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- PDB-4u2p: Full-length AMPA subtype ionotropic glutamate receptor GluA2 in t... -

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Basic information

Entry
Database: PDB / ID: 4u2p
TitleFull-length AMPA subtype ionotropic glutamate receptor GluA2 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 / 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
Response regulator / 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 ...Response regulator / 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 / Rossmann fold / 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: 3.2386 Å
AuthorsDuerr, K.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 1.2Nov 22, 2017Group: Derived calculations / Other ...Derived calculations / Other / Refinement description / Source and taxonomy / Structure summary
Category: entity / entity_src_gen ...entity / entity_src_gen / pdbx_database_status / pdbx_struct_oper_list / software
Item: _entity.pdbx_description / _entity_src_gen.pdbx_alt_source_flag ..._entity.pdbx_description / _entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_oper_list.symmetry_operation / _software.classification
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations ...Data collection / Derived calculations / Refinement description / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / refine_hist / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Dec 27, 2023Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
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 2
B: Glutamate receptor 2
D: Glutamate receptor 2
C: Glutamate receptor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)371,21112
Polymers369,5464
Non-polymers1,6668
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area23590 Å2
ΔGint-149 kcal/mol
Surface area138230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)107.810, 149.130, 352.790
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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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: 92386.383 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Gria2, Glur2 / Cell line (production host): HEK293S / Production host: Homo sapiens (human) / Variant (production host): GnTI- / References: UniProt: P19491
#2: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Chemical
ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
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: 3.84 Å3/Da / Density % sol: 67.95 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop
Details: 0.1 M MES, 5.8-6.2% PEG6000, 5% TMAO, 0.1-0.3 M sodium acetate
PH range: pH 6.2-6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 2, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.2→49.002 Å / Num. obs: 65917 / % possible obs: 96.6 % / Redundancy: 3.4 % / Biso Wilson estimate: 107.69 Å2 / Net I/σ(I): 7.77

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.8.2_1309)refinement
XDSdata reduction
Aimless3.14data scaling
PDB_EXTRACTdata extraction
PHASERphasing
RefinementResolution: 3.2386→49.002 Å / SU ML: 0.57 / Cross valid method: FREE R-VALUE / σ(F): 1.49 / Phase error: 33.07 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2876 3377 5.12 %
Rwork0.2503 --
obs0.2522 65917 72.19 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.2386→49.002 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms22284 0 104 0 22388
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00422870
X-RAY DIFFRACTIONf_angle_d0.92731143
X-RAY DIFFRACTIONf_dihedral_angle_d10.7747785
X-RAY DIFFRACTIONf_chiral_restr0.0623583
X-RAY DIFFRACTIONf_plane_restr0.0033988
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2386-3.28480.511850.3919113X-RAY DIFFRACTION3
3.2848-3.33380.4463120.3846312X-RAY DIFFRACTION9
3.3338-3.38590.4116360.383536X-RAY DIFFRACTION15
3.3859-3.44140.3622400.3766827X-RAY DIFFRACTION23
3.4414-3.50070.3962720.36951285X-RAY DIFFRACTION36
3.5007-3.56440.3741890.35921603X-RAY DIFFRACTION45
3.5644-3.63290.3644920.36441866X-RAY DIFFRACTION52
3.6329-3.7070.40831240.3552121X-RAY DIFFRACTION60
3.707-3.78760.37931410.33882373X-RAY DIFFRACTION67
3.7876-3.87570.39861410.33622634X-RAY DIFFRACTION73
3.8757-3.97260.37751650.31082881X-RAY DIFFRACTION80
3.9726-4.07990.39421790.30393150X-RAY DIFFRACTION88
4.0799-4.19990.34741780.29713416X-RAY DIFFRACTION95
4.1999-4.33540.29561860.26923419X-RAY DIFFRACTION96
4.3354-4.49030.29212020.24933534X-RAY DIFFRACTION98
4.4903-4.66990.29582070.23613522X-RAY DIFFRACTION98
4.6699-4.88230.27231850.22533522X-RAY DIFFRACTION98
4.8823-5.13940.26741750.21273592X-RAY DIFFRACTION98
5.1394-5.4610.27061900.22113568X-RAY DIFFRACTION99
5.461-5.8820.26141980.23333580X-RAY DIFFRACTION99
5.882-6.47280.28811820.23823657X-RAY DIFFRACTION99
6.4728-7.40660.26861950.23043635X-RAY DIFFRACTION99
7.4066-9.32110.23561890.21563680X-RAY DIFFRACTION99
9.3211-49.00770.24191940.23053714X-RAY DIFFRACTION95
Refinement TLS params.Method: refined / Origin x: 0.7617 Å / Origin y: 158.9574 Å / Origin z: 90.585 Å
111213212223313233
T0.9633 Å20.1248 Å20.0661 Å2-0.6794 Å20.0414 Å2--1.1655 Å2
L0.8357 °20.2227 °2-0.142 °2-1.04 °20.1382 °2--0.2434 °2
S-0.2218 Å °-0.0754 Å °-0.2011 Å °-0.2756 Å °0.2128 Å °-0.254 Å °0.0735 Å °0.0276 Å °0.0024 Å °
Refinement TLS groupSelection details: all

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