[English] 日本語
Yorodumi
- PDB-4u1w: Full length GluA2-kainate-(R,R)-2b complex crystal form A -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4u1w
TitleFull length GluA2-kainate-(R,R)-2b complex crystal form A
ComponentsGlutamate receptor 2
KeywordsTransport protein / Membrane protein / AMPA receptor
Function / homology
Function and homology information


spine synapse / dendritic spine neck / dendritic spine head / cellular response to amine stimulus / perisynaptic space / Activation of AMPA receptors / ligand-gated monoatomic cation channel activity / AMPA glutamate receptor activity / response to lithium ion / Trafficking of GluR2-containing AMPA receptors ...spine synapse / dendritic spine neck / dendritic spine head / cellular response to amine stimulus / perisynaptic space / Activation of AMPA receptors / ligand-gated monoatomic cation channel activity / AMPA glutamate receptor activity / response to lithium ion / Trafficking of GluR2-containing AMPA receptors / kainate selective glutamate receptor activity / AMPA glutamate receptor complex / cellular response to glycine / extracellularly glutamate-gated ion channel activity / immunoglobulin binding / asymmetric synapse / ionotropic glutamate receptor complex / conditioned place preference / regulation of receptor recycling / glutamate receptor binding / Unblocking of NMDA receptors, glutamate binding and activation / positive regulation of synaptic transmission / regulation of synaptic transmission, glutamatergic / response to fungicide / cytoskeletal protein binding / glutamate-gated receptor activity / regulation of long-term synaptic depression / extracellular ligand-gated monoatomic ion channel activity / cellular response to brain-derived neurotrophic factor stimulus / glutamate-gated calcium ion channel activity / presynaptic active zone membrane / somatodendritic compartment / dendrite membrane / ionotropic glutamate receptor binding / ligand-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / ionotropic glutamate receptor signaling pathway / dendrite cytoplasm / synaptic membrane / dendritic shaft / SNARE binding / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / synaptic transmission, glutamatergic / PDZ domain binding / protein tetramerization / establishment of protein localization / postsynaptic density membrane / cerebral cortex development / modulation of chemical synaptic transmission / receptor internalization / Schaffer collateral - CA1 synapse / terminal bouton / synaptic vesicle / synaptic vesicle membrane / presynapse / signaling receptor activity / amyloid-beta binding / presynaptic membrane / growth cone / scaffold protein binding / perikaryon / chemical synaptic transmission / dendritic spine / postsynaptic membrane / neuron projection / postsynaptic density / axon / external side of plasma membrane / neuronal cell body / synapse / dendrite / protein kinase binding / protein-containing complex binding / glutamatergic synapse / cell surface / endoplasmic reticulum / protein-containing complex / 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 II / Periplasmic binding protein-like I / D-Maltodextrin-Binding Protein; domain 2 / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-FWF / 3-(CARBOXYMETHYL)-4-ISOPROPENYLPROLINE / Glutamate receptor 2
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3.25 Å
AuthorsChen, L. / Gouaux, E.
CitationJournal: Cell / Year: 2014
Title: Structure and Dynamics of AMPA Receptor GluA2 in Resting, Pre-Open, and Desensitized States.
Authors: Durr, K.L. / Chen, L. / Stein, R.A. / De Zorzi, R. / Folea, I.M. / Walz, T. / Mchaourab, H.S. / Gouaux, E.
History
DepositionJul 16, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 20, 2014Provider: repository / Type: Initial release
Revision 1.1Oct 1, 2014Group: Database references
Revision 1.2Nov 22, 2017Group: Derived calculations / Other ...Derived calculations / Other / Refinement description / Source and taxonomy / Structure summary
Category: entity / entity_src_gen ...entity / entity_src_gen / pdbx_database_status / pdbx_struct_oper_list / software
Item: _entity.pdbx_description / _entity_src_gen.pdbx_alt_source_flag ..._entity.pdbx_description / _entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations ...Data collection / Derived calculations / Refinement description / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / refine_hist / struct_conn / 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 / _refine_hist.pdbx_number_atoms_nucleic_acid / _refine_hist.pdbx_number_atoms_protein / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Dec 27, 2023Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
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 2
B: Glutamate receptor 2
C: Glutamate receptor 2
D: Glutamate receptor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)372,24514
Polymers369,5464
Non-polymers2,69910
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area23150 Å2
ΔGint-175 kcal/mol
Surface area134470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.500, 151.110, 332.530
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein
Glutamate receptor 2 / GluR-2 / AMPA-selective glutamate receptor 2 / GluR-B / GluR-K2 / Glutamate receptor ionotropic / ...GluR-2 / AMPA-selective glutamate receptor 2 / GluR-B / GluR-K2 / Glutamate receptor ionotropic / AMPA 2 / GluA2


