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- PDB-4u1y: Full length GluA2-FW-(R,R)-2b complex -

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Basic information

Entry
Database: PDB / ID: 4u1y
TitleFull length GluA2-FW-(R,R)-2b complex
ComponentsGlutamate receptor 2
KeywordsTransport protein / Membrane protein / AMPA receptor
Function / homology
Function and homology information


spine synapse / dendritic spine cytoplasm / dendritic spine neck / cellular response to amine stimulus / dendritic spine head / Activation of AMPA receptors / ligand-gated monoatomic cation channel activity / perisynaptic space / Trafficking of GluR2-containing AMPA receptors / AMPA glutamate receptor activity ...spine synapse / dendritic spine cytoplasm / dendritic spine neck / cellular response to amine stimulus / dendritic spine head / Activation of AMPA receptors / ligand-gated monoatomic cation channel activity / perisynaptic space / Trafficking of GluR2-containing AMPA receptors / AMPA glutamate receptor activity / response to lithium ion / AMPA glutamate receptor clustering / kainate selective glutamate receptor activity / immunoglobulin binding / asymmetric synapse / AMPA glutamate receptor complex / regulation of receptor recycling / extracellularly glutamate-gated ion channel activity / cellular response to glycine / ionotropic glutamate receptor complex / Unblocking of NMDA receptors, glutamate binding and activation / conditioned place preference / glutamate receptor binding / positive regulation of synaptic transmission / response to fungicide / regulation of synaptic transmission, glutamatergic / extracellular ligand-gated monoatomic ion channel activity / glutamate-gated receptor activity / cytoskeletal protein binding / cellular response to brain-derived neurotrophic factor stimulus / regulation of long-term synaptic depression / somatodendritic compartment / glutamate-gated calcium ion channel activity / presynaptic active zone membrane / excitatory synapse / ionotropic glutamate receptor binding / dendrite membrane / ionotropic glutamate receptor signaling pathway / dendrite cytoplasm / ligand-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / positive regulation of excitatory postsynaptic potential / dendritic shaft / synaptic membrane / SNARE binding / PDZ domain binding / synaptic transmission, glutamatergic / establishment of protein localization / protein tetramerization / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / cerebral cortex development / receptor internalization / postsynaptic density membrane / modulation of chemical synaptic transmission / Schaffer collateral - CA1 synapse / terminal bouton / synaptic vesicle / long-term synaptic potentiation / synaptic vesicle membrane / amyloid-beta binding / growth cone / presynapse / signaling receptor activity / presynaptic membrane / scaffold protein binding / dendritic spine / chemical synaptic transmission / perikaryon / postsynaptic membrane / neuron projection / postsynaptic density / external side of plasma membrane / axon / neuronal cell body / synapse / dendrite / protein kinase binding / protein-containing complex binding / glutamatergic synapse / cell surface / endoplasmic reticulum / protein-containing complex / membrane / identical protein binding / 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. / Periplasmic binding protein-like II ...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. / Periplasmic binding protein-like II / Receptor, ligand binding region / Receptor family ligand binding region / D-Maltodextrin-Binding Protein; domain 2 / Periplasmic binding protein-like I / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-FWD / Chem-FWF / Glutamate receptor 2
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3.8999 Å
AuthorsChen, 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 16, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 20, 2014Provider: repository / Type: Initial release
Revision 1.1Oct 1, 2014Group: Database references
Revision 1.2Apr 6, 2016Group: Source and taxonomy
Revision 1.3Nov 22, 2017Group: Derived calculations / Refinement description / Category: pdbx_struct_oper_list / software / Item: _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / 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 1.5Dec 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 1.6Nov 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
A: Glutamate receptor 2
B: Glutamate receptor 2
C: Glutamate receptor 2
D: Glutamate receptor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)370,55013
Polymers368,0574
Non-polymers2,4949
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area23990 Å2
ΔGint-155 kcal/mol
Surface area131290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.250, 151.440, 330.490
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 A and resid 8:383
21chain B and resid 8:383
31chain C and resid 8:383
41chain D and resid 8:383
12chain A and resid 393:505
22chain B and resid 393:505
32chain C and resid 393:505
42chain D and resid 393:505
13chain A and resid 635:769
23chain B and resid 635:769
33chain C and resid 635:769
43chain D and resid 635:769
14chain A and resid 514:544
24chain B and resid 514:544
34chain C and resid 514:544
44chain D and resid 514:544
15chain A and resid 597:622
25chain B and resid 597:622
35chain C and resid 597:622
45chain D and resid 597:622
16chain A and resid 790:816
26chain B and resid 790:816
36chain C and resid 790:816
46chain D and resid 790:816

