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- PDB-3h5v: Crystal structure of the GluR2-ATD -

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Basic information

Entry
Database: PDB / ID: 3h5v
TitleCrystal structure of the GluR2-ATD
ComponentsGlutamate receptor 2
KeywordsTRANSPORT PROTEIN / Glutamate receptor / Ligand-gated ion channel / synapse / Cell junction / Cell membrane / Endoplasmic reticulum / Glycoprotein / Ion transport / Ionic channel / Lipoprotein / Membrane / Palmitate / Phosphoprotein / Postsynaptic cell membrane / Receptor / RNA editing / Transmembrane / Transport
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 / cellular response to glycine / AMPA glutamate receptor complex / 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 / cellular response to brain-derived neurotrophic factor stimulus / extracellular ligand-gated monoatomic ion channel activity / glutamate-gated calcium ion channel activity / presynaptic active zone membrane / 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 / signaling receptor activity / presynapse / amyloid-beta binding / growth cone / presynaptic membrane / scaffold protein binding / perikaryon / dendritic spine / chemical synaptic transmission / postsynaptic membrane / neuron projection / postsynaptic density / axon / external side of plasma membrane / neuronal cell body / synapse / dendrite / 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 I / 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 / SAD / Resolution: 2.33 Å
AuthorsJin, R. / Singh, S.K. / Gu, S. / Furukawa, H. / Sobolevsky, A. / Zhou, J. / Jin, Y. / Gouaux, E.
CitationJournal: Embo J. / Year: 2009
Title: Crystal structure and association behaviour of the GluR2 amino-terminal domain.
Authors: Jin, R. / Singh, S.K. / Gu, S. / Furukawa, H. / Sobolevsky, A.I. / Zhou, J. / Jin, Y. / Gouaux, E.
History
DepositionApr 22, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 9, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_special_symmetry / pdbx_unobs_or_zero_occ_atoms / struct_asym / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.auth_asym_id / _atom_site.auth_seq_id ..._atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_special_symmetry.label_asym_id / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 6, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_unobs_or_zero_occ_atoms
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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
C: Glutamate receptor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)134,3775
Polymers133,5283
Non-polymers8492
Water6,630368
1
A: Glutamate receptor 2
B: Glutamate receptor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,8674
Polymers89,0192
Non-polymers8492
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3840 Å2
ΔGint3 kcal/mol
Surface area32510 Å2
MethodPISA
2
C: Glutamate receptor 2

C: Glutamate receptor 2


Theoretical massNumber of molelcules
Total (without water)89,0192
Polymers89,0192
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
Buried area2730 Å2
ΔGint-16 kcal/mol
Surface area31860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.003, 362.993, 61.434
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11C-392-

HOH

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Components

#1: Protein Glutamate receptor 2 / GluR-2 / GluR-B / GluR-K2 / Glutamate receptor ionotropic / AMPA 2 / AMPA-selective glutamate receptor 2


Mass: 44509.250 Da / Num. of mol.: 3 / Fragment: UNP residues 21-404
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Gria2, Glur2 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P19491
#2: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 368 / 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: 2.67 Å3/Da / Density % sol: 53.97 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 14-16% PEG3350, 100mM TrisHCl, 10mM MgCl2, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jan 30, 2008
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.33→50 Å / Num. obs: 61441 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.3 % / Rmerge(I) obs: 0.061 / Net I/σ(I): 35.8
Reflection shellResolution: 2.33→2.41 Å / Redundancy: 7.4 % / Rmerge(I) obs: 0.605 / Mean I/σ(I) obs: 2.2 / % possible all: 99.9

