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- PDB-4u5e: Crystal structure of GluA2 T625G, con-ikot-ikot snail toxin, part... -

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Basic information

Entry
Database: PDB / ID: 4u5e
TitleCrystal structure of GluA2 T625G, con-ikot-ikot snail toxin, partial agonist KA and postitive modulator (R,R)-2b complex
Components
  • Con-ikot-ikot
  • Glutamate receptor 2GRIA2
KeywordsTransport protein/Toxin / AMPA receptors / 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 / Activation of AMPA receptors / response to lithium ion / perisynaptic space / cellular response to glycine / AMPA glutamate receptor activity ...host cell postsynaptic membrane / ion channel regulator activity / spine synapse / dendritic spine neck / dendritic spine head / Activation of AMPA receptors / response to lithium ion / perisynaptic space / cellular response to glycine / AMPA glutamate receptor activity / Trafficking of GluR2-containing AMPA receptors / immunoglobulin binding / AMPA glutamate receptor complex / kainate selective glutamate receptor activity / ionotropic glutamate receptor complex / extracellularly glutamate-gated ion channel activity / asymmetric synapse / regulation of receptor recycling / Unblocking of NMDA receptors, glutamate binding and activation / glutamate receptor binding / positive regulation of synaptic transmission / glutamate-gated receptor activity / presynaptic active zone membrane / response to fungicide / regulation of synaptic transmission, glutamatergic / cellular response to brain-derived neurotrophic factor stimulus / somatodendritic compartment / dendrite membrane / ligand-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / ionotropic glutamate receptor binding / ionotropic glutamate receptor signaling pathway / dendrite cytoplasm / cytoskeletal protein binding / SNARE binding / dendritic shaft / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / synaptic membrane / synaptic transmission, glutamatergic / PDZ domain binding / postsynaptic density membrane / protein tetramerization / modulation of chemical synaptic transmission / Schaffer collateral - CA1 synapse / establishment of protein localization / terminal bouton / receptor internalization / synaptic vesicle membrane / cerebral cortex development / synaptic vesicle / presynapse / signaling receptor activity / presynaptic membrane / amyloid-beta binding / growth cone / toxin activity / perikaryon / chemical synaptic transmission / postsynaptic membrane / scaffold protein binding / dendritic spine / postsynaptic density / neuron projection / axon / dendrite / neuronal cell body / glutamatergic synapse / synapse / protein-containing complex binding / endoplasmic reticulum membrane / protein kinase binding / cell surface / endoplasmic reticulum / protein-containing complex / extracellular region / membrane / identical protein binding / plasma membrane
Similarity search - Function
Four Helix Bundle (Hemerythrin (Met), subunit A) - #1800 / Bacterial extracellular solute-binding proteins, family 3 / Solute-binding protein family 3/N-terminal domain of MltF / Ionotropic glutamate receptor, metazoa / Ligated ion channel L-glutamate- and glycine-binding site / : / Ligand-gated ion channel / Ionotropic glutamate receptor, L-glutamate and glycine-binding domain / Ligated ion channel L-glutamate- and glycine-binding site / Ionotropic glutamate receptor ...Four Helix Bundle (Hemerythrin (Met), subunit A) - #1800 / Bacterial extracellular solute-binding proteins, family 3 / Solute-binding protein family 3/N-terminal domain of MltF / Ionotropic glutamate receptor, metazoa / Ligated ion channel L-glutamate- and glycine-binding site / : / Ligand-gated ion channel / Ionotropic glutamate receptor, L-glutamate and glycine-binding domain / Ligated ion channel L-glutamate- and glycine-binding site / 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: 3.5073 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 1.5Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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
D: Glutamate receptor 2
E: Con-ikot-ikot
F: Con-ikot-ikot
hetero molecules


Theoretical massNumber of molelcules
Total (without water)387,57116
Polymers384,8716
Non-polymers2,69910
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area27120 Å2
ΔGint-196 kcal/mol
Surface area139100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)161.270, 366.690, 109.010
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 / GRIA2 / 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: 91341.273 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Gria2, Glur2 / Cell (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 / Kainic acid


