[English] 日本語
Yorodumi
- PDB-3h6g: Crystal structure of the GluR6 amino terminal domain dimer assembly -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3h6g
TitleCrystal structure of the GluR6 amino terminal domain dimer assembly
ComponentsGlutamate receptor, ionotropic kainate 2
KeywordsMEMBRANE PROTEIN / MEMBRANE PROTEIN GLYCOPROTEIN / Cell junction / Cell membrane / Glycoprotein / Ion transport / Ionic channel / Isopeptide bond / Membrane / Postsynaptic cell membrane / Receptor / RNA editing / Synapse / Transmembrane / Transport
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 / negative regulation of synaptic transmission, glutamatergic / regulation of short-term neuronal synaptic plasticity / inhibitory postsynaptic potential / glutamate receptor activity / ubiquitin conjugating enzyme binding ...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 / positive regulation of synaptic transmission / 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 / regulation of membrane potential / SNARE binding / 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 / regulation of long-term neuronal synaptic plasticity / modulation of chemical synaptic transmission / terminal bouton / intracellular calcium ion homeostasis / positive regulation of neuron apoptotic process / presynaptic membrane / scaffold protein binding / chemical synaptic transmission / perikaryon / postsynaptic membrane / neuron apoptotic process / negative regulation of neuron apoptotic process / postsynaptic density / axon / neuronal cell body / glutamatergic synapse / ubiquitin protein ligase binding / dendrite / synapse / identical protein binding / membrane / plasma membrane
Similarity search - Function
Response regulator / 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 ...Response regulator / 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 / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
L(+)-TARTARIC ACID / Glutamate receptor ionotropic, kainate 2
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.697 Å
AuthorsKumar, J. / Mayer, M.L.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2009
Title: The N-terminal domain of GluR6-subtype glutamate receptor ion channels.
Authors: Kumar, J. / Schuck, P. / Jin, R. / Mayer, M.L.
History
DepositionApr 23, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 26, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Jul 29, 2020Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / database_PDB_caveat ...chem_comp / database_PDB_caveat / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_conn_type / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _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_type.id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Mar 31, 2021Group: Source and taxonomy / Structure summary / Category: chem_comp / entity_src_gen
Item: _chem_comp.pdbx_synonyms / _entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_strain
Revision 1.4Sep 6, 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.5Nov 6, 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 kainate 2
B: Glutamate receptor, ionotropic kainate 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,65014
Polymers89,5002
Non-polymers2,15012
Water79344
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6140 Å2
ΔGint-9 kcal/mol
Surface area32470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)172.074, 172.074, 111.547
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Ens-ID: 1 / End auth comp-ID: GLU / End label comp-ID: GLU

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11THRTHRchain A and (resseq 2:268 or resseq 275:384 ) and (not element H)AA2 - 2682 - 268
12LYSLYSchain A and (resseq 2:268 or resseq 275:384 ) and (not element H)AA275 - 384275 - 384
21THRTHRchain B and (resseq 2:268 or resseq 275:384 ) and (not element H)BB2 - 2682 - 268
22LYSLYSchain B and (resseq 2:268 or resseq 275:384 ) and (not element H)BB275 - 384275 - 384

-
Components

#1: Protein Glutamate receptor, ionotropic kainate 2 / Glutamate receptor 6 / GluR-6 / GluR6


Mass: 44750.121 Da / Num. of mol.: 2 / Fragment: UNP residues 32-420
Source method: isolated from a genetically manipulated source
Details: The last six amino acids are vector encoded. The protein is a secreted product in which the 31 amino acid signal peptide was cleaved by the expression system between residues 31 and 32 and ...Details: The last six amino acids are vector encoded. The protein is a secreted product in which the 31 amino acid signal peptide was cleaved by the expression system between residues 31 and 32 and verified by N-terminal sequencing.
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Glur6, Grik2 / Plasmid: pRK8 / Cell line (production host): HEK-293 / Production host: Homo Sapiens (human) / References: UniProt: P42260
#2: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Chemical ChemComp-TLA / L(+)-TARTARIC ACID


Mass: 150.087 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H6O6
#4: Chemical ChemComp-CA / CALCIUM ION


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


Mass: 18.015 Da / Num. of mol.: 44 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 5.33 Å3/Da / Density % sol: 76.91 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 600 mM NaKTartrate, 200 mM NaCl, 20 mM NaAcetate, 1 mM EDTA, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 6, 2008
RadiationMonochromator: Si(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.69→50 Å / Num. all: 50708 / Num. obs: 50708 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 1 / Redundancy: 4.4 % / Biso Wilson estimate: 68.93 Å2 / Rmerge(I) obs: 0.073 / Net I/σ(I): 14
Reflection shellResolution: 2.69→2.74 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.63 / Mean I/σ(I) obs: 2.1 / % possible all: 99.4