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111chain A and resid 8:383A8 - 383
211chain B and resid 8:383B8 - 383
311chain C and resid 8:383C8 - 383
411chain D and resid 8:383D8 - 383
112chain A and resid 393:505A393 - 505
212chain B and resid 393:505B393 - 505
312chain C and resid 393:505C393 - 505
412chain D and resid 393:505D393 - 505
113chain A and resid 635:769A635 - 769
213chain B and resid 635:769B635 - 769
313chain C and resid 635:769C635 - 769
413chain D and resid 635:769D635 - 769
114chain A and resid 514:544A514 - 544
214chain B and resid 514:544B514 - 544
314chain C and resid 514:544C514 - 544
414chain D and resid 514:544D514 - 544
115chain A and resid 597:622A597 - 622
215chain B and resid 597:622B597 - 622
315chain C and resid 597:622C597 - 622
415chain D and resid 597:622D597 - 622
116chain A and resid 790:816A790 - 816
216chain B and resid 790:816B790 - 816
316chain C and resid 790:816C790 - 816
416chain D and resid 790:816D790 - 816

NCS ensembles :
ID
1
2
3
4
5
6

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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: 92014.125 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): Ric15 / Production host: Homo sapiens (human) / 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.: 3
Source method: isolated from a genetically manipulated source
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-FWD / 2-AMINO-3-(5-FLUORO-2,4-DIOXO-3,4-DIHYDRO-2H-PYRIMIDIN-1-YL)-PROPIONIC ACID / FLUORO-WILLARDIINE


Mass: 217.155 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C7H8FN3O4
#4: Chemical ChemComp-FWF / N,N'-[biphenyl-4,4'-diyldi(2R)propane-2,1-diyl]dipropane-2-sulfonamide


Mass: 480.684 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C24H36N2O4S2
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: 3.58 Å3/Da / Density % sol: 65.63 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / Details: 0.1 M imidazole pH 6.2, 9% PEG1450, 3% TMAO

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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: Jan 12, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.7→64.99 Å / Num. obs: 56784 / % possible obs: 99.1 % / Redundancy: 4.12 % / Biso Wilson estimate: 140.44 Å2 / Net I/σ(I): 6.93

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Processing

Software
NameVersionClassification
PHENIX1.8.2_1309refinement
XDSdata reduction
Aimlessdata scaling
PDB_EXTRACT3.14data extraction
XSCALEdata scaling
RefinementResolution: 3.8999→19.973 Å / FOM work R set: 0.7232 / SU ML: 0.64 / Cross valid method: FREE R-VALUE / σ(F): 1.99 / Phase error: 33.77 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3035 2275 5 %
Rwork0.2682 43245 -
obs0.27 45520 93.65 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 421.67 Å2 / Biso mean: 175.6 Å2 / Biso min: 61.5 Å2
Refinement stepCycle: final / Resolution: 3.8999→19.973 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms22093 0 124 0 22217
Biso mean--144.23 --
Num. residues----2911
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00522718
X-RAY DIFFRACTIONf_angle_d1.02130846
X-RAY DIFFRACTIONf_chiral_restr0.0413563
X-RAY DIFFRACTIONf_plane_restr0.0063874
X-RAY DIFFRACTIONf_dihedral_angle_d12.2787882
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A6407X-RAY DIFFRACTION11.227TORSIONAL
12B6407X-RAY DIFFRACTION11.227TORSIONAL
13C6407X-RAY DIFFRACTION11.227TORSIONAL
14D6407X-RAY DIFFRACTION11.227TORSIONAL
21A2078X-RAY DIFFRACTION11.227TORSIONAL
22B2078X-RAY DIFFRACTION11.227TORSIONAL
23C2078X-RAY DIFFRACTION11.227TORSIONAL
24D2078X-RAY DIFFRACTION11.227TORSIONAL
31A2486X-RAY DIFFRACTION11.227TORSIONAL
32B2486X-RAY DIFFRACTION11.227TORSIONAL
33C2486X-RAY DIFFRACTION11.227TORSIONAL
34D2486X-RAY DIFFRACTION11.227TORSIONAL
41A483X-RAY DIFFRACTION11.227TORSIONAL
42B483X-RAY DIFFRACTION11.227TORSIONAL
43C483X-RAY DIFFRACTION11.227TORSIONAL
44D483X-RAY DIFFRACTION11.227TORSIONAL
51A423X-RAY DIFFRACTION11.227TORSIONAL
52B423X-RAY DIFFRACTION11.227TORSIONAL
53C423X-RAY DIFFRACTION11.227TORSIONAL
54D423X-RAY DIFFRACTION11.227TORSIONAL
61A409X-RAY DIFFRACTION11.227TORSIONAL
62B409X-RAY DIFFRACTION11.227TORSIONAL
63C409X-RAY DIFFRACTION11.227TORSIONAL
64D409X-RAY DIFFRACTION11.227TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 16

