[English] 日本語
Yorodumi
- PDB-2r1b: Crystal Structure of rat neurexin 1beta with a splice insert at SS#4 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2r1b
TitleCrystal Structure of rat neurexin 1beta with a splice insert at SS#4
ComponentsNeurexin-1-beta
KeywordsCELL ADHESION / SPLICING / beta-sandwich
Function / homology
Function and homology information


positive regulation of protein kinase A signaling / protein-containing complex assembly involved in synapse maturation / cell-cell adhesion involved in synapse maturation / positive regulation of presynaptic active zone assembly / gephyrin clustering involved in postsynaptic density assembly / type 1 fibroblast growth factor receptor binding / protein complex involved in cell-cell adhesion / positive regulation of neuromuscular synaptic transmission / guanylate kinase-associated protein clustering / neuron to neuron synapse ...positive regulation of protein kinase A signaling / protein-containing complex assembly involved in synapse maturation / cell-cell adhesion involved in synapse maturation / positive regulation of presynaptic active zone assembly / gephyrin clustering involved in postsynaptic density assembly / type 1 fibroblast growth factor receptor binding / protein complex involved in cell-cell adhesion / positive regulation of neuromuscular synaptic transmission / guanylate kinase-associated protein clustering / neuron to neuron synapse / neuroligin clustering involved in postsynaptic membrane assembly / postsynaptic density protein 95 clustering / regulation of trans-synaptic signaling by endocannabinoid, modulating synaptic transmission / cerebellar granule cell differentiation / trans-synaptic signaling, modulating synaptic transmission / postsynaptic membrane assembly / gamma-aminobutyric acid receptor clustering / presynaptic membrane assembly / negative regulation of filopodium assembly / synapse maturation / maintenance of synapse structure / vocal learning / slit diaphragm / neuroligin family protein binding / positive regulation of synapse maturation / neuron cell-cell adhesion / positive regulation of fibroblast growth factor receptor signaling pathway / synaptic vesicle clustering / regulation of grooming behavior / inhibitory synapse / synaptic membrane adhesion / regulation of postsynaptic specialization assembly / receptor localization to synapse / presynapse assembly / NMDA glutamate receptor clustering / vocalization behavior / calcium-dependent cell-cell adhesion via plasma membrane cell adhesion molecules / protein localization to synapse / regulation of postsynaptic density assembly / neurotransmitter secretion / filopodium assembly / neuron maturation / acetylcholine receptor binding / AMPA selective glutamate receptor signaling pathway / positive regulation of synapse assembly / regulation of synaptic vesicle cycle / NMDA selective glutamate receptor signaling pathway / heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules / positive regulation of phospholipase C-activating G protein-coupled receptor signaling pathway / adult behavior / social behavior / neuromuscular process controlling balance / positive regulation of excitatory postsynaptic potential / excitatory synapse / regulation of presynapse assembly / endocytic vesicle / calcium channel regulator activity / prepulse inhibition / axonal growth cone / synapse assembly / cell adhesion molecule binding / presynaptic active zone membrane / cellular response to calcium ion / positive regulation of synaptic transmission, glutamatergic / neuron projection morphogenesis / GABA-ergic synapse / learning / positive regulation of synaptic transmission, GABAergic / positive regulation of protein localization to plasma membrane / establishment of protein localization / neuromuscular junction / Schaffer collateral - CA1 synapse / positive regulation of neuron projection development / circadian rhythm / neuron projection development / calcium-dependent protein binding / transmembrane signaling receptor activity / presynaptic membrane / nuclear membrane / angiogenesis / 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 / MOLECULAR REPLACEMENT / Resolution: 1.72 Å
AuthorsRudenko, G.
CitationJournal: Structure / Year: 2008
Title: Regulation of Neurexin 1beta Tertiary Structure and Ligand Binding through Alternative Splicing
Authors: Shen, K.C. / Kuczynska, D.A. / Wu, I.J. / Murray, B.H. / Sheckler, L.R. / Rudenko, G.
History
DepositionAug 22, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 25, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Jul 24, 2019Group: Data collection / Refinement description / Category: software
Item: _software.classification / _software.name / _software.version
Revision 1.4Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ncs_dom_lim / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Neurexin-1-beta
B: Neurexin-1-beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,0704
Polymers47,9902
Non-polymers802
Water6,359353
1
A: Neurexin-1-beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,0352
Polymers23,9951
Non-polymers401
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Neurexin-1-beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,0352
Polymers23,9951
Non-polymers401
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)84.122, 39.260, 85.410
Angle α, β, γ (deg.)90.00, 115.47, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31A
41B
51A
61B
71A
81B
91A
101B
111A
121B
131A
141B

NCS domain segments:

