[English] 日本語
Yorodumi
- PDB-3qlv: Crystal structure of the GluK2/GluK5 (GluR6/KA2) ATD tetramer assembly -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3qlv
TitleCrystal structure of the GluK2/GluK5 (GluR6/KA2) ATD tetramer assembly
Components
  • Glutamate receptor, ionotropic kainate 2
  • Glutamate receptor, ionotropic kainate 5
KeywordsMEMBRANE PROTEIN / Glycosylation
Function / homology
Function and homology information


regulation of synaptic vesicle fusion to presynaptic active zone membrane / protein retention in ER lumen / chemical synaptic transmission, postsynaptic / 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 / negative regulation of synaptic transmission, glutamatergic / regulation of short-term neuronal synaptic plasticity ...regulation of synaptic vesicle fusion to presynaptic active zone membrane / protein retention in ER lumen / chemical synaptic transmission, postsynaptic / 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 / negative regulation of synaptic transmission, glutamatergic / regulation of short-term neuronal synaptic plasticity / inhibitory postsynaptic potential / glutamate receptor activity / ubiquitin conjugating enzyme binding / receptor clustering / modulation of excitatory postsynaptic potential / regulation of JNK cascade / kainate selective glutamate receptor activity / ionotropic glutamate receptor complex / extracellularly glutamate-gated ion channel activity / neuronal action potential / behavioral fear response / regulation of postsynaptic membrane potential / positive regulation of synaptic transmission / glutamate-gated receptor activity / monoatomic ion transmembrane transport / ligand-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / presynaptic modulation of chemical synaptic transmission / excitatory postsynaptic potential / dendrite cytoplasm / hippocampal mossy fiber to CA3 synapse / SNARE binding / synaptic transmission, glutamatergic / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / establishment of localization in cell / PDZ domain binding / regulation of membrane potential / cellular response to glucose stimulus / postsynaptic density membrane / regulation of long-term neuronal synaptic plasticity / modulation of chemical synaptic transmission / terminal bouton / SH3 domain binding / intracellular calcium ion homeostasis / positive regulation of neuron apoptotic process / presynaptic membrane / scaffold protein binding / chemical synaptic transmission / postsynaptic membrane / perikaryon / neuron apoptotic process / negative regulation of neuron apoptotic process / postsynaptic density / axon / neuronal cell body / glutamatergic synapse / ubiquitin protein ligase binding / synapse / dendrite / endoplasmic reticulum / identical protein binding / membrane / plasma membrane
Similarity search - Function
Response regulator / Ionotropic glutamate receptor, metazoa / Ligated ion channel L-glutamate- and glycine-binding site / : / Ligand-gated ion channel / Ionotropic glutamate receptor, L-glutamate and glycine-binding domain / Ligated ion channel L-glutamate- and glycine-binding site / Ionotropic glutamate receptor / Eukaryotic homologues of bacterial periplasmic substrate binding proteins. / Receptor, ligand binding region ...Response regulator / Ionotropic glutamate receptor, metazoa / Ligated ion channel L-glutamate- and glycine-binding site / : / Ligand-gated ion channel / Ionotropic glutamate receptor, L-glutamate and glycine-binding domain / Ligated ion channel L-glutamate- and glycine-binding site / 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 / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Glutamate receptor ionotropic, kainate 2 / Glutamate receptor ionotropic, kainate 5
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.94 Å
AuthorsKumar, J. / Mayer, M.L.
CitationJournal: Neuron / Year: 2011
Title: Structure and assembly mechanism for heteromeric kainate receptors.
Authors: Kumar, J. / Schuck, P. / Mayer, M.L.
History
DepositionFeb 3, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 3, 2011Provider: repository / Type: Initial release
Revision 1.1Oct 10, 2012Group: Database references
Revision 1.2Mar 31, 2021Group: Database references / Source and taxonomy / Category: entity_src_gen / struct_ref_seq_dif
Item: _entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_strain / _struct_ref_seq_dif.details
Revision 1.3Sep 13, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Glutamate receptor, ionotropic kainate 5
B: Glutamate receptor, ionotropic kainate 5
C: Glutamate receptor, ionotropic kainate 2
D: Glutamate receptor, ionotropic kainate 2
E: Glutamate receptor, ionotropic kainate 5
F: Glutamate receptor, ionotropic kainate 2
G: Glutamate receptor, ionotropic kainate 5
H: Glutamate receptor, ionotropic kainate 2
I: Glutamate receptor, ionotropic kainate 5
J: Glutamate receptor, ionotropic kainate 2


Theoretical massNumber of molelcules
Total (without water)442,74110
Polymers442,74110
Non-polymers00
Water00
1
A: Glutamate receptor, ionotropic kainate 5
B: Glutamate receptor, ionotropic kainate 5
C: Glutamate receptor, ionotropic kainate 2
D: Glutamate receptor, ionotropic kainate 2


