[English] 日本語
Yorodumi
- PDB-7f3o: Crystal structure of the GluA2o LBD in complex with glutamate and... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7f3o
TitleCrystal structure of the GluA2o LBD in complex with glutamate and TAK-653
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 / chemical synaptic transmission / dendritic spine / 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-0YK / ACETATE ION / GLUTAMIC ACID / Glutamate receptor 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.44 Å
AuthorsSogabe, S. / Igaki, S. / Hirokawa, A. / Zama, Y. / Lane, W. / Snell, G.
CitationJournal: Sci Rep / Year: 2021
Title: Strictly regulated agonist-dependent activation of AMPA-R is the key characteristic of TAK-653 for robust synaptic responses and cognitive improvement.
Authors: Suzuki, A. / Kunugi, A. / Tajima, Y. / Suzuki, N. / Suzuki, M. / Toyofuku, M. / Kuno, H. / Sogabe, S. / Kosugi, Y. / Awasaki, Y. / Kaku, T. / Kimura, H.
History
DepositionJun 16, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 28, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 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 1.2Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
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
E: Glutamate receptor 2
F: Glutamate receptor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)179,10531
Polymers176,0276
Non-polymers3,07825
Water24,0501335
1
A: Glutamate receptor 2
B: Glutamate receptor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,4096
Polymers58,6762
Non-polymers7334
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Glutamate receptor 2
D: Glutamate receptor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,03215
Polymers58,6762
Non-polymers1,35613
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
E: Glutamate receptor 2
F: Glutamate receptor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,66410
Polymers58,6762
Non-polymers9888
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)114.313, 163.508, 47.558
Angle α, β, γ (deg.)90.00, 89.99, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14A
24E
15A
25F
16B
26C
17B
27D
18B
28E
19B
29F
110C
210D
111C
211E
112C
212F
113D
213E
114D
214F
115E
215F

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11SERSERCYSCYSAA412 - 7942 - 261
21SERSERCYSCYSBB412 - 7942 - 261
12GLYGLYGLYGLYAA411 - 7951 - 262
22GLYGLYGLYGLYCC411 - 7951 - 262
13GLYGLYGLYGLYAA411 - 7951 - 262
23GLYGLYGLYGLYDD411 - 7951 - 262
14GLYGLYGLYGLYAA411 - 7951 - 262
24GLYGLYGLYGLYEE411 - 7951 - 262
15SERSERCYSCYSAA412 - 7942 - 261
25SERSERCYSCYSFF412 - 7942 - 261
16SERSERCYSCYSBB412 - 7942 - 261
26SERSERCYSCYSCC412 - 7942 - 261
17SERSERCYSCYSBB412 - 7942 - 261
27SERSERCYSCYSDD412 - 7942 - 261
18SERSERCYSCYSBB412 - 7942 - 261
28SERSERCYSCYSEE412 - 7942 - 261
19SERSERGLYGLYBB412 - 7952 - 262
29SERSERGLYGLYFF412 - 7952 - 262
110GLYGLYGLYGLYCC411 - 7951 - 262
210GLYGLYGLYGLYDD411 - 7951 - 262
111GLYGLYGLYGLYCC411 - 7951 - 262
211GLYGLYGLYGLYEE411 - 7951 - 262
112SERSERCYSCYSCC412 - 7942 - 261
212SERSERCYSCYSFF412 - 7942 - 261
113GLYGLYGLYGLYDD411 - 7951 - 262
213GLYGLYGLYGLYEE411 - 7951 - 262
114SERSERCYSCYSDD412 - 7942 - 261
214SERSERCYSCYSFF412 - 7942 - 261
115SERSERCYSCYSEE412 - 7942 - 261
215SERSERCYSCYSFF412 - 7942 - 261

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15

-
Components

-
Protein , 1 types, 6 molecules ABCDEF

#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: 29337.830 Da / Num. of mol.: 6 / Fragment: UNP residues 413-527, 653-796
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GRIA2, GLUR2 / Production host: Escherichia coli (E. coli) / References: UniProt: P42262

