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- PDB-4u2r: Crystal structure of the GLUR2 ligand binding core (S1S2J, flip v... -

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Basic information

Entry
Database: PDB / ID: 4u2r
TitleCrystal structure of the GLUR2 ligand binding core (S1S2J, flip variant) in the apo state
ComponentsGlutamate receptor 2
KeywordsTransport protein / Membrane protein / AMPA receptor
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
Glutamate receptor 2
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.4114 Å
AuthorsDuerr, K.L. / Chen, L. / Gouaux, E.
CitationJournal: Cell / Year: 2014
Title: Structure and Dynamics of AMPA Receptor GluA2 in Resting, Pre-Open, and Desensitized States.
Authors: Durr, K.L. / Chen, L. / Stein, R.A. / De Zorzi, R. / Folea, I.M. / Walz, T. / Mchaourab, H.S. / Gouaux, E.
History
DepositionJul 17, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 20, 2014Provider: repository / Type: Initial release
Revision 1.1Oct 1, 2014Group: Database references
Revision 1.2Feb 4, 2015Group: Derived calculations
Revision 1.3Nov 22, 2017Group: Advisory / Derived calculations ...Advisory / Derived calculations / Other / Refinement description / Source and taxonomy
Category: entity_src_gen / pdbx_database_status ...entity_src_gen / pdbx_database_status / pdbx_struct_oper_list / pdbx_validate_symm_contact / software
Item: _entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible ..._entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_oper_list.symmetry_operation / _pdbx_validate_symm_contact.auth_asym_id_1 / _pdbx_validate_symm_contact.auth_asym_id_2 / _pdbx_validate_symm_contact.auth_atom_id_2 / _pdbx_validate_symm_contact.auth_comp_id_1 / _pdbx_validate_symm_contact.auth_comp_id_2 / _pdbx_validate_symm_contact.auth_seq_id_1 / _pdbx_validate_symm_contact.auth_seq_id_2 / _pdbx_validate_symm_contact.dist / _pdbx_validate_symm_contact.site_symmetry_2 / _software.classification
Revision 1.4Dec 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / refine_hist / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.pdbx_number_atoms_nucleic_acid / _refine_hist.pdbx_number_atoms_protein / _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 1.5Nov 6, 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
B: Glutamate receptor 2
A: Glutamate receptor 2
C: Glutamate receptor 2
D: Glutamate receptor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,9676
Polymers116,7754
Non-polymers1922
Water35,1651952
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5310 Å2
ΔGint-51 kcal/mol
Surface area49810 Å2
2
B: Glutamate receptor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,2902
Polymers29,1941
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
A: Glutamate receptor 2


Theoretical massNumber of molelcules
Total (without water)29,1941
Polymers29,1941
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
C: Glutamate receptor 2


Theoretical massNumber of molelcules
Total (without water)29,1941
Polymers29,1941
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
D: Glutamate receptor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,2902
Polymers29,1941
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)66.659, 91.936, 201.344
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain B
21chain A
31chain C
41chain D

NCS domain segments:

Component-ID: 1 / Ens-ID: 1

Dom-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1GLYGLYSERSERchain BBA1 - 2631 - 263
2ASNASNCYSCYSchain AAB3 - 2613 - 261
3ALAALACYSCYSchain CCC2 - 2612 - 261
4ASNASNSERSERchain DDD3 - 2633 - 263

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Components

#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: 29193.670 Da / Num. of mol.: 4 / Mutation: A796S,A796S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Gria2, Glur2 / Production host: Escherichia coli (E. coli) / References: UniProt: P19491
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1952 / 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: 2.64 Å3/Da / Density % sol: 53.44 %
Crystal growTemperature: 297 K / Method: vapor diffusion, hanging drop
Details: 17-20% PEG8000, 0.2M lithium sulfate, 0.1 M sodium acetate
PH range: 4.2-4.8

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 10, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.41→63.28 Å / Num. obs: 404918 / % possible obs: 97.3 % / Redundancy: 3.5 % / Net I/σ(I): 8.68

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Processing

Software
NameVersionClassification
XDSdata reduction
PDB_EXTRACT3.14data extraction
PHENIX(phenix.refine: 1.8.2_1309)refinement
PHASERphasing
Aimlessdata scaling
RefinementResolution: 1.4114→63.28 Å / FOM work R set: 0.7731 / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 0.8 / Phase error: 29.61 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2317 20269 5.01 %
Rwork0.2121 384648 -
obs0.2131 404917 88.1 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 66.56 Å2 / Biso mean: 25.96 Å2 / Biso min: 13.27 Å2
Refinement stepCycle: final / Resolution: 1.4114→63.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8069 0 10 1952 10031
Biso mean--32.54 34.38 -
Num. residues----1043
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0118229
X-RAY DIFFRACTIONf_angle_d1.21411081
X-RAY DIFFRACTIONf_chiral_restr0.0871233
X-RAY DIFFRACTIONf_plane_restr0.0051387
X-RAY DIFFRACTIONf_dihedral_angle_d12.2653068
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11B4980X-RAY DIFFRACTION7.527TORSIONAL
12A4980X-RAY DIFFRACTION7.527TORSIONAL
13C4980X-RAY DIFFRACTION7.527TORSIONAL
14D4980X-RAY DIFFRACTION7.527TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.4114-1.42740.5639280.52114404683
1.4274-1.44420.46411110.46751893200413
1.4442-1.46180.46852830.44855360564337
1.4618-1.48030.42794250.4268550897559
1.4803-1.49980.40215580.4122108811143975
1.4998-1.52030.37646710.3786130401371190
1.5203-1.54210.3967660.3694139321469896
1.5421-1.56510.38017580.3567142831504198
1.5651-1.58950.33978020.338144001520299
1.5895-1.61560.35716890.3329145331522299
1.6156-1.64350.337810.3252144061518799
1.6435-1.67340.32777660.31181445915225100
1.6734-1.70550.31797560.30781452315279100
1.7055-1.74040.30997620.3077144371519999
1.7404-1.77820.31967440.27691451915263100
1.7782-1.81960.28517540.25951449115245100
1.8196-1.86510.26647670.24751448715254100
1.8651-1.91550.26797110.2292145211523299
1.9155-1.97190.25367430.22251449115234100
1.9719-2.03550.24876930.2156145791527299
2.0355-2.10830.22987800.205144121519299
2.1083-2.19270.2177850.19331450815293100
2.1927-2.29250.22298040.1878144241522899
2.2925-2.41340.20997750.1864144451522099
2.4134-2.56460.23127760.1986143531512999
2.5646-2.76260.23167970.1904142361503398
2.7626-3.04060.20717100.1889142241493498
3.0406-3.48060.18168010.1684139421474396
3.4806-4.3850.17267110.1558139921470396
4.385-63.34480.17547620.1697138871464996

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