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- PDB-3h03: Crystal structure of the binding domain of the AMPA subunit GluR2... -

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Basic information

Entry
Database: PDB / ID: 3h03
TitleCrystal structure of the binding domain of the AMPA subunit GluR2 bound to UBP277
ComponentsGlutamate receptor 2
KeywordsMEMBRANE PROTEIN / glutamate receptor / glur2 / AMPA receptor / neurotransmitter receptor / S1S2
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 / extracellularly glutamate-gated ion channel activity ...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 / extracellularly glutamate-gated ion channel activity / immunoglobulin binding / AMPA glutamate receptor complex / kainate selective glutamate receptor activity / ionotropic glutamate receptor complex / cellular response to glycine / asymmetric synapse / regulation of receptor recycling / Unblocking of NMDA receptors, glutamate binding and activation / glutamate receptor binding / positive regulation of synaptic transmission / extracellular ligand-gated monoatomic ion channel activity / glutamate-gated receptor activity / response to fungicide / glutamate-gated calcium ion channel activity / presynaptic active zone membrane / regulation of synaptic transmission, glutamatergic / ionotropic glutamate receptor binding / somatodendritic compartment / dendrite membrane / cellular response to brain-derived neurotrophic factor stimulus / ligand-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / cytoskeletal protein binding / dendrite cytoplasm / ionotropic glutamate receptor signaling pathway / SNARE binding / dendritic shaft / synaptic transmission, glutamatergic / synaptic membrane / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / PDZ domain binding / protein tetramerization / postsynaptic density membrane / establishment of protein localization / modulation of chemical synaptic transmission / Schaffer collateral - CA1 synapse / terminal bouton / receptor internalization / cerebral cortex development / synaptic vesicle membrane / synaptic vesicle / presynapse / signaling receptor activity / presynaptic membrane / amyloid-beta binding / growth cone / scaffold protein binding / chemical synaptic transmission / perikaryon / postsynaptic membrane / dendritic spine / postsynaptic density / neuron projection / axon / neuronal cell body / glutamatergic synapse / dendrite / synapse / protein-containing complex binding / protein kinase binding / 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-UBP / Glutamate receptor 2
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsAhmed, A.H. / Oswald, R.E.
CitationJournal: Biochemistry / Year: 2009
Title: Mechanisms of antagonism of the GluR2 AMPA receptor: structure and dynamics of the complex of two willardiine antagonists with the glutamate binding domain.
Authors: Ahmed, A.H. / Thompson, M.D. / Fenwick, M.K. / Romero, B. / Loh, A.P. / Jane, D.E. / Sondermann, H. / Oswald, R.E.
History
DepositionApr 8, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 5, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 23, 2017Group: Data collection / Source and taxonomy / Category: diffrn_detector / entity_src_gen / Item: _diffrn_detector.detector
Revision 1.3Jun 27, 2018Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Source and taxonomy / Structure summary
Category: entity_name_com / entity_src_gen ...entity_name_com / entity_src_gen / pdbx_struct_assembly / pdbx_struct_assembly_gen / struct_ref / struct_ref_seq_dif
Item: _entity_name_com.name / _entity_src_gen.gene_src_common_name ..._entity_name_com.name / _entity_src_gen.gene_src_common_name / _entity_src_gen.pdbx_gene_src_gene / _entity_src_gen.pdbx_seq_type / _struct_ref.pdbx_db_isoform
Revision 1.4Sep 6, 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 / 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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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_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_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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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
D: Glutamate receptor 2
G: Glutamate receptor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,94916
Polymers115,3414
Non-polymers1,60812
Water11,602644
1
A: Glutamate receptor 2
hetero molecules

B: Glutamate receptor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,4758
Polymers57,6712
Non-polymers8046
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_545x,y-1,z1
Buried area1130 Å2
ΔGint-124 kcal/mol
Surface area25000 Å2
MethodPISA
2
D: Glutamate receptor 2
G: Glutamate receptor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,4758
Polymers57,6712
Non-polymers8046
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1300 Å2
ΔGint-133 kcal/mol
Surface area24730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.953, 57.719, 105.461
Angle α, β, γ (deg.)90.00, 114.88, 90.00
Int Tables number4
Space group name H-MP1211

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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: 28835.320 Da / Num. of mol.: 4 / Fragment: UNP residues 414-527, 652-794
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Gria2, Glur2 / Plasmid: pET-22b(+) / Production host: Escherichia coli (E. coli) / Strain (production host): Origami B (DE3) / References: UniProt: P19491
#2: Chemical
ChemComp-UBP / 3-[3-(2-carboxyethyl)-2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl]-L-alanine / (S)-1-(2-amino-2-carboxyethyl)-3-(2-carboxyethyl)pyrimidine-2,4-dione


Mass: 271.227 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H13N3O6
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 644 / Source method: isolated from a natural source / Formula: H2O

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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: 2.37 Å3/Da / Density % sol: 48.07 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 14-16% PEG8K, 0.1-0.15 M Zn acetate, 0.25 M ammonium sulfate, 0.1 M Na cacodylate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.977 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 21, 2007
RadiationMonochromator: Rh coated Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.977 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 56999 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.7 % / Rmerge(I) obs: 0.22 / Rsym value: 0.22 / Net I/σ(I): 12.48
Reflection shellResolution: 1.9→1.93 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.22 / Mean I/σ(I) obs: 2.307 / Num. unique all: 4154 / Rsym value: 0.22 / % possible all: 99.1

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Processing

Software
NameClassification
HKL-2000data collection
PHENIXmodel building
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1FTL

1ftl


Resolution: 1.9→28.1 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2584 5981 -random
Rwork0.2208 ---
all-85484 --
obs-56999 69 %-
Displacement parametersBiso mean: 12.3 Å2
Baniso -1Baniso -2Baniso -3
1--0.14 Å21.22 Å2-1.08 Å2
2--0 Å2-0.42 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.29 Å0.244 Å
Luzzati sigma a0.2 Å0.1733 Å
Refinement stepCycle: LAST / Resolution: 1.9→28.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8040 0 84 644 8768
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.2
LS refinement shellResolution: 1.9→2.02 Å / Rfactor Rfree error: 0.01
RfactorNum. reflection% reflection
Rfree0.311 931 -
Rwork0.26 --
obs-8037 63.5 %

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