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- PDB-1m5b: X-RAY STRUCTURE OF THE GLUR2 LIGAND BINDING CORE (S1S2J) IN COMPL... -

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Basic information

Entry
Database: PDB / ID: 1m5b
TitleX-RAY STRUCTURE OF THE GLUR2 LIGAND BINDING CORE (S1S2J) IN COMPLEX WITH 2-Me-Tet-AMPA AT 1.85 A RESOLUTION.
ComponentsGlutamate receptor 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 / 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 / presynaptic active zone membrane / glutamate-gated calcium ion channel activity / 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 / dendrite / synapse / 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
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-BN1 / Glutamate receptor 2
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / Difference Fourier. / Resolution: 1.85 Å
AuthorsHogner, A. / Kastrup, J.S. / Jin, R. / Liljefors, T. / Mayer, M.L. / Egebjerg, J. / Larsen, I.K. / Gouaux, E.
Citation
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.S. / Jin, R. / Liljefors, T. / Mayer, M.L. / Egebjerg, J. / Larsen, I.K. / Gouaux, E.
#1: 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.
#2: Journal: Nature / Year: 2002
Title: Mechanism of glutamate receptor desensitization.
Authors: Sun, Y. / Olson, R. / Horning, M. / Armstrong, N. / Mayer, M. / Gouaux, E.
#3: 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, R. / Jin, R. / Gouaux, E.
History
DepositionJul 9, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 18, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Aug 16, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 1.4Nov 13, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_initial_refinement_model / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn / 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 / _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.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _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.ptnr3_symmetry / _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.ptnr1_symmetry / _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_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 999Sequence Native GluR2 is a membrane protein. The protein crystallized is the extracellular ligand ...Sequence Native GluR2 is a membrane protein. The protein crystallized is the extracellular ligand binding domain of GluR2. Transmembrane regions were genetically removed and replaced with a GLY-THR linker (residues 118 and 119). Therefore, the sequence matches discontinuously with the reference database (413-527, 653-796). Residues GLY1 and ALA2 are cloning artifacts.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)88,75511
Polymers87,6653
Non-polymers1,0908
Water20,8971160
1
A: Glutamate receptor 2
C: Glutamate receptor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,1487
Polymers58,4432
Non-polymers7055
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: Glutamate receptor 2
hetero molecules

B: Glutamate receptor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,2138
Polymers58,4432
Non-polymers7706
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
Buried area3060 Å2
ΔGint-95 kcal/mol
Surface area23630 Å2
MethodPISA, PQS
3
C: Glutamate receptor 2
hetero molecules

A: Glutamate receptor 2
B: Glutamate receptor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,75511
Polymers87,6653
Non-polymers1,0908
Water543
TypeNameSymmetry operationNumber
crystal symmetry operation4_557x+1/2,-y+1/2,-z+21
identity operation1_555x,y,z1
Buried area3890 Å2
ΔGint-161 kcal/mol
Surface area35830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)114.410, 164.330, 47.310
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
DetailsThe biological assembly is a dimer. Chain A and chain C of the asymmetric unit form a non-crystallographic dimer. The dimer of chain B can be generated by the two fold axis: -x, -y, z.

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Components

#1: Protein Glutamate receptor 2 / GLUR-2 / GLUR-B / GLUR-K2 / GLUTAMATE RECEPTOR IONOTROPIC AMPA 2


Mass: 29221.682 Da / Num. of mol.: 3 / Fragment: flop ligand binding core (S1S2J)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: GluR-2 / 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-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-BN1 / (S)-2-AMINO-3-[3-HYDROXY-5-(2-METHYL-2H-TETRAZOL-5-YL)ISOXAZOL-4-YL]PROPIONIC ACID / 2-ME-TET-AMPA


Mass: 254.203 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C8H10N6O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1160 / 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: 2.54 Å3/Da / Density % sol: 0.515 %
Crystal growTemperature: 279 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: PEG 8000, Zn(OAc)2, cacodylate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 279K
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 7
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
110 mg/mlprotein1drop
210 mMHEPES1droppH7.0
320 mM1dropNaCl
41 mMEDTA1drop
53 mM(S)-2-Me-Tet-AMPA1drop
612-18 %(w/v)PEG80001reservoir
70.15-0.28 Mzinc acetate1reservoir
80.1 Msodium cacodylate1reservoirpH6.5

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Mar 31, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.85→20 Å / Num. all: 76427 / Num. obs: 76427 / % possible obs: 99 % / Observed criterion σ(I): -3 / Redundancy: 6.3 % / Biso Wilson estimate: 21.5 Å2 / Rmerge(I) obs: 0.063 / Net I/σ(I): 19
Reflection shellResolution: 1.85→1.97 Å / Rmerge(I) obs: 0.284 / Mean I/σ(I) obs: 2.4 / % possible all: 91.4
Reflection
*PLUS
Lowest resolution: 20 Å / Redundancy: 4.4 %
Reflection shell
*PLUS
% possible obs: 91.4 %

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
CNS0.5refinement
CNS0.5phasing
RefinementMethod to determine structure: Difference Fourier.
Starting model: PDB entry 1FTM(S1S2J-AMPA, molecule A).

1ftm


Resolution: 1.85→20 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 2171714 / Data cutoff high rms absF: 2171714 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: Residues 1-3 and 262-263 were not located in the electron density map. The side chains of the following residues are not fully defined: LYS A21, GLU A24, GLU A122, ARG A172, LYS B183, LYS ...Details: Residues 1-3 and 262-263 were not located in the electron density map. The side chains of the following residues are not fully defined: LYS A21, GLU A24, GLU A122, ARG A172, LYS B183, LYS C21, MET C25, GLU C27, ARG C163, LYS C204
RfactorNum. reflection% reflectionSelection details
Rfree0.234 7648 0.1 %Random.
Rwork0.196 ---
all-76361 --
obs-76361 98.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 42.9979 Å2 / ksol: 0.349853 e/Å3
Displacement parametersBiso mean: 22.9 Å2
Baniso -1Baniso -2Baniso -3
1-0.48 Å20.93 Å2-1.41 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.25 Å0.2 Å
Luzzati d res low-5 Å
Luzzati sigma a0.17 Å0.15 Å
Refinement stepCycle: LAST / Resolution: 1.85→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6054 0 59 1160 7273
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_dihedral_angle_d21.6
X-RAY DIFFRACTIONc_improper_angle_d0.74
X-RAY DIFFRACTIONc_mcbond_it0.841.5
X-RAY DIFFRACTIONc_mcangle_it1.392
X-RAY DIFFRACTIONc_scbond_it1.32
X-RAY DIFFRACTIONc_scangle_it2.042.5
LS refinement shellResolution: 1.85→1.97 Å / Rfactor Rfree error: 0.009 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.31 1249 0.104 %
Rwork0.265 10777 -
obs-12026 94.7 %
Xplor fileSerial no: 1 / Param file: PROTEIN_REP.PARAM / Topol file: PROTEIN.TOP
Refinement
*PLUS
Lowest resolution: 20 Å / % reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg21.6
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.74

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