[English] 日本語
Yorodumi
- PDB-5l2e: Crystal structure of rat Glutamate receptor delta-2 extracellular... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5l2e
TitleCrystal structure of rat Glutamate receptor delta-2 extracellular domain
ComponentsGlutamate receptor ionotropic, delta-2,Glutamate receptor ionotropic, delta-2
KeywordsPROTEIN BINDING / Synapse Protein / Cell Surface Protein / Glycoprotein / Nervous System
Function / homology
Function and homology information


excitatory synapse assembly / cerebellar granule cell differentiation / positive regulation of long-term synaptic depression / regulation of postsynaptic density assembly / glutamate receptor activity / positive regulation of synapse assembly / parallel fiber to Purkinje cell synapse / heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules / regulation of neuron projection development / regulation of postsynaptic membrane neurotransmitter receptor levels ...excitatory synapse assembly / cerebellar granule cell differentiation / positive regulation of long-term synaptic depression / regulation of postsynaptic density assembly / glutamate receptor activity / positive regulation of synapse assembly / parallel fiber to Purkinje cell synapse / heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules / regulation of neuron projection development / regulation of postsynaptic membrane neurotransmitter receptor levels / ionotropic glutamate receptor complex / regulation of presynapse assembly / prepulse inhibition / regulation of neuron apoptotic process / somatodendritic compartment / excitatory postsynaptic potential / synaptic transmission, glutamatergic / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / PDZ domain binding / postsynaptic density membrane / modulation of chemical synaptic transmission / protein localization / scaffold protein binding / postsynaptic membrane / dendritic spine / glutamatergic synapse / synapse / identical protein binding / membrane / plasma membrane
Similarity search - Function
Ionotropic glutamate receptor, metazoa / Ligated ion channel L-glutamate- and glycine-binding site / Ionotropic glutamate receptor, L-glutamate and glycine-binding domain / Ligated ion channel L-glutamate- and glycine-binding site / Ligand-gated ion channel / : / Ionotropic glutamate receptor / Eukaryotic homologues of bacterial periplasmic substrate binding proteins. / Receptor, ligand binding region / Receptor family ligand binding region / Periplasmic binding protein-like I
Similarity search - Domain/homology
Glutamate receptor ionotropic, delta-2
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.152 Å
AuthorsCheng, S. / Ozkan, E.
CitationJournal: Structure / Year: 2016
Title: Conformational Plasticity in the Transsynaptic Neurexin-Cerebellin-Glutamate Receptor Adhesion Complex.
Authors: Cheng, S. / Seven, A.B. / Wang, J. / Skiniotis, G. / Ozkan, E.
History
DepositionAug 1, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 28, 2016Provider: repository / Type: Initial release
Revision 1.1Oct 4, 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 / pdbx_reflns_twin
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_reflns_twin.operator
Revision 1.2Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Glutamate receptor ionotropic, delta-2,Glutamate receptor ionotropic, delta-2
B: Glutamate receptor ionotropic, delta-2,Glutamate receptor ionotropic, delta-2
C: Glutamate receptor ionotropic, delta-2,Glutamate receptor ionotropic, delta-2


Theoretical massNumber of molelcules
Total (without water)233,5013
Polymers233,5013
Non-polymers00
Water00
1
A: Glutamate receptor ionotropic, delta-2,Glutamate receptor ionotropic, delta-2

A: Glutamate receptor ionotropic, delta-2,Glutamate receptor ionotropic, delta-2


Theoretical massNumber of molelcules
Total (without water)155,6682
Polymers155,6682
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_467y-1,x+1,-z+21
Buried area3640 Å2
ΔGint-16 kcal/mol
Surface area58950 Å2
MethodPISA
2
B: Glutamate receptor ionotropic, delta-2,Glutamate receptor ionotropic, delta-2
C: Glutamate receptor ionotropic, delta-2,Glutamate receptor ionotropic, delta-2


Theoretical massNumber of molelcules
Total (without water)155,6682
Polymers155,6682
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3750 Å2
ΔGint-17 kcal/mol
Surface area58760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)179.172, 179.172, 214.390
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

-
Components

#1: Protein Glutamate receptor ionotropic, delta-2,Glutamate receptor ionotropic, delta-2 / GluR delta-2 subunit


Mass: 77833.812 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Grid2 / Cell line (production host): High Five (BTI-TN-5B1-4) / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q63226
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 4.25 Å3/Da / Density % sol: 71.09 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 6.6
Details: 0.1 M Sodium cacodylate pH 6.6, 1.3 M Ammonium dihydrogen phosphate

-
Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.0332 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 19, 2016
RadiationMonochromator: Double crystal cryo-cooled Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
Reflection twinOperator: -h,-k,l / Fraction: 0.49
ReflectionResolution: 4.15→50 Å / Num. obs: 30494 / % possible obs: 100 % / Redundancy: 4.2 % / Rmerge(I) obs: 0.157 / Rsym value: 0.157 / Net I/av σ(I): 8.9 / Net I/σ(I): 8.9
Reflection shellResolution: 4.15→4.22 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.795 / Mean I/σ(I) obs: 1.6 / CC1/2: 0.457 / % possible all: 100

-
Processing

Software
NameVersionClassification
PHENIX(dev_2481: ???)refinement
HKL-20000.98.712data reduction
PHASER2.7.12phasing
Coot0.8.3model building
HKL-20000.98.712data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2VT3 and 5KC8

2vt3

5kc8


Resolution: 4.152→46.583 Å / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 24.5
Details: Refined with twin law -h,-k,l and twin fraction of 0.49.
RfactorNum. reflection% reflection
Rfree0.2604 1994 6.62 %
Rwork0.2112 --
obs0.2176 30109 98.54 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 4.152→46.583 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15408 0 0 0 15408
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00315717
X-RAY DIFFRACTIONf_angle_d0.61321294
X-RAY DIFFRACTIONf_dihedral_angle_d10.3959426
X-RAY DIFFRACTIONf_chiral_restr0.0462376
X-RAY DIFFRACTIONf_plane_restr0.0042760
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
4.1566-4.26040.27171230.21361764X-RAY DIFFRACTION82
4.2604-4.37550.26741310.19461970X-RAY DIFFRACTION92
4.3755-4.50420.29581390.1951972X-RAY DIFFRACTION93
4.5042-4.64940.29861400.19362004X-RAY DIFFRACTION93
4.6494-4.81540.23871400.18821998X-RAY DIFFRACTION93
4.8154-5.00790.23131390.18362008X-RAY DIFFRACTION93
5.0079-5.23550.24261410.19192012X-RAY DIFFRACTION93
5.2355-5.5110.23321420.21952012X-RAY DIFFRACTION93
5.511-5.85560.24521440.22862012X-RAY DIFFRACTION93
5.8556-6.30650.28791440.23032035X-RAY DIFFRACTION93
6.3065-6.93890.26751440.22932048X-RAY DIFFRACTION93
6.9389-7.93790.2441420.21552034X-RAY DIFFRACTION93
7.9379-9.98180.23811500.20962088X-RAY DIFFRACTION93
9.9818-44.10030.28191540.27952150X-RAY DIFFRACTION93

+
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