Mass: 92386.383 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Gria2, Glur2 / Production host: Homo sapiens (human) / References: UniProt: P19491
#2: Chemical
ChemComp-KAI / 3-(CARBOXYMETHYL)-4-ISOPROPENYLPROLINE / KAINATE


Mass: 213.230 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H15NO4
#3: 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.: 4 / Source method: obtained synthetically / 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
#4: Chemical ChemComp-FWF / N,N'-[biphenyl-4,4'-diyldi(2R)propane-2,1-diyl]dipropane-2-sulfonamide


Mass: 480.684 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C24H36N2O4S2
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.55 Å3/Da / Density % sol: 65.37 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: 0.1 M MES, pH 6.5, 6%PEG6K, 3% TMAO, 0.006M Taurine

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 27, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.23→83.21 Å / Num. obs: 83881 / % possible obs: 98.4 % / Redundancy: 4.1 % / Biso Wilson estimate: 107.96 Å2 / Net I/σ(I): 11.1

-
Processing

Software
NameVersionClassification
PHENIXrefinement
PDB_EXTRACT3.14data extraction
RefinementResolution: 3.25→29.91 Å / FOM work R set: 0.6735 / SU ML: 0.59 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 37.87 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3161 3359 5.03 %
Rwork0.2702 63389 -
obs0.2725 66748 79.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 298.36 Å2 / Biso mean: 147.51 Å2 / Biso min: 43.69 Å2
Refinement stepCycle: final / Resolution: 3.25→29.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms22831 0 180 0 23011
Biso mean--118.4 --
Num. residues----2968
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00423489
X-RAY DIFFRACTIONf_angle_d0.84931847
X-RAY DIFFRACTIONf_chiral_restr0.0563644
X-RAY DIFFRACTIONf_plane_restr0.0034017
X-RAY DIFFRACTIONf_dihedral_angle_d13.1848342
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 24