-
Processing

Software
NameClassification
HKL-2000data collection
PHASERphasing
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3H5V

3h5v


Resolution: 2.697→46.8 Å / SU ML: 0.31 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2271 2571 5.07 %Throughout
Rwork0.2038 ---
obs0.2049 50708 97.86 %-
all-50708 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 54.644 Å2 / ksol: 0.371 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--11.6145 Å2--
2---11.6145 Å2-
3---23.229 Å2
Refinement stepCycle: LAST / Resolution: 2.697→46.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6055 0 134 44 6233
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONf_bond_d0.009
X-RAY DIFFRACTIONf_angle_deg0.841
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A3004X-RAY DIFFRACTIONPOSITIONAL0.03
12B3004X-RAY DIFFRACTIONPOSITIONAL0.03
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.697-2.74850.3002930.28351869X-RAY DIFFRACTION70
2.7485-2.80460.36311290.29992735X-RAY DIFFRACTION99
2.8046-2.86560.3121440.28992741X-RAY DIFFRACTION100
2.8656-2.93220.32791670.27382698X-RAY DIFFRACTION100
2.9322-3.00560.24311430.2512695X-RAY DIFFRACTION100
3.0056-3.08680.2911520.23482716X-RAY DIFFRACTION100
3.0868-3.17760.27051690.23132677X-RAY DIFFRACTION100
3.1776-3.28020.21041610.20312727X-RAY DIFFRACTION100
3.2802-3.39740.20881260.20492722X-RAY DIFFRACTION100
3.3974-3.53330.25081440.19642716X-RAY DIFFRACTION100
3.5333-3.69410.19281310.20412747X-RAY DIFFRACTION100
3.6941-3.88880.20881400.18272711X-RAY DIFFRACTION100
3.8888-4.13230.21631530.16712723X-RAY DIFFRACTION100
4.1323-4.45110.18591380.15562728X-RAY DIFFRACTION100
4.4511-4.89860.18191400.15252741X-RAY DIFFRACTION99
4.8986-5.60640.18371570.16072697X-RAY DIFFRACTION99
5.6064-7.05960.22951400.19182750X-RAY DIFFRACTION99
7.0596-46.80730.17241440.19462744X-RAY DIFFRACTION98
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)
11.4228-0.78131.55282.5370.2049-1.9213-0.03310.2416-0.2945-0.3241-0.13870.28110.0618-0.230.11160.44760.06360.0370.4928-0.00680.241-80.696428.59416.6412
20.4214-0.3301-1.0740.56760.2812.5218-0.03110.00660.5729-0.15990.0448-0.5215-0.2436-0.00350.01970.5073-0.0531-0.07070.32260.07140.7739-54.22210.31789.4732
30.9741-0.92280.23852.63450.51822.259-0.1629-0.2594-0.08190.77650.1751-0.38660.0833-0.27590.00380.5455-0.0332-0.0550.36530.05710.408-69.060223.369624.2822
42.4774-0.0324-1.42551.94090.7363-1.3338-0.3161-0.21510.1610.17670.039-0.27620.0979-0.2410.13580.45630.0106-0.10680.61670.04780.3141-76.503638.7077-12.6766
52.69791.61690.44880.3748-0.31472.13590.0794-0.0183-0.8634-0.0736-0.0812-0.01470.1189-0.11240.0030.4228-0.08330.05120.30650.00540.7537-45.048431.926-6.7014
64.6197-0.0922-0.1361.02670.37852.0381-0.22250.8636-0.291-0.21650.1365-0.1915-0.0304-0.20350.07870.5488-0.09850.02150.4753-0.00470.4503-65.180535.0122-20.756
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 2:120) or (chain C and resid 1:2)A2 - 120
2X-RAY DIFFRACTION1(chain A and resid 2:120) or (chain C and resid 1:2)A1 - 397
3X-RAY DIFFRACTION2(chain A and resid 121:242)A121 - 242
4X-RAY DIFFRACTION3(chain A and resid 243:384) or (chain C and resid 3:5)A243 - 384
5X-RAY DIFFRACTION3(chain A and resid 243:384) or (chain C and resid 3:5)A3 - 400
6X-RAY DIFFRACTION4(chain B and resid 2:121) or (chain C and resid 6)B2 - 121
7X-RAY DIFFRACTION4(chain B and resid 2:121) or (chain C and resid 6)B6 - 396
8X-RAY DIFFRACTION5(chain B and resid 122:242)B122 - 242
9X-RAY DIFFRACTION6(chain B and resid 243:384) or (chain C and resid 8:9)B243 - 384
10X-RAY DIFFRACTION6(chain B and resid 243:384) or (chain C and resid 8:9)B8 - 398

+
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