Theoretical massNumber of molelcules
Total (without water)177,0974
Polymers177,0974
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
E: Glutamate receptor, ionotropic kainate 5
F: Glutamate receptor, ionotropic kainate 2
G: Glutamate receptor, ionotropic kainate 5
H: Glutamate receptor, ionotropic kainate 2


Theoretical massNumber of molelcules
Total (without water)177,0974
Polymers177,0974
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
I: Glutamate receptor, ionotropic kainate 5
J: Glutamate receptor, ionotropic kainate 2

I: Glutamate receptor, ionotropic kainate 5
J: Glutamate receptor, ionotropic kainate 2


Theoretical massNumber of molelcules
Total (without water)177,0974
Polymers177,0974
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
4
A: Glutamate receptor, ionotropic kainate 5
C: Glutamate receptor, ionotropic kainate 2


Theoretical massNumber of molelcules
Total (without water)88,5482
Polymers88,5482
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3090 Å2
ΔGint-16 kcal/mol
Surface area33480 Å2
MethodPISA
5
B: Glutamate receptor, ionotropic kainate 5
D: Glutamate receptor, ionotropic kainate 2


Theoretical massNumber of molelcules
Total (without water)88,5482
Polymers88,5482
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3000 Å2
ΔGint-15 kcal/mol
Surface area33560 Å2
MethodPISA
6
E: Glutamate receptor, ionotropic kainate 5
F: Glutamate receptor, ionotropic kainate 2


Theoretical massNumber of molelcules
Total (without water)88,5482
Polymers88,5482
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3190 Å2
ΔGint-16 kcal/mol
Surface area33330 Å2
MethodPISA
7
G: Glutamate receptor, ionotropic kainate 5
H: Glutamate receptor, ionotropic kainate 2


Theoretical massNumber of molelcules
Total (without water)88,5482
Polymers88,5482
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3090 Å2
ΔGint-16 kcal/mol
Surface area33490 Å2
MethodPISA
8
I: Glutamate receptor, ionotropic kainate 5
J: Glutamate receptor, ionotropic kainate 2


Theoretical massNumber of molelcules
Total (without water)88,5482
Polymers88,5482
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2900 Å2
ΔGint-14 kcal/mol
Surface area33720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)366.552, 109.176, 155.469
Angle α, β, γ (deg.)90.00, 97.54, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
41
51
12
22
32
42
52

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111chain C and (resseq 10:35 or resseq 45: 104 or...
211chain D and (resseq 10:35 or resseq 45: 104 or...
311chain F and (resseq 10:35 or resseq 45: 104 or...
411chain H and (resseq 10:35 or resseq 45: 104 or...
511chain J and (resseq 10:35 or resseq 45: 104 or...
112chain A and (resseq 3:10 or resseq 22:37 or resseq...
212chain B and (resseq 3:10 or resseq 22:37 or resseq...
312chain E and (resseq 3:10 or resseq 22:37 or resseq...
412chain G and (resseq 3:10 or resseq 22:37 or resseq...
512chain I and (resseq 3:10 or resseq 22:37 or resseq...

NCS ensembles :
ID
1
2

-
Components

#1: Protein
Glutamate receptor, ionotropic kainate 5 / Glutamate receptor KA-2 / KA2


Mass: 43798.176 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Grik5 / Plasmid: PRK-IRES_EGFP / Cell line (production host): HEK 293 GNTI(-) / Production host: Homo Sapiens (human) / References: UniProt: Q63273
#2: Protein
Glutamate receptor, ionotropic kainate 2 / Glutamate receptor 6 / GluR-6 / GluR6


Mass: 44750.121 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Glur6, Grik2 / Plasmid: PRK-IRES_EGFP / Cell line (production host): HEK 293 GNTI(-) / Production host: Homo Sapiens (human) / References: UniProt: P42260

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.48 Å3/Da / Density % sol: 64.68 %
Crystal growTemperature: 293 K / pH: 8
Details: 10% Ethylene Glycol, 0.1 M HEPES, 5% PEG 8K, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.0332
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 24, 2009
RadiationMonochromator: SI(111) DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 3.94→50 Å / Num. obs: 54061 / % possible obs: 100 % / Observed criterion σ(I): 1 / Redundancy: 13.3 % / Biso Wilson estimate: 131 Å2 / Rmerge(I) obs: 0.139 / Net I/σ(I): 18.6
Reflection shellResolution: 3.95→4.1 Å / Redundancy: 13.4 % / Rmerge(I) obs: 0.895 / Mean I/σ(I) obs: 2.8 / % possible all: 100

-
Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine: 1.6.4_486)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3OM0 AND 3H6H

