[English] 日本語
Yorodumi
- PDB-3pmx: Ligand-binding domain of GluA2 (flip) ionotropic glutamate recept... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3pmx
TitleLigand-binding domain of GluA2 (flip) ionotropic glutamate receptor in complex with an allosteric modulator
ComponentsGlutamate receptor 2GRIA2
KeywordsTRANSPORT PROTEIN / Membrane Protein / Fusion protein / chimera protein
Function / homology
Function and homology information


spine synapse / dendritic spine neck / dendritic spine head / Activation of AMPA receptors / perisynaptic space / AMPA glutamate receptor activity / Trafficking of GluR2-containing AMPA receptors / response to lithium ion / immunoglobulin binding / AMPA glutamate receptor complex ...spine synapse / dendritic spine neck / dendritic spine head / Activation of AMPA receptors / perisynaptic space / AMPA glutamate receptor activity / Trafficking of GluR2-containing AMPA receptors / response to lithium ion / immunoglobulin binding / AMPA glutamate receptor complex / kainate selective glutamate receptor activity / ionotropic glutamate receptor complex / extracellularly glutamate-gated ion channel activity / cellular response to glycine / asymmetric synapse / regulation of receptor recycling / Unblocking of NMDA receptors, glutamate binding and activation / glutamate receptor binding / positive regulation of synaptic transmission / presynaptic active zone membrane / glutamate-gated receptor activity / response to fungicide / regulation of synaptic transmission, glutamatergic / somatodendritic compartment / cellular response to brain-derived neurotrophic factor stimulus / dendrite membrane / ligand-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / ionotropic glutamate receptor binding / cytoskeletal protein binding / ionotropic glutamate receptor signaling pathway / dendrite cytoplasm / SNARE binding / dendritic shaft / synaptic membrane / synaptic transmission, glutamatergic / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / PDZ domain binding / protein tetramerization / postsynaptic density membrane / Schaffer collateral - CA1 synapse / modulation of chemical synaptic transmission / establishment of protein localization / receptor internalization / terminal bouton / cerebral cortex development / synaptic vesicle membrane / synaptic vesicle / presynapse / presynaptic membrane / signaling receptor activity / amyloid-beta binding / growth cone / scaffold protein binding / chemical synaptic transmission / perikaryon / postsynaptic membrane / dendritic spine / postsynaptic density / neuron projection / axon / neuronal cell body / glutamatergic synapse / synapse / dendrite / protein-containing complex binding / endoplasmic reticulum membrane / protein kinase binding / cell surface / endoplasmic reticulum / protein-containing complex / membrane / identical protein binding / plasma membrane
Similarity search - Function
Bacterial extracellular solute-binding proteins, family 3 / Solute-binding protein family 3/N-terminal domain of MltF / 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. ...Bacterial extracellular solute-binding proteins, family 3 / Solute-binding protein family 3/N-terminal domain of MltF / 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 II / Periplasmic binding protein-like I / D-Maltodextrin-Binding Protein; domain 2 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-808 / GLUTAMIC ACID / Glutamate receptor 2
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.87 Å
AuthorsMaclean, J.K.F. / Jamieson, C. / Brown, C.I. / Campbell, R.A. / Gillen, K.J. / Gillespie, J. / Kazemier, B. / Kiczun, M. / Lamont, Y. / Lyons, A.J. ...Maclean, J.K.F. / Jamieson, C. / Brown, C.I. / Campbell, R.A. / Gillen, K.J. / Gillespie, J. / Kazemier, B. / Kiczun, M. / Lamont, Y. / Lyons, A.J. / Moir, E.M. / Morrow, J.A. / Pantling, J. / Rankovic, Z. / Smith, L.
CitationJournal: Bioorg.Med.Chem.Lett. / Year: 2011
Title: Structure based evolution of a novel series of positive modulators of the AMPA receptor.
Authors: Jamieson, C. / Maclean, J.K. / Brown, C.I. / Campbell, R.A. / Gillen, K.J. / Gillespie, J. / Kazemier, B. / Kiczun, M. / Lamont, Y. / Lyons, A.J. / Moir, E.M. / Morrow, J.A. / Pantling, J. / ...Authors: Jamieson, C. / Maclean, J.K. / Brown, C.I. / Campbell, R.A. / Gillen, K.J. / Gillespie, J. / Kazemier, B. / Kiczun, M. / Lamont, Y. / Lyons, A.J. / Moir, E.M. / Morrow, J.A. / Pantling, J. / Rankovic, Z. / Smith, L.
History
DepositionNov 18, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 12, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 9, 2017Group: Advisory / Refinement description / Source and taxonomy
Category: entity_src_gen / pdbx_unobs_or_zero_occ_atoms / software