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Processing

Software
NameVersionClassification
HKL-2000data collection
SOLVEphasing
PHENIX(phenix.refine)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.33→19.912 Å / SU ML: 0.34 / σ(F): 1.33 / Phase error: 23.2 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2355 5084 8.14 %
Rwork0.1859 --
obs0.1899 61441 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 72.811 Å2 / ksol: 0.316 e/Å3
Refinement stepCycle: LAST / Resolution: 2.33→19.912 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8968 0 56 368 9392
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0089213
X-RAY DIFFRACTIONf_angle_d1.08912459
X-RAY DIFFRACTIONf_dihedral_angle_d17.8723338
X-RAY DIFFRACTIONf_chiral_restr0.0741380
X-RAY DIFFRACTIONf_plane_restr0.0041603
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.33-2.35640.30661580.23611912X-RAY DIFFRACTION100
2.3564-2.38410.26631780.21291853X-RAY DIFFRACTION100
2.3841-2.41310.27821750.19231859X-RAY DIFFRACTION100
2.4131-2.44360.27181660.19591895X-RAY DIFFRACTION100
2.4436-2.47570.28321670.20091889X-RAY DIFFRACTION100
2.4757-2.50960.29071570.19211848X-RAY DIFFRACTION100
2.5096-2.54540.28871680.19341920X-RAY DIFFRACTION100
2.5454-2.58330.26971470.18291899X-RAY DIFFRACTION100
2.5833-2.62360.2431760.1811864X-RAY DIFFRACTION100
2.6236-2.66650.25481510.181953X-RAY DIFFRACTION100
2.6665-2.71230.24741760.18291835X-RAY DIFFRACTION100
2.7123-2.76150.23411660.17551903X-RAY DIFFRACTION100
2.7615-2.81450.25971690.19061889X-RAY DIFFRACTION100
2.8145-2.87180.26451730.18731876X-RAY DIFFRACTION100
2.8718-2.93410.25021620.18961922X-RAY DIFFRACTION100
2.9341-3.00210.25031700.18591872X-RAY DIFFRACTION100
3.0021-3.07690.25921680.18371953X-RAY DIFFRACTION100
3.0769-3.15980.29321910.19981843X-RAY DIFFRACTION100
3.1598-3.25240.25541740.21031922X-RAY DIFFRACTION100
3.2524-3.35690.21281610.19321898X-RAY DIFFRACTION100
3.3569-3.47620.25761720.19341907X-RAY DIFFRACTION100
3.4762-3.61460.24421750.18671926X-RAY DIFFRACTION100
3.6146-3.77810.23271610.18121923X-RAY DIFFRACTION100
3.7781-3.97580.24421800.17631910X-RAY DIFFRACTION100
3.9758-4.22270.21681720.15891940X-RAY DIFFRACTION100
4.2227-4.54510.16751620.1481938X-RAY DIFFRACTION100
4.5451-4.9960.18761680.14971965X-RAY DIFFRACTION100
4.996-5.7040.2231810.1781959X-RAY DIFFRACTION100
5.704-7.13110.22711780.19612008X-RAY DIFFRACTION100
7.1311-19.91320.21691820.18352085X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.7921-0.1356-0.72451.9607-0.36932.6411-0.05320.1327-0.05610.0677-0.0824-0.0925-0.1679-0.0940.10780.14820.0073-0.05910.27880.05390.23358.9746105.875130.5343
22.0305-0.0097-0.46780.7837-1.08433.52720.0717-0.13240.1250.35-0.5804-0.2202-0.77920.52930.37690.8137-0.0818-0.13940.44170.06910.348217.4609121.995550.3735
30.8817-0.0545-0.51782.0515-0.30372.136-0.12680.0703-0.07520.2169-0.010.3169-0.0615-0.48130.08750.15230.03950.02720.39850.01540.30651.0773102.711537.6585
41.0568-0.3979-0.46582.6815-0.14332.18450.01960.06340.0981-0.4979-0.1967-0.2453-0.20090.21970.0850.335-0.0420.06060.34270.14660.269230.225118.927613.1791
51.27840.2478-0.57790.2144-2.73612.5933-0.0142-0.12760.03740.08130.04710.004-1.19410.06740.0050.979-0.0251-0.0770.28780.0510.396316.9537135.586234.2973
61.7407-0.0777-0.28683.5269-0.47782.40230.0320.06180.3026-0.0912-0.1405-0.469-0.94390.30060.10260.5424-0.1729-0.10410.24130.10980.220727.6526134.94219.8315
71.8215-0.23421.34520.6919-0.6421.17160.72210.2232-0.93630.13690.3368-0.10461.27-0.0454-0.74621.83030.6389-0.6270.9956-0.20241.0584-12.5476159.5835-17.0472
81.9225-1.42771.20350.9931-1.59681.90090.34090.3305-0.2196-0.3301-0.1460.2956-0.49840.3621-0.15361.86130.5608-0.0130.4342-0.03330.4387-6.2346174.2626-1.4828
9-1.1481.07230.72043.6657-2.9449-4.1919-0.8305-0.0411-0.89981.5063-1.4946-0.8345-0.23691.50820.85091.48190.1867-0.11130.75910.31651.056813.3274166.065713.7522
102.0485-0.91041.4781.4777-0.98831.25090.1930.1074-0.6585-0.12990.23630.8911-0.3068-0.0299-0.36381.3240.39590.02920.50220.09040.8295-12.8041163.17030.4173
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(CHAIN A AND RESID 3:149)A3 - 149
2X-RAY DIFFRACTION2(CHAIN A AND RESID 150:208)A150 - 208
3X-RAY DIFFRACTION3(CHAIN A AND RESID 209:378)A209 - 378
4X-RAY DIFFRACTION4(CHAIN B AND RESID 3:109)B3 - 109
5X-RAY DIFFRACTION5(CHAIN B AND RESID 110:164)B110 - 164
6X-RAY DIFFRACTION6(CHAIN B AND RESID 165:378)B165 - 378
7X-RAY DIFFRACTION7(CHAIN C AND RESID 6:38)C6 - 38
8X-RAY DIFFRACTION8(CHAIN C AND RESID 39:164)C39 - 164
9X-RAY DIFFRACTION9(CHAIN C AND RESID 165:178)C165 - 178
10X-RAY DIFFRACTION10(CHAIN C AND RESID 179:378)C179 - 378

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