3om0

3h6h


Resolution: 3.94→48.95 Å / SU ML: 0.5 / σ(F): 0 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.28 2595 5.1 %
Rwork0.264 --
obs0.264 50913 94.1 %
all-50913 -
Solvent computationShrinkage radii: 0.77 Å / VDW probe radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 107.93 Å2 / ksol: 0.32 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--18.0599 Å20 Å214.6265 Å2
2--23.7176 Å20 Å2
3----5.6576 Å2
Refinement stepCycle: LAST / Resolution: 3.94→48.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms29634 0 0 0 29634
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00530270
X-RAY DIFFRACTIONf_angle_d0.59340955
X-RAY DIFFRACTIONf_dihedral_angle_d13.14911215
X-RAY DIFFRACTIONf_chiral_restr0.0424655
X-RAY DIFFRACTIONf_plane_restr0.0035235
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11C2395X-RAY DIFFRACTIONPOSITIONAL
12D2395X-RAY DIFFRACTIONPOSITIONAL0.014
13F2395X-RAY DIFFRACTIONPOSITIONAL0.052
14H2395X-RAY DIFFRACTIONPOSITIONAL0.004
15J2395X-RAY DIFFRACTIONPOSITIONAL0.061
21A2277X-RAY DIFFRACTIONPOSITIONAL
22B2277X-RAY DIFFRACTIONPOSITIONAL0.013
23E2277X-RAY DIFFRACTIONPOSITIONAL0.053
24G2277X-RAY DIFFRACTIONPOSITIONAL0.021
25I2277X-RAY DIFFRACTIONPOSITIONAL0.054
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.942-4.08280.34712120.36334206X-RAY DIFFRACTION82
4.0828-4.24620.32992620.32354461X-RAY DIFFRACTION88
4.2462-4.43930.34992460.2954631X-RAY DIFFRACTION90
4.4393-4.67320.28492450.26294773X-RAY DIFFRACTION94
4.6732-4.96570.27312720.24434866X-RAY DIFFRACTION95
4.9657-5.34870.27572670.25384929X-RAY DIFFRACTION96
5.3487-5.88610.34252690.28714969X-RAY DIFFRACTION97
5.8861-6.7360.29972780.2735076X-RAY DIFFRACTION98
6.736-8.47950.2382720.21185139X-RAY DIFFRACTION99
8.4795-48.95310.24062720.25395268X-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)
11.26390.5596-0.73511.3374-0.77831.0576-0.19370.3449-0.1670.0315-0.24050.40040.1642-0.1235-0.00160.54370.0326-0.24870.9223-0.33270.4841-9.8529-33.303349.767
20.3847-0.23180.64931.75350.92212.020.3416-0.0888-0.2348-0.0354-0.1135-0.1353-0.21520.49890.00010.5287-0.02860.02060.95370.11950.769181.4568-14.921183.9502
32.5393-0.6960.07912.08430.7250.48380.00010.13640.3859-0.0580.04440.0897-0.04760.129200.6911-0.0518-0.11530.78820.14880.57969.9516-6.75361.5578
41.4823-0.38760.13081.6259-1.3451.10860.0821-0.0823-0.13390.1104-0.19090.08630.0388-0.2895-00.7192-0.0833-0.01090.6040.05450.763253.1759-34.877391.0049
52.26581.2138-0.14442.43180.82990.3105-0.18590.5209-0.037-0.14790.24240.39810.2769-0.15190.00010.77970.1714-0.04941.08040.31710.820735.1769-50.9644-11.8811
62.45190.05290.4219-0.0643-0.01410.40810.1263-0.48930.21210.3932-0.08040.04630.0734-0.072-00.8230.2460.19140.7190.06070.552245.3341-45.300721.1019
70.9093-0.0095-0.11550.828-1.00021.10250.08430.15820.09350.5488-0.1283-0.58810.01410.3508-01.061-0.2525-0.13920.87470.04291.3243117.406-39.754642.2448
81.3221-0.81350.22981.9242-0.12520.18540.03760.42170.08310.0101-0.04960.07010.2770.1456-00.93570.04460.04320.9588-0.10520.8031102.3773-62.933620.4746
90.22880.31760.19520.35370.41352.18-0.1097-0.3488-1.04930.29290.32910.70290.63940.224201.21350.5091-0.05280.73680.1862.558148.492410.345610.4926
101.45110.14860.33480.72511.16121.60630.2287-0.5993-1.3804-0.1021-0.1437-0.02530.2028-0.12301.50190.13460.12721.21350.82682.353917.369421.043923.9411
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A
2X-RAY DIFFRACTION2CHAIN B
3X-RAY DIFFRACTION3CHAIN C
4X-RAY DIFFRACTION4CHAIN D
5X-RAY DIFFRACTION5CHAIN E
6X-RAY DIFFRACTION6CHAIN F
7X-RAY DIFFRACTION7CHAIN G
8X-RAY DIFFRACTION8CHAIN H
9X-RAY DIFFRACTION9CHAIN I
10X-RAY DIFFRACTION10CHAIN J

+
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://pdbjlvh1.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