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- PDB-1mqd: X-ray structure of the GluR2 ligand-binding core (S1S2J) in compl... -

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Basic information

Entry
Database: PDB / ID: 1mqd
TitleX-ray structure of the GluR2 ligand-binding core (S1S2J) in complex with (S)-Des-Me-AMPA at 1.46 A resolution. Crystallization in the presence of lithium sulfate.
ComponentsGlutamate receptor subunit 2
KeywordsMEMBRANE PROTEIN / Ionotropic glutamate receptor GluR2 / ligand-binding core / agonist complex.
Function / homology
Function and homology information


spine synapse / dendritic spine neck / dendritic spine head / Activation of AMPA receptors / perisynaptic space / AMPA glutamate receptor activity / ligand-gated monoatomic cation channel activity / Trafficking of GluR2-containing AMPA receptors / response to lithium ion / immunoglobulin binding ...spine synapse / dendritic spine neck / dendritic spine head / Activation of AMPA receptors / perisynaptic space / AMPA glutamate receptor activity / ligand-gated monoatomic cation channel 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 / cellular response to glycine / extracellularly glutamate-gated ion channel activity / asymmetric synapse / regulation of receptor recycling / Unblocking of NMDA receptors, glutamate binding and activation / positive regulation of synaptic transmission / glutamate receptor binding / glutamate-gated receptor activity / regulation of synaptic transmission, glutamatergic / response to fungicide / cytoskeletal protein binding / ionotropic glutamate receptor binding / presynaptic active zone membrane / extracellular ligand-gated monoatomic ion channel activity / somatodendritic compartment / glutamate-gated calcium ion channel activity / cellular response to brain-derived neurotrophic factor stimulus / ligand-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / dendrite membrane / dendrite cytoplasm / ionotropic glutamate receptor signaling pathway / SNARE binding / dendritic shaft / 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 / synaptic membrane / modulation of chemical synaptic transmission / postsynaptic density membrane / terminal bouton / Schaffer collateral - CA1 synapse / cerebral cortex development / receptor internalization / synaptic vesicle membrane / synaptic vesicle / presynapse / signaling receptor activity / amyloid-beta binding / presynaptic membrane / growth cone / scaffold protein binding / chemical synaptic transmission / dendritic spine / perikaryon / postsynaptic membrane / neuron projection / postsynaptic density / axon / neuronal cell body / synapse / dendrite / protein-containing complex binding / protein kinase binding / glutamatergic synapse / cell surface / endoplasmic reticulum / protein-containing complex / identical protein binding / membrane / 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-SHI / Glutamate receptor 2
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.46 Å
AuthorsKasper, C. / Lunn, M.-L. / Liljefors, T. / Gouaux, E. / Egebjerg, J. / Kastrup, J.S.
Citation
Journal: FEBS Lett. / Year: 2002
Title: GluR2 ligand-binding core complexes: Importance of the isoxazolol moiety and 5-substituent for the binding mode of AMPA-type agonists.
Authors: Kasper, C. / Lunn, M.L. / Liljefors, T. / Gouaux, E. / Egebjerg, J. / Kastrup, J.S.
#1: Journal: J.Mol.Biol. / Year: 2002
Title: Structural basis for AMPA receptor activation and ligand selectivity: Crystal structures of five agonist complexes with the GluR2 ligand binding core.
Authors: Hogner, A. / Kastrup, J. / Jin, R. / Liljefors, T. / Mayer, M. / Egebjerg, J. / Larsen, I. / Gouaux, E.
#2: Journal: Neuron / Year: 2000
Title: Mechanisms for activation and antagonism of an AMPA-sensitive glutamate receptor: Crystal structures of the GluR2 ligand binding core.
Authors: Armstrong, N. / Gouaux, E.
#3: Journal: Nature / Year: 2002
Title: Mechanism of glutamate receptor desensitization.
Authors: Sun, Y. / Olson, R. / Horning, M. / Armstrong, N. / Mayer, M. / Gouaux, E.
#4: Journal: Protein Sci. / Year: 1998
Title: Probing the ligand binding domain of the GluR2 receptor by proteolysis and deletion mutagenesis defines domain boundaries and yields a crystallizable construct.
Authors: Chen, G.Q. / Sun, Y. / Jin, R. / Gouaux, E.
History
DepositionSep 16, 2002Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 1, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Aug 23, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 1.4Oct 25, 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 / diffrn_source / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glutamate receptor subunit 2
B: Glutamate receptor subunit 2
C: Glutamate receptor subunit 2
D: Glutamate receptor subunit 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)117,37912
Polymers116,3104
Non-polymers1,0698
Water47,3072626
1
A: Glutamate receptor subunit 2
hetero molecules

A: Glutamate receptor subunit 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,8768
Polymers58,1552
Non-polymers7216
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_756-x+2,y,-z+11
2
B: Glutamate receptor subunit 2
hetero molecules

B: Glutamate receptor subunit 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,6926
Polymers58,1552
Non-polymers5364
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
3
C: Glutamate receptor subunit 2
hetero molecules

C: Glutamate receptor subunit 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,4994
Polymers58,1552
Non-polymers3442
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
4
D: Glutamate receptor subunit 2
hetero molecules