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.8999-3.9840.3631610.35291318137946
3.984-4.07590.39111090.35021945205468
4.0759-4.1770.39271170.33452471258886
4.177-4.28880.36461510.3252811296299
4.2888-4.41370.33441450.319828372982100
4.4137-4.55450.41121570.31742839299699
4.5545-4.71530.34761510.294728583009100
4.7153-4.90140.28341560.263228382994100
4.9014-5.12090.33351630.26328643027100
5.1209-5.38590.36341480.261628653013100
5.3859-5.71590.31191410.265328693010100
5.7159-6.14530.32481600.272829133073100
6.1453-6.7420.29351580.256728703028100
6.742-7.66880.26631580.24429313089100
7.6688-9.48640.24841380.236529663104100
9.4864-19.97310.26521620.248230503212100
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)
13.37160.4303-0.77352.9-0.15714.0885-0.684-0.0191-0.5802-0.3498-0.2431-0.95290.13711.32781.04551.3788-0.40730.45821.21860.14011.527897.1306-11.341854.1828
23.9101-1.3772-0.0912.3999-0.78661.1830.4696-0.03250.44580.2253-0.2263-1.1881-0.59030.9733-0.03151.06710.32050.02221.5495-0.49191.585886.41842.3098104.936
30.75670.02340.69432.4971.40121.40520.60390.19540.40642.1796-0.4814-0.369-0.350.17810.40982.58890.00170.50021.1221-0.28492.606451.059616.8466154.6733
41.01410.87360.08362.1544-0.36452.32990.0423-0.3977-0.25360.76330.54690.2665-1.21940.5386-1.02411.6260.5269-0.00811.9216-0.20781.394661.257214.7413123.3025
51.18520.0051.38490.88640.65591.33780.4402-0.3112-0.8863-0.03590.3218-0.0089-1.0433-1.0956-1.31771.66990.19910.00181.37340.13451.408871.6184-2.0759124.7918
62.4864-1.89140.63443.24321.68042.8393-0.17080.43960.6122-0.82550.14950.1489-0.2433-0.4534-0.06120.9553-0.4677-0.05221.24290.24851.240180.270919.483145.6479
72.4647-0.1434-0.43623.0595-0.11292.6217-1.77420.97172.28371.1798-1.1064-2.5362-1.99221.4966-0.0076-0.06461.29222.3397-0.4113-1.2831-0.87943.400637.933992.3638
83.90591.10661.12420.86690.61240.425-0.7899-0.6055-0.533-0.9065-0.7286-0.03741.16280.46151.91890.86481.53591.36632.05621.03543.630624.712511.8728152.3529
90.71920.3747-0.02380.48760.97223.29630.0996-0.0326-0.37880.1073-0.3067-0.37140.8012-0.5419-0.50991.81180.4250.35241.22090.08441.504435.925631.2091123.9717
100.93681.33141.20510.8191-0.81562.84270.2575-0.0474-0.28350.57350.1328-0.03180.23090.2995-0.07381.4780.49590.26970.9056-0.13061.182338.424525.6441119.0066
113.0463-0.4987-0.05841.97691.2392.21880.8595-1.0731.5482-0.3551-0.1160.752-1.21441.0769-0.59251.7784-1.1020.50212.2973-0.44692.486814.754334.963147.0777
121.7065-0.31680.3842.883-0.03623.6842-0.0547-0.4625-0.39440.13230.01621.76821.6042-0.99860.10280.880.23540.42221.4683-0.02161.443613.437520.426993.4917
