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- PDB-4u5d: Crystal structure of GluA2, con-ikot-ikot snail toxin, partial ag... -

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Basic information

Entry
Database: PDB / ID: 4u5d
TitleCrystal structure of GluA2, con-ikot-ikot snail toxin, partial agonist KA and postitive modulator (R,R)-2b complex
Components
  • Con-ikot-ikot
  • Glutamate receptor 2
KeywordsTransport protein/toxin / AMPA receptor / Transport protein-toxin complex
Function / homology
Function and homology information


host cell postsynaptic membrane / ion channel regulator activity / 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 ...host cell postsynaptic membrane / ion channel regulator activity / 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 / 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 / presynapse / signaling receptor activity / amyloid-beta binding / toxin activity / 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 / synapse / dendrite / protein kinase binding / protein-containing complex binding / glutamatergic synapse / cell surface / endoplasmic reticulum / protein-containing complex / extracellular region / identical protein binding / membrane / plasma membrane
Similarity search - Function
Four Helix Bundle (Hemerythrin (Met), subunit A) - #1800 / 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 ...Four Helix Bundle (Hemerythrin (Met), subunit A) - #1800 / 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 / Four Helix Bundle (Hemerythrin (Met), subunit A) / Periplasmic binding protein-like I / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-FWF / 3-(CARBOXYMETHYL)-4-ISOPROPENYLPROLINE / Con-ikot-ikot / Glutamate receptor 2
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
Conus striatus (striated cone)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3.5757 Å
AuthorsChen, L. / Gouaux, E.
CitationJournal: Science / Year: 2014
Title: X-ray structures of AMPA receptor-cone snail toxin complexes illuminate activation mechanism.
Authors: Chen, L. / Durr, K.L. / Gouaux, E.
History
DepositionJul 25, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 13, 2014Provider: repository / Type: Initial release
Revision 1.1Aug 27, 2014Group: Database references
Revision 1.2Oct 1, 2014Group: Database references
Revision 1.3Nov 22, 2017Group: Database references / Derived calculations ...Database references / Derived calculations / Other / Refinement description / Source and taxonomy / Structure summary
Category: citation / entity ...citation / entity / entity_src_gen / pdbx_database_status / pdbx_struct_oper_list / software
Item: _citation.journal_id_CSD / _entity.pdbx_description ..._citation.journal_id_CSD / _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 1.4Jul 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 1.5Dec 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 1.6Oct 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
C: Glutamate receptor 2
D: Glutamate receptor 2
E: Con-ikot-ikot
F: Con-ikot-ikot
hetero molecules


Theoretical massNumber of molelcules
Total (without water)387,74716
Polymers385,0486
Non-polymers2,69910
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area27180 Å2
ΔGint-201 kcal/mol
Surface area140370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)161.510, 367.580, 109.380
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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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: 91385.320 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 GNTI- / Production host: Homo sapiens (human) / References: UniProt: P19491
#2: Protein Con-ikot-ikot


Mass: 9753.155 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Conus striatus (striated cone) / Production host: Escherichia coli (E. coli) / References: UniProt: P0CB20
#3: Chemical
ChemComp-KAI / 3-(CARBOXYMETHYL)-4-ISOPROPENYLPROLINE / KAINATE


Mass: 213.230 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H15NO4
#4: 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
#5: 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: 4.22 Å3/Da / Density % sol: 70.83 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / Details: 0.1 M MES pH 5.8-6.3, 0.1 M NaCl, 5%-6% PEG3350

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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: Aug 2, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.52→97.62 Å / Num. obs: 77844 / % possible obs: 96 % / Redundancy: 3.2 % / Biso Wilson estimate: 128.68 Å2 / Net I/σ(I): 5.1