-
Non-polymers , 6 types, 1360 molecules

#2: Chemical
ChemComp-GLU / GLUTAMIC ACID


Type: L-peptide linking / Mass: 147.129 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C5H9NO4
#3: Chemical ChemComp-0YK / 7-(4-cyclohexyloxyphenyl)-9-methyl-4$l^{6}-thia-1$l^{4},5,8-triazabicyclo[4.4.0]deca-1(10),6,8-triene 4,4-dioxide


Mass: 373.469 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C19H23N3O3S / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 10 / Source method: isolated from a natural source / Formula: Zn
#5: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H3O2
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1335 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.53 Å3/Da / Density % sol: 51.46 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 4.9
Details: 15% PEG 3350, 0.1M SODIUM ACETATE, 0.1M ZINC ACETATE,

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.3 / Wavelength: 0.9765 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 7, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9765 Å / Relative weight: 1
ReflectionResolution: 1.44→50 Å / Num. obs: 304104 / % possible obs: 97.1 % / Redundancy: 4 % / Rsym value: 0.053 / Net I/σ(I): 21.2
Reflection shellResolution: 1.44→1.46 Å / Mean I/σ(I) obs: 1.6 / Num. unique obs: 14115 / Rsym value: 0.867 / % possible all: 91

-
Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1FTJ

1ftj


Resolution: 1.44→40 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.956 / SU B: 2.487 / SU ML: 0.049 / Cross valid method: THROUGHOUT / ESU R: 0.07 / ESU R Free: 0.07 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.21381 15331 5 %RANDOM
Rwork0.19386 ---
obs0.19486 288550 97.05 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.633 Å2
Baniso -1Baniso -2Baniso -3
1-0.53 Å2-0 Å2-0.03 Å2
2---0.26 Å2-0 Å2
3----0.27 Å2
Refinement stepCycle: 1 / Resolution: 1.44→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12274 0 176 1335 13785
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.01212880
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.8151.65617353
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.23451622
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.45222.633581
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.492152460
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.3131567
X-RAY DIFFRACTIONr_chiral_restr0.1120.21663
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.029489
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_it1.7781.1986354
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.4551.7957931
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.2041.5366526
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined6.26917.9520097
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A83690.09
12B83690.09
21A83050.1
22C83050.1
31A83090.1
32D83090.1
41A85990.06
42E85990.06
51A83570.1
52F83570.1
61B82850.09
62C82850.09
71B82910.09
72D82910.09
81B83020.09
82E83020.09
91B84790.07
92F84790.07
101C86810.06
102D86810.06
111C83420.1
112E83420.1
121C83940.09
122F83940.09
131D83790.1
132E83790.1
141D84220.09
142F84220.09
151E83880.09
152F83880.09
LS refinement shellResolution: 1.441→1.478 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.324 1033 -
Rwork0.295 20157 -
obs--92.01 %
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)
10.96850.2037-0.11190.49120.04940.67650.0040.0666-0.0265-0.0544-0.0056-0.01880.0523-0.01990.00160.08670.0326-0.00830.0663-0.0060.081232.982-55.53818.145
20.4575-0.3636-0.00210.74450.00360.6907-0.0110.00250.0004-0.0372-0.0103-0.00120.0005-0.00110.02130.0064-0.0090.00170.0694-00.017628.5860.02928.553
30.95840.20490.11930.4845-0.04360.69150.00510.0670.0271-0.0612-0.00540.0233-0.05250.0120.00030.08870.03180.01460.06710.00880.086424.18355.5918.156
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A411 - 795
2X-RAY DIFFRACTION1A801
3X-RAY DIFFRACTION1B412 - 795
4X-RAY DIFFRACTION1B801
5X-RAY DIFFRACTION2C411 - 795
6X-RAY DIFFRACTION2C802
7X-RAY DIFFRACTION2D411 - 795
8X-RAY DIFFRACTION2D801
9X-RAY DIFFRACTION3E411 - 795
10X-RAY DIFFRACTION3E801
11X-RAY DIFFRACTION3F412 - 795
12X-RAY DIFFRACTION3F801

+
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