133.4593-0.2306-0.02880.81960.4170.21170.80131.91760.09120.28580.2232-0.5939-0.2788-0.2355-0.72913.3345-0.10430.28041.71050.17892.156331.1828-13.7954147.0925
14-0.26940.03160.04220.261-1.4691.2204-0.41720.013-0.53230.04330.1995-0.53340.83980.0869-0.50962.33880.40160.57081.11680.09721.870330.65311.6615114.9676
151.69460.4448-2.04480.5732-0.64791.64440.1441-0.95350.07150.7565-0.1323-0.8294-0.4373-0.0361-0.24131.5813-0.08170.06291.30480.04621.319620.269616.9204119.2691
162.5098-0.63280.79511.46230.14451.2326-0.0016-0.1183-1.1666-0.90440.2302-0.4857-0.0297-0.3417-0.33231.6721-0.88790.30912.58-0.26882.244431.4414.782939.4897
174.4911-1.10310.40383.5708-0.01553.7586-0.4712-0.3982-0.957-0.60960.40620.48980.2899-0.03050.06371.34780.13030.37360.66620.02970.872160.0528-12.321988.8329
180.7846-0.32340.86130.1855-0.37550.8529-0.28250.1346-1.1554-1.36420.80290.32421.29920.9353-0.05972.92842.57580.17063.0322-0.54941.215155.1012-8.4777147.6586
190.81422.00451.11481.99640.09244.178-0.0916-0.0995-0.88421.1609-0.1949-1.12331.8601-1.2295-0.91762.31140.71740.3291.50660.7872.528155.0706-15.8588119.1335
200.14140.2308-1.86890.352-0.24562.3656-0.982-0.46910.39430.74310.51240.47181.01240.60820.38762.33940.65970.63411.097-0.11591.478854.5675-9.0573116.1023
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 1:382)A1 - 382
2X-RAY DIFFRACTION2(chain A and resid 383:507)A383 - 507
3X-RAY DIFFRACTION3(chain A and resid 508:545)A508 - 545
4X-RAY DIFFRACTION4(chain A and resid 550:721)A550 - 721
5X-RAY DIFFRACTION5(chain A and resid 722:817)A722 - 817
6X-RAY DIFFRACTION6(chain B and resid 1:382)B1 - 382
7X-RAY DIFFRACTION7(chain B and resid 383:507)B383 - 507
8X-RAY DIFFRACTION8(chain B and resid 508:545)B508 - 545
9X-RAY DIFFRACTION9(chain B and resid 550:721)B550 - 721
10X-RAY DIFFRACTION10(chain B and resid 722:817)B722 - 817
11X-RAY DIFFRACTION11(chain C and resid 1:382)C1 - 382
12X-RAY DIFFRACTION12(chain C and resid 383:507)C383 - 507
13X-RAY DIFFRACTION13(chain C and resid 508:545)C508 - 545
14X-RAY DIFFRACTION14(chain C and resid 550:721)C550 - 721
15X-RAY DIFFRACTION15(chain C and resid 722:817)C722 - 817
16X-RAY DIFFRACTION16(chain D and resid 1:382)D1 - 382
17X-RAY DIFFRACTION17(chain D and resid 383:507)D383 - 507
18X-RAY DIFFRACTION18(chain D and resid 508:545)D508 - 545
19X-RAY DIFFRACTION19(chain D and resid 550:721)D550 - 721
20X-RAY DIFFRACTION20(chain D and resid 722:817)D722 - 817

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Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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