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.8.2_1309)refinement
XDSdata scaling
PDB_EXTRACT3.14data extraction
RefinementResolution: 3.5757→19.995 Å / SU ML: 0.54 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 33.04 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2972 3028 5.03 %
Rwork0.2558 --
obs0.2579 60144 77.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.5757→19.995 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms23540 0 180 0 23720
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00324228
X-RAY DIFFRACTIONf_angle_d0.75332915
X-RAY DIFFRACTIONf_dihedral_angle_d11.758389
X-RAY DIFFRACTIONf_chiral_restr0.033802
X-RAY DIFFRACTIONf_plane_restr0.0034176
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.5757-3.63130.522130.356840X-RAY DIFFRACTION1
3.6313-3.69040.785240.5704154X-RAY DIFFRACTION5
3.6904-3.75370.3889220.4349443X-RAY DIFFRACTION13
3.7537-3.82140.4497390.3693850X-RAY DIFFRACTION26
3.8214-3.89440.4276770.4051232X-RAY DIFFRACTION38
3.8944-3.97330.4732840.43691840X-RAY DIFFRACTION55
3.9733-4.0590.31991480.35282783X-RAY DIFFRACTION83
4.059-4.15260.33761930.3313179X-RAY DIFFRACTION97
4.1526-4.25550.3561570.32873233X-RAY DIFFRACTION97
4.2555-4.36940.33651690.313216X-RAY DIFFRACTION97
4.3694-4.49650.31081910.29613252X-RAY DIFFRACTION99
4.4965-4.63990.29841830.29123288X-RAY DIFFRACTION99
4.6399-4.80360.31431830.27113305X-RAY DIFFRACTION99
4.8036-4.9930.33121670.25253343X-RAY DIFFRACTION100
4.993-5.21640.26091750.24713337X-RAY DIFFRACTION100
5.2164-5.48610.30161900.24243320X-RAY DIFFRACTION100
5.4861-5.82180.30431820.25733331X-RAY DIFFRACTION100
5.8218-6.25850.32181470.25973383X-RAY DIFFRACTION100
6.2585-6.86510.26181770.24273365X-RAY DIFFRACTION99
6.8651-7.80620.27221860.22873387X-RAY DIFFRACTION99
7.8062-9.64760.25791810.20163381X-RAY DIFFRACTION99
9.6476-19.99540.26911700.21033454X-RAY DIFFRACTION97
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)
11.92851.3197-0.30287.8711-3.09752.7211-0.12040.52330.3293-0.63710.44930.12050.0313-0.036-0.24780.70140.00790.14270.93450.02460.8505-60.153234.2995-18.6479
21.9197-0.20660.31322.19511.34793.4299-0.11220.64620.3526-1.0395-0.0885-0.183-0.3218-0.22460.18151.25710.1766-0.09921.0437-0.06721.0137-54.3768-25.1528-11.641
30.1384-1.13630.79062.8229-1.3366-1.12880.46730.9243-0.20871.3326-0.6666-0.1849-0.2360.84790.16252.59680.5041-0.03121.36140.05341.9805-33.9894-76.988220.6053
43.2118-0.8631-0.61520.53030.56341.4960.08320.0171-0.2873-0.20850.122-0.28990.29230.418-0.1541.08760.2731-0.21231.0235-0.12211.1804-48.1062-34.32890.9686
5-0.2469-0.11660.87510.06420.29560.21030.57210.770.38090.27620.46330.20891.9224-0.9682-0.4654.2794-0.0695-0.63620.4572-0.35612.0408-41.8377-85.70174.2967
61.39570.6036-0.79941.8365-1.63925.0120.0068-0.01540.1347-0.05270.127-0.2745-0.19020.4701-0.10031.0334-0.04290.20671.2365-0.24760.9192-28.489339.3131-2.8246
70.24240.01020.82463.2928-1.47243.4875-0.14390.14090.23090.0769-0.1231-1.0242-0.29410.73780.19460.88650.0726-0.28321.15970.08941.8772-12.8489-19.32725.9765
80.6172-1.16311.44761.5186-1.5706-0.95250.8395-0.46190.3974-0.06890.22512.5249-0.17560.2142-0.94082.3401-0.2656-0.09221.20570.3162.0357-36.535-75.636338.1751
