[English] 日本語
Yorodumi
- PDB-4bdl: Crystal structure of the GluK2 K531A LBD dimer in complex with gl... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4bdl
TitleCrystal structure of the GluK2 K531A LBD dimer in complex with glutamate
ComponentsGLUTAMATE RECEPTOR, IONOTROPIC KAINATE 2
KeywordsMETAL TRANSPORT / IONOTROPIC GLUTAMATE RECEPTOR / KAINATE RECEPTOR
Function / homology
Function and homology information


mossy fiber rosette / detection of cold stimulus involved in thermoception / Activation of Na-permeable kainate receptors / kainate selective glutamate receptor complex / Activation of Ca-permeable Kainate Receptor / regulation of short-term neuronal synaptic plasticity / glutamate receptor activity / negative regulation of synaptic transmission, glutamatergic / ubiquitin conjugating enzyme binding / regulation of JNK cascade ...mossy fiber rosette / detection of cold stimulus involved in thermoception / Activation of Na-permeable kainate receptors / kainate selective glutamate receptor complex / Activation of Ca-permeable Kainate Receptor / regulation of short-term neuronal synaptic plasticity / glutamate receptor activity / negative regulation of synaptic transmission, glutamatergic / ubiquitin conjugating enzyme binding / regulation of JNK cascade / inhibitory postsynaptic potential / receptor clustering / kainate selective glutamate receptor activity / modulation of excitatory postsynaptic potential / extracellularly glutamate-gated ion channel activity / ionotropic glutamate receptor complex / positive regulation of synaptic transmission / behavioral fear response / neuronal action potential / glutamate-gated receptor activity / glutamate-gated calcium ion channel activity / ligand-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / presynaptic modulation of chemical synaptic transmission / dendrite cytoplasm / hippocampal mossy fiber to CA3 synapse / SNARE binding / regulation of membrane potential / excitatory postsynaptic potential / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / synaptic transmission, glutamatergic / PDZ domain binding / regulation of long-term neuronal synaptic plasticity / postsynaptic density membrane / modulation of chemical synaptic transmission / intracellular calcium ion homeostasis / terminal bouton / positive regulation of neuron apoptotic process / presynaptic membrane / scaffold protein binding / neuron apoptotic process / perikaryon / chemical synaptic transmission / negative regulation of neuron apoptotic process / postsynaptic membrane / postsynaptic density / axon / neuronal cell body / synapse / dendrite / ubiquitin protein ligase binding / glutamatergic 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 ...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 II / Periplasmic binding protein-like I / D-Maltodextrin-Binding Protein; domain 2 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
GLUTAMIC ACID / Glutamate receptor ionotropic, kainate 2
Similarity search - Component
Biological speciesRATTUS NORVEGICUS (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsNayeem, N. / Mayans, O. / Green, T.
CitationJournal: Open Biol. / Year: 2013
Title: Correlating Efficacy and Desensitization with Gluk2 Ligand-Binding Domain Movements.
Authors: Nayeem, N. / Mayans, O. / Green, T.
History
DepositionOct 5, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 10, 2013Provider: repository / Type: Initial release
Revision 1.1Jun 12, 2013Group: Database references
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _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_conn.ptnr2_label_seq_id / _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: GLUTAMATE RECEPTOR, IONOTROPIC KAINATE 2
B: GLUTAMATE RECEPTOR, IONOTROPIC KAINATE 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,4766
Polymers59,1362
Non-polymers3404
Water9,080504
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2030 Å2
ΔGint-33.9 kcal/mol
Surface area22590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.568, 106.611, 113.904
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-2104-

HOH

Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.5052, -0.863, -0.0006), (-0.8628, -0.5051, -0.0236), (0.0201, 0.0125, -0.9997)
Vector: 23.5707, 41.5805, 40.6379)

-
Components

#1: Protein GLUTAMATE RECEPTOR, IONOTROPIC KAINATE 2 / GLUTAMATE RECEPTOR 6 / GLUR-6 / GLUR6


Mass: 29567.842 Da / Num. of mol.: 2 / Fragment: LIGAND BINDING DOMAIN, RESIDUES 429-544,667-806 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) RATTUS NORVEGICUS (Norway rat) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P42260
#2: Chemical ChemComp-GLU / GLUTAMIC ACID


Type: L-peptide linking / Mass: 147.129 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H9NO4
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 504 / 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: 2.5 Å3/Da / Density % sol: 52 % / Description: NONE
Crystal growDetails: 19% PEG 4,000, 3% PROPAN-2-OL, 80MM NA ACETATE

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.75→33.92 Å / Num. obs: 59953 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 4.5 % / Biso Wilson estimate: 19.81 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 15.5
Reflection shellResolution: 1.75→1.78 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.77 / Mean I/σ(I) obs: 2.2 / % possible all: 99.9

