBiso mean: 38.2 Å2
Baniso -1Baniso -2Baniso -3
1-10.96 Å20 Å20 Å2
2---12.35 Å20 Å2
3---1.39 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.4 Å0.35 Å
Luzzati d res low-5 Å
Luzzati sigma a0.39 Å0.29 Å
Refinement stepCycle: LAST / Resolution: 2.6→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10888 0 0 10951 21839
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.014
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.8
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d27.6
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.08
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
Refine LS restraints NCSNCS model details: CONSTR
LS refinement shellResolution: 2.6→2.76 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.374 441 3.7 %
Rwork0.309 11531 -
obs--99 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAM
Software
*PLUS
Name: CNS / Version: 0.5 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg27.6
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.08

+
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