92.179-0.66030.68982.1008-0.67590.30.16060.0311-0.5521-0.2709-0.33880.21950.17110.3250.17011.18920.1853-0.29841.35210.06151.4127-12.86-35.210432.8867
100.4629-0.1883-0.67280.0779-0.003-0.0032-0.7061-0.346-0.92810.91530.53620.0219-0.52010.1788-0.02631.5645-0.0525-0.13691.29980.11472.6088-22.6938-83.647930.2491
112.1471-1.3195-0.65155.30042.08433.29480.0227-0.46960.1265-0.14990.1276-0.45640.11870.1865-0.11560.91310.04430.34361.1536-0.08790.9679-13.34136.388365.3479
121.31681.03960.04992.04341.46862.7876-0.0652-0.16390.5050.519-0.41620.3712-0.18190.16420.49051.48640.3069-0.44721.2896-0.10481.129-31.4117-20.17255.1831
131.28024.27220.03236.3513-0.1469-0.75530.4987-1.4931-0.5336-1.4243-1.816-0.5986-1.0675-0.30631.46682.4124-0.1591-0.14921.32190.00182.0012-54.4188-75.55332.4776
141.25560.504-0.20150.17180.40240.336-0.0223-0.6421-0.39920.0745-0.2367-0.063-0.0718-0.09440.19491.3701-0.0096-0.30651.49420.12211.4368-37.8338-30.918744.4807
152.5293-1.7689-0.1790.64790.28671.5803-0.2246-0.74370.1311.16621.1403-0.0943-0.42710.1679-0.87352.4074-0.0532-0.18021.4616-0.03241.8732-43.235-75.102548.8404
162.2115-0.3055-0.25081.49141.97113.14620.0738-0.31660.41580.05070.04630.2466-0.4009-0.3639-0.12941.41350.1280.25881.24090.0630.9237-45.210342.730650.1355
171.8409-0.5346-1.36483.10160.04521.5728-0.1045-0.37210.3050.21190.17840.6191-0.1938-0.0815-0.10540.87860.0729-0.17360.8616-0.07731.1449-72.9872-19.123716.7146
180.1027-0.226-1.64480.22331.06160.95221.61120.78680.61330.0075-0.57-1.2218-0.4426-0.7571-1.12212.7820.277-0.31231.0073-0.16532.8004-51.5089-77.949814.9466
192.6641-0.37680.94411.72880.66511.85730.2636-0.1552-0.9805-0.148-0.03430.40920.2977-0.2186-0.20670.98880.1058-0.18660.8939-0.04751.1682-73.8076-35.690112.6949
20-0.52980.08810.20380.42280.01581.6360.18940.4178-0.9007-0.947-0.90770.5908-0.0956-0.63670.65951.63690.24620.05331.4942-0.32572.8956-64.5384-80.217325.5426
211.7147-0.3874-1.52422.81690.85312.13160.09310.4491-0.0559-0.1778-0.31640.3468-0.08090.37140.2960.93250.1754-0.15631.00310.02041.41-49.4002-2.44997.4772
222.5492-0.94640.25323.4212-0.01061.43770.0126-0.3750.13760.2703-0.05-0.3615-0.3312-0.08170.06931.42940.0683-0.43681.0925-0.11721.604-35.7821-0.448732.5113
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 1:382)
2X-RAY DIFFRACTION2(chain A and resid 383:507)
3X-RAY DIFFRACTION3(chain A and resid 508:635)
4X-RAY DIFFRACTION4(chain A and resid 636:771)
5X-RAY DIFFRACTION5(chain A and resid 772:817)
6X-RAY DIFFRACTION6(chain B and resid 1:382)
7X-RAY DIFFRACTION7(chain B and resid 383:507)
8X-RAY DIFFRACTION8(chain B and resid 508:635)
9X-RAY DIFFRACTION9(chain B and resid 636:771)
10X-RAY DIFFRACTION10(chain B and resid 772:817)
11X-RAY DIFFRACTION11(chain C and resid 1:382)
12X-RAY DIFFRACTION12(chain C and resid 383:507)
13X-RAY DIFFRACTION13(chain C and resid 508:635)
14X-RAY DIFFRACTION14(chain C and resid 636:771)
15X-RAY DIFFRACTION15(chain C and resid 772:817)
16X-RAY DIFFRACTION16(chain D and resid 1:382)
17X-RAY DIFFRACTION17(chain D and resid 383:507)
18X-RAY DIFFRACTION18(chain D and resid 508:635)
19X-RAY DIFFRACTION19(chain D and resid 636:771)
20X-RAY DIFFRACTION20(chain D and resid 772:817)
21X-RAY DIFFRACTION21(chain E)
22X-RAY DIFFRACTION22(chain F)

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