Mass: 213.230 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H15NO4 / Comment: neurotransmitter, agonist*YM
#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 / N-Acetylglucosamine


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

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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: 4.19 Å3/Da / Density % sol: 70.63 %
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: Sep 30, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.5→97.41 Å / Num. obs: 81049 / % possible obs: 98.8 % / Redundancy: 3.7 % / Biso Wilson estimate: 110.91 Å2 / Net I/σ(I): 9.4

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.8.2_1309)refinement
XDSdata scaling
PDB_EXTRACT3.14data extraction
RefinementStarting model: PDB ENTRY 3H5V, 1FW0, 3KG2

3h5v

1fw0

3kg2


Resolution: 3.5073→19.988 Å / SU ML: 0.44 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 28.29 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2757 3255 5.03 %
Rwork0.2404 --
obs0.2421 64765 79.57 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.5073→19.988 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms23551 0 180 0 23731
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00324239
X-RAY DIFFRACTIONf_angle_d0.78832928
X-RAY DIFFRACTIONf_dihedral_angle_d12.0038392
X-RAY DIFFRACTIONf_chiral_restr0.0323798
X-RAY DIFFRACTIONf_plane_restr0.0034182
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.5073-3.55940.400150.454698X-RAY DIFFRACTION3
3.5594-3.61470.3113130.4407345X-RAY DIFFRACTION10
3.6147-3.67360.6258340.6231533X-RAY DIFFRACTION16
3.6736-3.73650.5841360.4341901X-RAY DIFFRACTION27
3.7365-3.8040.4099560.3631311X-RAY DIFFRACTION39
3.804-3.87670.42531130.39561801X-RAY DIFFRACTION54
3.8767-3.95520.51251390.45622780X-RAY DIFFRACTION84
3.9552-4.04050.32821720.31413338X-RAY DIFFRACTION99
4.0405-4.13370.30171990.29463266X-RAY DIFFRACTION99
4.1337-4.23610.31061590.27773346X-RAY DIFFRACTION100
4.2361-4.34950.27771740.25713324X-RAY DIFFRACTION99
4.3495-4.47610.27541840.24063284X-RAY DIFFRACTION99
4.4761-4.61890.27361890.23323326X-RAY DIFFRACTION99
4.6189-4.78180.25471860.22283336X-RAY DIFFRACTION100
4.7818-4.97040.2411710.21433338X-RAY DIFFRACTION100
4.9704-5.19290.22351730.21163372X-RAY DIFFRACTION100
5.1929-5.46140.28641930.20573326X-RAY DIFFRACTION100
5.4614-5.79570.24261810.22063348X-RAY DIFFRACTION100
5.7957-6.23060.26251500.22493383X-RAY DIFFRACTION99
6.2306-6.83470.23811790.22373411X-RAY DIFFRACTION100
6.8347-7.77240.24821820.20313413X-RAY DIFFRACTION100
7.7724-9.60780.22311880.18423414X-RAY DIFFRACTION99
9.6078-19.98810.27091790.22753516X-RAY DIFFRACTION98
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)
10.21550.9326-0.00332.7692-1.14710.2367-0.02780.35070.139-0.27380.41760.0811-0.05820.0152-00.85890.02360.14550.9670.10680.922-60.051834.2264-18.0415
20.0027-0.1938-0.0571.61090.54771.3855-0.03510.13510.1905-0.6285-0.0990.0352-0.4114-0.119201.35160.1483-0.10991.1486-0.10981.0862-54.3298-25.0234-11.0935