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.25-3.29640.196460.55021301364
3.2964-3.34550.3929170.428537439111
3.3455-3.39770.3855310.424362765819
3.3977-3.45330.4995410.419192696728
3.4533-3.51280.4122740.39891357143141
3.5128-3.57660.42241030.38721978208161
3.5766-3.64520.42741370.37162482261976
3.6452-3.71950.40431590.35792958311790
3.7195-3.80020.36131700.35253215338599
3.8002-3.88850.41072030.36253217342098
3.8885-3.98550.3881850.36073167335297
3.9855-4.0930.42511470.33783256340398
4.093-4.21310.38211540.31153260341499
4.2131-4.34870.3421730.2923271344499
4.3487-4.50360.30841740.27133237341199
4.5036-4.68330.30981690.26433276344599
4.6833-4.89560.30551740.2463246342098
4.8956-5.15240.28561790.24123251343098
5.1524-5.47340.29821830.24583301348499
5.4734-5.8930.28821580.26653331348999
5.893-6.48060.32191850.26663319350499
6.4806-7.40590.2951880.25173363355199
7.4059-9.28420.24871620.22273382354499
9.2842-29.91080.27691870.22283465365298
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)
13.7033-0.46871.94835.225-1.42786.7375-0.6404-0.34840.60020.3465-0.1719-1.2203-0.3910.63860.750.77810.2976-0.15740.93550.05641.0531-8.073610.1697-54.7344
24.45550.0307-0.06312.5108-0.83573.54670.22840.5366-0.8259-0.06730.0291-1.33640.80450.8692-0.0411.0337-0.1072-0.12911.0753-0.42241.8504-17.8209-3.5817-104.6346
32.4542-0.11760.18424.0158-0.77220.58970.92580.24310.3908-0.7305-1.119-0.03890.710.7791-0.14592.0617-0.2159-0.05562.0499-0.21641.0054-51.8199-15.7107-154.4395
40.61660.43370.92050.36090.52532.42770.20150.4107-0.1063-0.60390.04090.29220.51050.6547-0.09761.7438-0.41050.0381.4417-0.26581.0728-42.896-15.7832-123.5824
5-0.33650.6633-0.3095-0.33031.70683.32570.54380.24510.32540.1159-0.5531-0.01821.5286-1.4969-0.08761.5814-0.214-0.1771.5512-0.1271.2458-33.05592.0412-124.4299
64.3882-0.03471.90442.96540.4613.6727-0.4055-0.8658-0.26640.47570.10240.4390.1765-0.42970.27860.82210.30820.17730.9780.18680.9418-24.454-20.6946-45.4983
74.2410.40172.29573.1629-0.63245.3156-0.1838-0.00950.0928-0.26650.0265-0.2918-0.15310.45660.17570.6699-0.135-0.13840.6563-0.0610.4877-61.6055-38.8229-93.7781
82.69522.4911-0.16642.5296-2.16647.78691.07290.43241.30870.664-0.23591.6582-1.80981.5056-0.74092.3266-0.0289-0.25871.0413-0.46162.505-75.8332-16.0288-150.8097
91.02830.2481-0.83521.6434-0.36673.18180.1860.3411-0.1167-0.9101-0.22160.2397-0.3748-0.3350.02071.3624-0.2679-0.18990.9746-0.04750.9029-69.0142-31.4642-125.4902
101.075-0.42061.54121.01611.64364.2492-0.24410.54030.3482-0.97820.1095-0.2656-1.60971.25060.15261.4491-0.3937-0.15670.83360.14091.0908-64.8698-25.6409-121.9339
112.29210.5959-1.49642.78030.29154.39440.01940.1053-0.70970.41430.33070.08170.30660.5924-0.36430.90440.5481-0.081.4214-0.161.2316-90.1396-35.4932-47.2348
125.8811.8872-2.32994.34280.38064.2409-0.10220.36780.53050.35150.16140.8832-0.1818-1.10040.05710.5530.0498-0.18110.76820.13630.8266-91.8584-22.8595-92.9329
133.41570.98121.51320.2180.41020.64780.9619-0.19010.22751.0791-0.1744-0.08891.6236-2.219-0.55763.88950.5007-0.59311.8929-0.43891.5074-75.274311.1033-145.9166
140.11831.4642-0.79161.8065-2.39262.78410.04340.2774-0.06-0.3330.303-0.0777-0.7193-0.2724-0.21151.4540.0812-0.31860.97710.12531.3382-74.003-3.3229-114.3007
151.6617-1.15151.76060.0372-0.37110.7197-0.06830.99150.611-0.671-0.20410.2017-0.13120.42630.38641.622-0.2072-0.50131.2090.36911.1706-84.9579-18.6757-119.1772
166.77751.3982-1.96173.8507-0.97163.24620.3611-0.81321.5191.2128-0.1573-0.1859-0.41930.2397-0.17731.21790.3783-0.18321.6489-0.50241.643-73.5787-4.9246-39.6879
175.09551.08010.88365.83170.3042.7539-0.3103-0.48230.53880.57470.20060.6493-0.41760.0340.09130.8852-0.0492-0.16750.4691-0.04760.5673-45.446911.2072-88.0026
183.4951-1.32040.51643.64-4.03714.8144-2.27161.15370.0976-0.15370.5713-1.0142-2.15931.01171.57462.8881-1.316-0.05161.7785-0.20641.3638-50.76619.0153-147.0551
190.3418-1.10631.11512.3049-1.67583.5971-0.01790.35930.9054-1.0899-0.2261-0.466-0.49560.60230.21811.6078-0.5834-0.0941.41460.30111.3427-48.947113.7422-121.7818
200.2229-0.38830.31782.91860.57212.9567-0.70590.2338-0.0259-1.2764-0.01660.2601-0.2427-0.62270.53591.5241-0.453-0.36750.895-0.14561.0275-50.90618.0178-116.5156
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 1:382)A1 - 382
2X-RAY DIFFRACTION2(chain A and resid 383:507)A383 - 507
3X-RAY DIFFRACTION3(chain A and resid 508:545)A508 - 545
4X-RAY DIFFRACTION4(chain A and resid 550:721)A550 - 721
5X-RAY DIFFRACTION5(chain A and resid 722:817)A722 - 817
6X-RAY DIFFRACTION6(chain B and resid 1:382)B1 - 382
7X-RAY DIFFRACTION7(chain B and resid 383:507)B383 - 507
8X-RAY DIFFRACTION8(chain B and resid 508:545)B508 - 545
9X-RAY DIFFRACTION9(chain B and resid 550:721)B550 - 721
10X-RAY DIFFRACTION10(chain B and resid 722:817)B722 - 817
11X-RAY DIFFRACTION11(chain C and resid 1:382)C1 - 382
12X-RAY DIFFRACTION12(chain C and resid 383:507)C383 - 507
13X-RAY DIFFRACTION13(chain C and resid 508:545)C508 - 545
14X-RAY DIFFRACTION14(chain C and resid 550:721)C550 - 721
15X-RAY DIFFRACTION15(chain C and resid 722:817)C722 - 817
16X-RAY DIFFRACTION16(chain D and resid 1:382)D1 - 382
17X-RAY DIFFRACTION17(chain D and resid 383:507)D383 - 507
18X-RAY DIFFRACTION18(chain D and resid 508:545)D508 - 545
19X-RAY DIFFRACTION19(chain D and resid 550:721)D550 - 721
20X-RAY DIFFRACTION20(chain D and resid 722:817)D722 - 817

+
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