-
Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1XXR

1xxr


Resolution: 1.75→33.924 Å / SU ML: 0.19 / σ(F): 1.99 / Phase error: 18.73 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2016 2998 5 %
Rwork0.1693 --
obs0.1709 59953 99.87 %
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 31.374 Å2 / ksol: 0.328 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-1.9166 Å20 Å20 Å2
2---3.0992 Å20 Å2
3---1.1827 Å2
Refinement stepCycle: LAST / Resolution: 1.75→33.924 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3967 0 22 504 4493
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0064075
X-RAY DIFFRACTIONf_angle_d1.0285486
X-RAY DIFFRACTIONf_dihedral_angle_d11.9641526
X-RAY DIFFRACTIONf_chiral_restr0.071613
X-RAY DIFFRACTIONf_plane_restr0.004691
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.75-1.77870.30021410.26272683X-RAY DIFFRACTION100
1.7787-1.80940.25611420.24012698X-RAY DIFFRACTION100
1.8094-1.84230.2331400.21082668X-RAY DIFFRACTION100
1.8423-1.87770.24761430.20032699X-RAY DIFFRACTION100
1.8777-1.9160.22251400.19132666X-RAY DIFFRACTION100
1.916-1.95770.23741420.17972699X-RAY DIFFRACTION100
1.9577-2.00320.21561410.16982690X-RAY DIFFRACTION100
2.0032-2.05330.20821420.15732692X-RAY DIFFRACTION100
2.0533-2.10880.20551410.15822676X-RAY DIFFRACTION100
2.1088-2.17090.18441410.16092678X-RAY DIFFRACTION100
2.1709-2.24090.21251440.16362741X-RAY DIFFRACTION100
2.2409-2.3210.21521410.16872671X-RAY DIFFRACTION100
2.321-2.41390.21781430.16652725X-RAY DIFFRACTION100
2.4139-2.52370.23691420.16892691X-RAY DIFFRACTION100
2.5237-2.65670.20211430.17572712X-RAY DIFFRACTION100
2.6567-2.82310.23161420.18262707X-RAY DIFFRACTION100
2.8231-3.0410.221440.17642742X-RAY DIFFRACTION100
3.041-3.34670.20531440.17232734X-RAY DIFFRACTION100
3.3467-3.83040.17241450.15812746X-RAY DIFFRACTION100
3.8304-4.82370.14091460.13182773X-RAY DIFFRACTION100
4.8237-33.93060.1931510.1762864X-RAY DIFFRACTION99
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)
12.03670.73710.42880.567-0.05770.8768-0.08840.17890.2135-0.03110.05230.006-0.22740.10610.03820.12-0.0223-0.01350.0973-0.01210.135142.034528.340313.9602
20.71680.0295-0.10320.9933-0.12130.0696-0.00080.3516-0.1501-0.38470.0256-0.0939-0.10280.1188-0.04890.2284-0.04780.05150.1974-0.06990.13838.057512.215-1.7529
30.43650.35310.61551.55920.63761.4082-0.1251-0.0132-0.0633-0.148-0.00340.125-0.1467-0.03420.08960.07580.0026-0.00740.0708-0.03290.065827.239515.41286.2981
43.2217-0.63221.4162.04380.92611.9115-0.1210.24860.1932-0.3359-0.12690.2267-0.29290.04570.24360.1565-0.0012-0.04320.1381-0.01090.15820.373519.16970.9398
50.60210.59330.11160.6437-0.10790.7720.0305-0.06690.01320.0688-0.08270.03480.0682-0.06660.04490.0953-0.00350.0050.0996-0.01830.103335.392318.700222.3294
66.0619-3.30814.34766.0888-5.36285.20560.18020.43580.0373-0.4614-0.2302-0.01510.5340.08310.04060.1817-0.0217-0.01620.2194-0.01060.130128.778617.05835.4178
70.49820.55520.2230.68930.14630.23130.0012-0.0504-0.21290.03640.03920.00120.0669-0.0292-0.03030.12160.00850.04150.07960.02910.208417.1795-9.115729.3163
82.61451.44510.2120.97890.7642.3262-0.1110.1238-1.0760.00850.1806-0.69160.49520.04960.09490.1913-0.00690.10940.1014-0.08920.440625.9767-10.044823.8264
91.38870.39820.52951.41830.10071.0548-0.0016-0.1145-0.29310.23870.0338-0.2525-0.03630.1104-0.03090.15390.0003-0.00950.13590.01810.164732.19472.633934.1245
101.8413-0.4935-0.84911.24090.09190.9706-0.0252-0.2518-0.09080.1812-0.01450.093-0.12430.10130.02570.14570.0090.0360.1196-0.01410.102115.411215.469340.3905
110.99420.6855-0.09740.7537-0.09680.6772-0.13280.148-0.2397-0.03360.1089-0.11170.01350.04770.01390.113-0.00650.03330.1139-0.03770.167625.22710.94118.8662
127.69280.1062-6.29422.34280.60365.3535-0.1143-0.59270.02850.05460.2964-0.193-0.2204-0.0391-0.18080.1860.06620.06830.2074-0.00010.170523.1057.483635.8142
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESID 430:482)
2X-RAY DIFFRACTION2(CHAIN A AND RESID 483:497)
3X-RAY DIFFRACTION3(CHAIN A AND RESID 498:681)
4X-RAY DIFFRACTION4(CHAIN A AND RESID 682:763)
5X-RAY DIFFRACTION5(CHAIN A AND RESID 764:806)
6X-RAY DIFFRACTION6(CHAIN A AND RESID 900)
7X-RAY DIFFRACTION7(CHAIN B AND RESID 430:467)
8X-RAY DIFFRACTION8(CHAIN B AND RESID 468:484)
9X-RAY DIFFRACTION9(CHAIN B AND RESID 485:536)
10X-RAY DIFFRACTION10(CHAIN B AND RESID 537:763)
11X-RAY DIFFRACTION11(CHAIN B AND RESID 764:806)
12X-RAY DIFFRACTION12(CHAIN B AND RESID 900)

+
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