D: Glutamate receptor subunit 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,6926
Polymers58,1552
Non-polymers5364
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,y,-z1
Unit cell
Length a, b, c (Å)105.445, 47.505, 123.920
Angle α, β, γ (deg.)90.00, 113.70, 90.00
Int Tables number3
Space group name H-MP121
Components on special symmetry positions
IDModelComponents
11B-4442-

HOH

21C-3641-

HOH

31D-4660-

HOH

DetailsThe biological assembly is a dimer. The dimer of chain A can be generated by -x, y, -z, shift 1 0 0. The dimer of chain B can be generated by -x, y, -z, shift 0 0 0. The dimer of chain C can be generated by -x, y, -z, shift -1 0 -1. The dimer of chain D can be generated by -x, y, -z, shift 0 0 -1.

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Components

#1: Protein
Glutamate receptor subunit 2 / GluR-2


Mass: 29077.553 Da / Num. of mol.: 4 / Fragment: GluR2-flop ligand-binding core (S1S2J)
Source method: isolated from a genetically manipulated source
Details: Tetherd dimer linked by GLY 115 and THR 116 / Source: (gene. exp.) Rattus norvegicus (Norway rat) / Plasmid: pET30B / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P19491
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-SHI / (S)-2-AMINO-3-(3-HYDROXY-ISOXAZOL-4-YL)PROPIONIC ACID / (S)-DES-ME-AMPA


Mass: 172.139 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H8N2O4
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2626 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.44 Å3/Da / Density % sol: 49.65 %
Crystal growTemperature: 279 K / Method: vapor diffusion, hanging drop / pH: 5.2
Details: 20% PEG 8000, 0.1M lithium sulfate, 0.1M cacodylate, pH 5.2, VAPOR DIFFUSION, HANGING DROP, temperature 279K
Crystal grow
*PLUS
Temperature: 6 ℃ / pH: 7.4 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
18 mg/mlprotein1drop
23 mM(S)-Des-Me-AMPA1drop
310 mMHEPES1droppH7.4
420 mM1dropNaCl
51 mMEDTA1drop
60.1 M1reservoirLi2SO4
720 %PEG80001reservoir
80.1 Mcacodylate1reservoirpH5.2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.8499 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Aug 15, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8499 Å / Relative weight: 1
ReflectionResolution: 1.46→20 Å / Num. all: 191888 / Num. obs: 191888 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.9 % / Biso Wilson estimate: 14.9 Å2 / Rmerge(I) obs: 0.042 / Net I/σ(I): 26.7
Reflection shellResolution: 1.46→1.49 Å / Rmerge(I) obs: 0.384 / Mean I/σ(I) obs: 2.4 / Num. unique all: 12223 / % possible all: 95.5
Reflection
*PLUS
Lowest resolution: 20 Å
Reflection shell
*PLUS
% possible obs: 95.5 %

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNS1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1M5B

1m5b


Resolution: 1.46→19.24 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 1705947 / Data cutoff high rms absF: 1705947 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
Details: The first three N-terminal residues and the last two C-terminal residues were not located in the electron density map. The side chains of the following residues are not fully defined: Lys ...Details: The first three N-terminal residues and the last two C-terminal residues were not located in the electron density map. The side chains of the following residues are not fully defined: Lys A1, Lys A18, Lys A66, Lys A104, Lys A126, Glu A129, Glu A142, Arg A146, Lys A180, Lys A246, Lys B1, Lys B18, Glu B21, Glu B24, Ala B63, Asp B64, Lys B66, Glu B119, Lys B126, Glu B142, Lys B255, Lys C1, Lys C47, Arg C61, Asp C64, Lys C66, Lys C126, Glu C129, Glu C142, Arg C146, Lys C148, Arg C180, Lys C246, Lys C255, Lys D1, Lys D18, Met D22, Lys D47, Lys D49, Ala D63, Lys D66, Lys D126, Glu D142
RfactorNum. reflection% reflectionSelection details
Rfree0.192 3852 2 %RANDOM
Rwork0.18 ---
all-191888 --
obs-191888 98.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 52.86 Å2 / ksol: 0.34 e/Å3
Displacement parametersBiso mean: 21.2 Å2
Baniso -1Baniso -2Baniso -3
1-1.75 Å2-1.69 Å2-0.07 Å2
2--0 Å21.38 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.17 Å0.15 Å
Luzzati d res low-5 Å
Luzzati sigma a0.17 Å0.16 Å
Refinement stepCycle: LAST / Resolution: 1.46→19.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8076 0 69 2626 10771
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d22.4
X-RAY DIFFRACTIONo_improper_angle_d0.82
LS refinement shellResolution: 1.46→1.55 Å / Rfactor Rfree error: 0.011 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.269 609 2.1 %
Rwork0.262 28754 -
obs-29363 90.7 %
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2water_rep.param
X-RAY DIFFRACTION3DAM_GOL_SO4.param
X-RAY DIFFRACTION4ion.param
Refinement
*PLUS
Lowest resolution: 20 Å / % reflection Rfree: 2 % / Rfactor Rwork: 0.18
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.4
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.82

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