3-0.6655-0.3008-1.70670.1368-0.6376-0.2228-0.19080.20630.23940.6871-0.325-0.71520.23210.017501.64580.1985-0.49931.1196-0.03011.7618-33.8518-76.866820.2185
4-0.194-0.259-0.9081-0.1603-0.32730.2028-0.00140.1701-0.0679-0.1907-0.0692-0.0128-0.06470.165401.08810.1877-0.21441.0344-0.08151.0639-48.0227-34.09941.5147
50.59490.6671.86680.06960.391-0.40080.53190.3619-0.7012-0.4606-0.0737-0.1196-0.0634-0.549102.08230.0493-0.11741.1157-0.24221.6527-42.7671-84.11624.7112
6-0.24540.4366-0.8909-0.7296-0.65462.77530.0350.0312-0.0326-0.08560.1965-0.1455-0.10630.3444-01.0249-0.09360.12921.2152-0.10220.9986-28.500539.0708-2.3272
7-1.20620.16210.49612.9125-0.98270.6135-0.0318-0.23220.11080.2024-0.0169-0.66240.12080.113200.81790.0368-0.21751.12090.16041.4328-12.9024-19.172326.2513
80.9897-2.00590.58711.2398-0.316-1.07940.312-0.48380.44970.16110.07911.367-0.54680.1541-01.7281-0.1656-0.43811.31430.31111.6393-35.632-75.774238.0724
90.7286-0.50040.57590.0967-1.0297-0.55270.1187-0.0525-0.17770.127-0.26790.2113-0.05860.196-01.09380.0789-0.25681.16320.07871.3711-12.8508-34.993533.2247
10-0.1494-0.3891-0.8985-0.12580.13181.291-0.9205-0.0665-0.08720.71850.8748-0.7392-0.4545-0.2077-00.960.0925-0.2751.03590.09381.9559-23.704-81.101628.5862
110.4769-0.3504-0.55042.32950.36521.95750.0502-0.2163-0.1331-0.33050.045-0.24110.318-0.0067-01.1937-0.07140.3091.2558-0.08571.2033-13.35736.150365.5929
120.06950.932-0.6057-0.78320.59310.7141-0.0234-0.31380.32670.3457-0.130.3197-0.060.1516-01.5960.1871-0.31961.3918-0.11691.2561-31.4178-20.203755.3629
130.9933-0.257-2.5870.3661-0.96020.53570.095-0.5773-0.0221-0.8589-0.54071.02830.30770.1049-01.5241-0.1348-0.51981.22520.2021.6606-54.4287-75.484432.6318
142.00390.23940.3016-0.1188-0.30360.0817-0.0124-0.3682-0.17690.26470.0502-0.32-0.09940.152601.32710.028-0.22841.22590.07551.3022-37.8211-30.737844.6654
151.1961-1.3107-0.61960.0506-0.5067-0.35850.0351-0.1775-0.28231.42820.0764-0.2008-0.477-0.3488-02.0098-0.0807-0.26491.33260.04511.6199-42.9948-75.041648.6903
160.6034-0.124-0.153-1.56411.28822.06430.0737-0.31820.12320.15060.05520.0521-0.1928-0.507401.38330.07740.18791.22260.00850.948-45.068442.467250.4839
170.22170.6677-0.36572.37850.316-0.6807-0.0161-0.0461-0.01210.02420.14510.20810.3010.0895-00.76890.0642-0.17160.8142-0.03650.8779-72.9817-19.612616.9742
181.05531.2521-1.54220.290.26270.80410.0577-0.0623-0.21440.94750.067-0.3357-0.06480.1383-01.38080.037-0.52460.7394-0.23021.7336-52.7345-77.414814.7072
190.0517-1.11090.10730.1440.11110.28480.1869-0.0661-0.395-0.0564-0.0980.17030.2095-0.1088-00.99770.0133-0.16710.9572-0.02731.1087-73.631-35.596413.0992
20-0.48580.4906-1.2543-0.0831-0.35022.1621-0.33580.3827-0.2008-0.09110.0030.37710.2629-0.589801.09720.1191-0.20121.22860.00032.352-64.8447-80.531125.0814
210.9074-0.1793-1.29750.9810.44720.18460.11910.09480.15290.232-0.3932-0.0843-0.07390.2178-00.80690.0628-0.15540.8735-0.00571.2313-49.4303-2.39987.9224
220.8075-1.45460.03661.62780.6250.1656-0.4078-0.11590.19910.21480.16-0.2967-0.3650.298801.35820.0019-0.37780.9751-0.02261.3858-35.6599-0.397732.831
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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