[English] 日本語
Yorodumi
- PDB-5zg2: Crystal structure of the GluA2o LBD in complex with ZK200775 and ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5zg2
TitleCrystal structure of the GluA2o LBD in complex with ZK200775 and Compound-2
ComponentsGlutamate receptor 2
KeywordsTRANSPORT PROTEIN / AMPA RECEPTOR LIGAND-BINDING DOMAIN / ALLOSTERIC MODULATION COMPLEX / MEMBRANE PROTEIN
Function / homology
Function and homology information


Activation of AMPA receptors / Trafficking of GluR2-containing AMPA receptors / postsynaptic endocytic zone / ligand-gated monoatomic cation channel activity / AMPA glutamate receptor activity / Unblocking of NMDA receptors, glutamate binding and activation / AMPA glutamate receptor complex / Long-term potentiation / asymmetric synapse / excitatory synapse ...Activation of AMPA receptors / Trafficking of GluR2-containing AMPA receptors / postsynaptic endocytic zone / ligand-gated monoatomic cation channel activity / AMPA glutamate receptor activity / Unblocking of NMDA receptors, glutamate binding and activation / AMPA glutamate receptor complex / Long-term potentiation / asymmetric synapse / excitatory synapse / glutamate-gated receptor activity / MECP2 regulates neuronal receptors and channels / ionotropic glutamate receptor signaling pathway / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / synaptic transmission, glutamatergic / postsynaptic density membrane / modulation of chemical synaptic transmission / endocytic vesicle membrane / amyloid-beta binding / dendritic spine / chemical synaptic transmission / postsynapse / postsynaptic density / external side of plasma membrane / neuronal cell body / dendrite / signal transduction / 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
Chem-9C0 / ACETATE ION / Chem-ZK1 / Glutamate receptor 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.25 Å
AuthorsSogabe, S. / Igaki, S. / Hirokawa, A. / Zama, Y. / Lane, W. / Snell, G.
CitationJournal: Neuropsychopharmacology / Year: 2019
Title: TAK-137, an AMPA-R potentiator with little agonistic effect, has a wide therapeutic window.
Authors: Kunugi, A. / Tanaka, M. / Suzuki, A. / Tajima, Y. / Suzuki, N. / Suzuki, M. / Nakamura, S. / Kuno, H. / Yokota, A. / Sogabe, S. / Kosugi, Y. / Awasaki, Y. / Kaku, T. / Kimura, H.
History
DepositionMar 7, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 16, 2019Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation.year
Revision 1.2Nov 22, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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.ptnr2_symmetry / _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_symmetry
Revision 1.3Nov 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,49915
Polymers58,6762
Non-polymers1,82313
Water11,746652
1
B: Glutamate receptor 2
hetero molecules

A: Glutamate receptor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,49915
Polymers58,6762
Non-polymers1,82313
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_545x,y-1,z1
Buried area2290 Å2
ΔGint-107 kcal/mol
Surface area25610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.384, 56.565, 90.779
Angle α, β, γ (deg.)90.00, 91.74, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

-
Protein , 1 types, 2 molecules AB

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


Mass: 29337.830 Da / Num. of mol.: 2 / Fragment: UNP residues 413-527,UNP residues 653-796
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GLUR2 / Production host: Escherichia coli (E. coli) / References: UniProt: P42262

-
Non-polymers , 6 types, 665 molecules

#2: Chemical ChemComp-ZK1 / {[7-morpholin-4-yl-2,3-dioxo-6-(trifluoromethyl)-3,4-dihydroquinoxalin-1(2H)-yl]methyl}phosphonic acid / [[3,4-Dihydro-7-(4-morpholinyl)-2,3-dioxo-6-(trifluorom ethyl)-1(2H)-quinoxalinyl]methyl]phosphonic acid


Mass: 409.254 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H15F3N3O6P / Comment: medication*YM
#3: Chemical ChemComp-9C0 / 9-(4-~{tert}-butylphenyl)-3,4-dihydropyrido[2,1-c][1,2,4]thiadiazine 2,2-dioxide


Mass: 316.418 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H20N2O2S
#4: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Zn
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 652 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.16 Å3/Da / Density % sol: 43.05 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 4.9
Details: 15% PEG 3350, 0.1 M SODIUM ACETATE, 0.1 M ZINC ACETATE

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.3 / Wavelength: 0.976486 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 27, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976486 Å / Relative weight: 1
ReflectionResolution: 1.25→50 Å / Num. obs: 128359 / % possible obs: 93.1 % / Redundancy: 3.3 % / Rsym value: 0.053 / Net I/σ(I): 19.5
Reflection shellResolution: 1.25→1.27 Å / Redundancy: 2.4 % / Mean I/σ(I) obs: 1.8 / Num. unique obs: 4044 / Rsym value: 0.517 / % possible all: 59

-
Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1FTJ

1ftj


Resolution: 1.25→40 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.956 / SU B: 1.461 / SU ML: 0.033 / Cross valid method: THROUGHOUT / ESU R: 0.048 / ESU R Free: 0.05
RfactorNum. reflection% reflectionSelection details
Rfree0.19034 6437 5 %RANDOM
Rwork0.16946 ---
obs0.17053 121789 93.02 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å
Displacement parametersBiso mean: 16.829 Å2
Baniso -1Baniso -2Baniso -3
1-0.26 Å20 Å20.26 Å2
2---0.34 Å2-0 Å2
3---0.06 Å2
Refinement stepCycle: 1 / Resolution: 1.25→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4058 0 105 652 4815
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0194319
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4992.0015829
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7535533
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.44524.226168
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.41715808
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.6421522
X-RAY DIFFRACTIONr_chiral_restr0.0950.2632
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.023146
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0091.0372094
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.541.5542615
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.0331.2982225
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined4.57416.0997010
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.251→1.283 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.25 274 -
Rwork0.269 5944 -
obs--61.29 %
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)
10.561-0.0256-0.0370.413-0.04010.3108-0.01530.01850.03750.0196-0.0131-0.0179-0.0248-0.02390.02840.01510.0037-0.00140.0039-0.00060.0078-9.20960.3373-22.471
20.3680.15860.01120.66-0.1210.27020.0244-0.0051-0.01240.0171-0.02710.04620.0304-0.01560.00260.0160.00220.00170.0061-0.00420.0099-10.1782-28.1446-24.0368
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A414 - 795
2X-RAY DIFFRACTION2B414 - 795

+
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