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- PDB-1c4r: THE STRUCTURE OF THE LIGAND-BINDING DOMAIN OF NEUREXIN 1BETA: REG... -

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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 / regulation of trans-synaptic signaling by endocannabinoid, modulating synaptic transmission / positive regulation of presynaptic active zone assembly / cell-cell adhesion involved in synapse maturation / gephyrin clustering involved in postsynaptic density assembly / regulation of postsynaptic specialization assembly / protein complex involved in cell-cell adhesion / positive regulation of neuromuscular synaptic transmission / guanylate kinase-associated protein clustering / type 1 fibroblast growth factor receptor binding ...protein-containing complex assembly involved in synapse maturation / regulation of trans-synaptic signaling by endocannabinoid, modulating synaptic transmission / positive regulation of presynaptic active zone assembly / cell-cell adhesion involved in synapse maturation / gephyrin clustering involved in postsynaptic density assembly / regulation of postsynaptic specialization assembly / protein complex involved in cell-cell adhesion / positive regulation of neuromuscular synaptic transmission / guanylate kinase-associated protein clustering / type 1 fibroblast growth factor receptor binding / neuron to neuron synapse / neuroligin clustering involved in postsynaptic membrane assembly / postsynaptic density protein 95 clustering / cerebellar granule cell differentiation / postsynaptic membrane assembly / gamma-aminobutyric acid receptor clustering / presynaptic membrane assembly / synapse maturation / NMDA glutamate receptor clustering / maintenance of synapse structure / negative regulation of filopodium assembly / neuroligin family protein binding / vocal learning / positive regulation of synapse maturation / positive regulation of fibroblast growth factor receptor signaling pathway / regulation of postsynaptic density assembly / synaptic membrane adhesion / synaptic vesicle clustering / receptor localization to synapse / inhibitory synapse / regulation of grooming behavior / neuron cell-cell adhesion / presynapse assembly / protein localization to synapse / regulation of synaptic vesicle cycle / vocalization behavior / calcium-dependent cell-cell adhesion via plasma membrane cell adhesion molecules / neurotransmitter secretion / regulation of AMPA receptor activity / filopodium assembly / neuron maturation / acetylcholine receptor binding / positive regulation of synapse assembly / heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules / adult behavior / positive regulation of protein kinase A signaling / regulation of NMDA receptor activity / social behavior / positive regulation of excitatory postsynaptic potential / calcium channel regulator activity / neuromuscular process controlling balance / excitatory synapse / regulation of presynapse assembly / endocytic vesicle / GABA-ergic synapse / prepulse inhibition / axonal growth cone / presynaptic active zone membrane / synapse assembly / cellular response to calcium ion / cell adhesion molecule binding / positive regulation of synaptic transmission, glutamatergic / neuron projection morphogenesis / learning / positive regulation of synaptic transmission, GABAergic / positive regulation of protein localization to plasma membrane / neuromuscular junction / Schaffer collateral - CA1 synapse / establishment of protein localization / positive regulation of neuron projection development / circadian rhythm / neuron projection development / calcium-dependent protein binding / transmembrane signaling receptor activity / presynaptic membrane / positive regulation of peptidyl-serine phosphorylation / chemical synaptic transmission / angiogenesis / nuclear membrane / vesicle / positive regulation of ERK1 and ERK2 cascade / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / negative regulation of gene expression / signaling receptor binding / neuronal cell body / glutamatergic synapse / calcium ion binding / protein-containing complex binding / positive regulation of gene expression / 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 / Concanavalin A-like lectin/glucanase domain superfamily ...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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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

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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 / Water


Mass: 18.015 Da / Num. of mol.: 108 / 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: 2

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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

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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

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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

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