Ens-ID: 1 / Refine code: 2

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLYGLYILEILEAA80 - 1156 - 41
21GLYGLYILEILEBB80 - 1156 - 41
32VALVALLEULEUAA120 - 12646 - 52
42VALVALLEULEUBB120 - 12646 - 52
53GLYGLYTYRTYRAA134 - 13860 - 64
63GLYGLYTYRTYRBB134 - 13860 - 64
74GLYGLYASPASPAA146 - 17072 - 96
84GLYGLYASPASPBB146 - 17072 - 96
95THRTHRGLUGLUAA179 - 196105 - 122
105THRTHRGLUGLUBB179 - 196105 - 122
116LEULEUGLNGLNAA219 - 233145 - 159
126LEULEUGLNGLNBB219 - 233145 - 159
137SERSERPROPROAA239 - 292165 - 218
147SERSERPROPROBB239 - 292165 - 218

-
Components

#1: Protein Neurexin-1-beta / neurexin I-beta


Mass: 23994.895 Da / Num. of mol.: 2 / Fragment: LNS/LG domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Nrxn1 / Plasmid: pGEX-KG / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q63373
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 353 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.65 Å3/Da / Density % sol: 53.64 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 17% Peg 8000, 0.1 M Tris pH 8.5, 0.2 M MgCl2, 5 mM CaCl2, 0.5% beta-octyl-glucoside, VAPOR DIFFUSION, HANGING DROP, temperature 277K

-
Data collection

DiffractionMean temperature: 103 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 32-ID / Wavelength: 1 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jan 1, 2005
RadiationMonochromator: see beam-line specifications / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.72→19.9 Å / Num. all: 49680 / Num. obs: 49680 / % possible obs: 92.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.2 % / Biso Wilson estimate: 22.5 Å2 / Rmerge(I) obs: 0.054 / Net I/σ(I): 25.9
Reflection shellResolution: 1.72→1.76 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.355 / Mean I/σ(I) obs: 3.1 / Num. unique all: 2877 / Rsym value: 0.355 / % possible all: 73.1

-
Processing

Software
NameVersionClassification
REFMAC5.2refinement
CNSrefinement
MAR345softwaredata collection
MOSFLMdata reduction
SCALAdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1C4R

1c4r


Resolution: 1.72→19.9 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.937 / SU B: 4.487 / SU ML: 0.076 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.113 / ESU R Free: 0.108 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.22474 3770 7.6 %RANDOM
Rwork0.19745 ---
all0.19956 49679 --
obs0.19956 45909 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 26.719 Å2
Baniso -1Baniso -2Baniso -3
1--1.48 Å20 Å2-0.91 Å2
2---0.17 Å20 Å2
3---0.86 Å2
Refinement stepCycle: LAST / Resolution: 1.72→19.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2980 0 2 353 3335
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0223075
X-RAY DIFFRACTIONr_angle_refined_deg1.7081.934168
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.265390
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.39724.286140
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.34515511
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.4411521
X-RAY DIFFRACTIONr_chiral_restr0.1570.2475
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022325
X-RAY DIFFRACTIONr_nbd_refined0.2230.21116
X-RAY DIFFRACTIONr_nbtor_refined0.2950.22046
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1660.2170
X-RAY DIFFRACTIONr_metal_ion_refined0.0550.26
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2530.267
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.4430.228
X-RAY DIFFRACTIONr_mcbond_it1.241.52032
X-RAY DIFFRACTIONr_mcangle_it1.72523112
X-RAY DIFFRACTIONr_scbond_it2.7631242
X-RAY DIFFRACTIONr_scangle_it4.1584.51056
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

NumberTypeRms dev position (Å)Weight position
632tight positional0.090.05
540medium positional0.330.5
632tight thermal0.260.5
540medium thermal0.852
LS refinement shellResolution: 1.72→1.765 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.415 209 -
Rwork0.356 2539 -
obs-2748 100 %
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)
12.5290.02931.0271.92690.5342.9277-0.0356-0.22850.1760.27770.0687-0.0557-0.1447-0.0386-0.033-0.09670.0122-0.0134-0.1759-0.0198-0.1995-9.928436.16262.6089
228.45558.278427.70892.40848.061326.9820.60380.1881-0.91550.19860.2012-0.05921.23140.4388-0.80490.21290.0581-0.1929-0.0162-0.09160.008215.603740.387481.1426
33.53820.6220.54161.64830.17311.4277-0.0404-0.1531-0.13530.08060.02530.10290.0729-0.0650.0151-0.1998-0.00330.0413-0.20630.0163-0.161343.8979-10.031844.7897
423.99743.91967.86380.95920.9133.0094-0.420.29730.6954-0.09610.18230.2529-0.3509-0.0190.2377-0.1083-0.0260.0001-0.13090.03380.021715.2238-14.533931.6886
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA80 - 1986 - 124
2X-RAY DIFFRACTION1AA238 - 294164 - 220
3X-RAY DIFFRACTION2AA216 - 237142 - 163
4X-RAY DIFFRACTION3BB80 - 1986 - 124
5X-RAY DIFFRACTION3BB238 - 292164 - 218
6X-RAY DIFFRACTION4BB216 - 237142 - 163

+
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