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Glutamate receptor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,68515
Polymers29,1781
Non-polymers1,50814
Water5,603311
1
A: Glutamate receptor 2
hetero molecules

A: Glutamate receptor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,37030
Polymers58,3552
Non-polymers3,01528
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Unit cell
Length a, b, c (Å)64.240, 88.170, 47.345
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

-
Components

-
Protein , 1 types, 1 molecules A

#1: Protein Glutamate receptor 2 / GRIA2 / GluR-2 / GluR-B / GluR-K2 / Glutamate receptor ionotropic / AMPA 2 / GluA2 / AMPA-selective ...GluR-2 / GluR-B / GluR-K2 / Glutamate receptor ionotropic / AMPA 2 / GluA2 / AMPA-selective glutamate receptor 2


Mass: 29177.670 Da / Num. of mol.: 1
Fragment: Ligand binding domain, residues 413 to 527 and 653 to 796
Source method: isolated from a genetically manipulated source
Details: S1-S2 fusion in which Gly118 and Thr119 replace a membrane-spanning region
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Gria2, Glur2 / Plasmid: pET-32a / Production host: Escherichia coli (E. coli) / Strain (production host): Origami B (de3) / References: UniProt: P19491

-
Non-polymers , 7 types, 325 molecules

#2: Chemical ChemComp-GLU / GLUTAMIC ACID / Glutamic acid


Type: L-peptide linking / Mass: 147.129 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H9NO4
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE / Dimethyl sulfoxide


Mass: 78.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#6: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#7: Chemical ChemComp-808 / N-[(2S)-5-{[5-(trifluoromethyl)furan-2-yl]methyl}-2,3-dihydro-1H-inden-2-yl]propane-2-sulfonamide / (S)-N-(5-((5-(trifluoromethyl)furan-2-yl)methyl)-2,3-dihydro-1H-inden-2-yl)propane-2-sulfonamide


Mass: 387.417 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H20F3NO3S
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 311 / 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: 2.3 Å3/Da / Density % sol: 46.44 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 4
Details: 18% PEG 4000, 50mM Lithium Sulphate, 2.5% Glycerol, 100mM Sodium Cacodylate pH 4.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.54178 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Sep 30, 2008 / Details: Mirrors
RadiationMonochromator: Graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 1.87→26.73 Å / Num. all: 21208 / Num. obs: 21208 / % possible obs: 92.9 % / Observed criterion σ(I): 2 / Redundancy: 4.4 % / Biso Wilson estimate: 31.2 Å2 / Rsym value: 0.051 / Net I/σ(I): 17.3
Reflection shellResolution: 1.87→1.92 Å / Redundancy: 4 % / Rmerge(I) obs: 0.661 / Mean I/σ(I) obs: 1.9 / Num. unique all: 1442 / % possible all: 86.5

-
Processing

Software
NameVersionClassification
CrystalCleardata collection
AMoREphasing
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.87→26.73 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.923 / SU B: 5.501 / SU ML: 0.162 / Cross valid method: THROUGHOUT / ESU R Free: 0.19 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28142 1089 5.1 %RANDOM
Rwork0.21754 ---
all0.22086 20080 --
obs0.22086 20080 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.358 Å2
Baniso -1Baniso -2Baniso -3
1--2.95 Å20 Å20 Å2
2--3.07 Å20 Å2
3----0.12 Å2
Refinement stepCycle: LAST / Resolution: 1.87→26.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2043 0 92 311 2446
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_refined_d0.014
X-RAY DIFFRACTIONr_bond_other_d0.006
X-RAY DIFFRACTIONr_angle_refined_deg1.442
X-RAY DIFFRACTIONr_angle_other_deg0.976
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.999
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.736
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.804
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.885
X-RAY DIFFRACTIONr_chiral_restr0.078
X-RAY DIFFRACTIONr_gen_planes_refined0.005
X-RAY DIFFRACTIONr_gen_planes_other0.001
X-RAY DIFFRACTIONr_nbd_refined0.199
X-RAY DIFFRACTIONr_nbd_other0.207
X-RAY DIFFRACTIONr_nbtor_refined0.17
X-RAY DIFFRACTIONr_nbtor_other0.087
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.172
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.159
X-RAY DIFFRACTIONr_symmetry_vdw_other0.28
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.247
X-RAY DIFFRACTIONr_mcbond_it1.492
X-RAY DIFFRACTIONr_mcbond_other0.258
X-RAY DIFFRACTIONr_mcangle_it1.599
X-RAY DIFFRACTIONr_scbond_it2.545
X-RAY DIFFRACTIONr_scangle_it3.277
LS refinement shellResolution: 1.87→1.916 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.517 87 -
Rwork0.411 1347 -
obs--100 %

+
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