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- PDB-4u5f: Crystal structure of GluA2, con-ikot-ikot snail toxin, partial ag... -

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Basic information

Entry
Database: PDB / ID: 4u5f
TitleCrystal structure of GluA2, con-ikot-ikot snail toxin, partial agonist KA and postitive modulator (R,R)-2b complex, GluA2cryst2 construct
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 / Activation of AMPA receptors / perisynaptic space / AMPA glutamate receptor activity / ligand-gated monoatomic cation channel activity / Trafficking of GluR2-containing AMPA receptors ...host cell postsynaptic membrane / ion channel regulator activity / spine synapse / dendritic spine neck / dendritic spine head / Activation of AMPA receptors / perisynaptic space / AMPA glutamate receptor activity / ligand-gated monoatomic cation channel activity / Trafficking of GluR2-containing AMPA receptors / response to lithium ion / immunoglobulin binding / AMPA glutamate receptor complex / kainate selective glutamate receptor activity / ionotropic glutamate receptor complex / extracellularly glutamate-gated ion channel activity / cellular response to glycine / asymmetric synapse / regulation of receptor recycling / Unblocking of NMDA receptors, glutamate binding and activation / positive regulation of synaptic transmission / glutamate receptor binding / extracellular ligand-gated monoatomic ion channel activity / glutamate-gated receptor activity / response to fungicide / glutamate-gated calcium ion channel activity / presynaptic active zone membrane / regulation of synaptic transmission, glutamatergic / somatodendritic compartment / dendrite membrane / cellular response to brain-derived neurotrophic factor stimulus / cytoskeletal protein binding / ligand-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / ionotropic glutamate receptor binding / dendrite cytoplasm / ionotropic glutamate receptor signaling pathway / SNARE binding / dendritic shaft / synaptic transmission, glutamatergic / synaptic membrane / PDZ domain binding / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / protein tetramerization / postsynaptic density membrane / establishment of protein localization / modulation of chemical synaptic transmission / Schaffer collateral - CA1 synapse / terminal bouton / receptor internalization / cerebral cortex development / synaptic vesicle membrane / synaptic vesicle / presynapse / signaling receptor activity / presynaptic membrane / amyloid-beta binding / toxin activity / growth cone / scaffold protein binding / chemical synaptic transmission / perikaryon / postsynaptic membrane / dendritic spine / postsynaptic density / neuron projection / axon / neuronal cell body / glutamatergic synapse / dendrite / synapse / protein-containing complex binding / protein kinase binding / 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. / Four Helix Bundle (Hemerythrin (Met), subunit A) ...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. / Four Helix Bundle (Hemerythrin (Met), subunit A) / Receptor, ligand binding region / Receptor family ligand binding region / 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: 3.7 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 24, 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 1.6Nov 13, 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)386,94216
Polymers384,2436
Non-polymers2,69910
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)160.290, 365.420, 108.860
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: 91184.055 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


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


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: 4.15 Å3/Da / Density % sol: 70.35 %
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: Dec 16, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.7→146.79 Å / Num. obs: 78943 / % possible obs: 98.4 % / Redundancy: 3.7 % / Biso Wilson estimate: 122.14 Å2 / Net I/σ(I): 8.3

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.8.2_1309)refinement
XDSdata scaling
PDB_EXTRACT3.14data extraction
RefinementResolution: 3.7→19.993 Å / SU ML: 0.58 / Cross valid method: FREE R-VALUE / σ(F): 1.98 / Phase error: 29.35 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.286 3247 5.06 %
Rwork0.2501 --
obs0.2519 64195 93.49 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.7→19.993 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms23520 0 180 0 23700
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00324208
X-RAY DIFFRACTIONf_angle_d0.74932879
X-RAY DIFFRACTIONf_dihedral_angle_d11.5458385
X-RAY DIFFRACTIONf_chiral_restr0.033786
X-RAY DIFFRACTIONf_plane_restr0.0034176
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.7-3.75550.4062420.40241006X-RAY DIFFRACTION35
3.7555-3.81380.4086870.38581768X-RAY DIFFRACTION63
3.8138-3.87590.37881440.38752320X-RAY DIFFRACTION83
3.8759-3.94220.37781350.38142683X-RAY DIFFRACTION96
3.9422-4.01340.39281310.3792763X-RAY DIFFRACTION98
4.0134-4.08990.3571660.34582727X-RAY DIFFRACTION98
4.0899-4.17270.35971540.32822753X-RAY DIFFRACTION99
4.1727-4.26250.31381530.30412763X-RAY DIFFRACTION99
4.2625-4.36070.32171390.29332814X-RAY DIFFRACTION99
4.3607-4.46860.29551560.28252739X-RAY DIFFRACTION99
4.4686-4.5880.25841550.26712815X-RAY DIFFRACTION99
4.588-4.72130.28711480.26152783X-RAY DIFFRACTION98
4.7213-4.87150.2951520.24272756X-RAY DIFFRACTION99
4.8715-5.04290.28041530.23782770X-RAY DIFFRACTION99
5.0429-5.24140.25631270.23092836X-RAY DIFFRACTION99
5.2414-5.47520.26891730.22792784X-RAY DIFFRACTION99
5.4752-5.75740.26661570.232809X-RAY DIFFRACTION99
5.7574-6.10840.28771270.23432820X-RAY DIFFRACTION99
6.1084-6.56450.25391360.23022843X-RAY DIFFRACTION99
6.5645-7.1970.23861590.21542834X-RAY DIFFRACTION99
7.197-8.17540.26071610.20792806X-RAY DIFFRACTION98
8.1754-10.07580.25751470.18782832X-RAY DIFFRACTION96
10.0758-19.9930.26841450.21962924X-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)
10.69860.7911-0.20782.6357-1.76560.8628-0.05620.39680.2087-0.280.3752-0.0223-0.04330.133900.70760.03320.1830.82360.10330.9297-59.79834.3914-17.9945
20.40540.26470.058-0.04320.36371.2109-0.1219-0.07390.4132-0.7923-0.1369-0.2438-0.0935-0.131901.18820.2111-0.17250.8159-0.11910.936-53.8053-24.8473-11.1479
3-0.21770.59880.37140.4403-0.113-1.48461.01621.35670.13241.5695-1.4773-0.5506-0.20760.791802.76880.5161-0.12971.38560.00631.8465-33.3516-76.443620.6647
40.2556-1.0714-0.6846-0.1236-1.02940.13030.04950.2649-0.2099-0.1712-0.0191-0.0185-0.14450.251100.94860.261-0.29050.9944-0.14411.1342-47.4494-33.98491.3959
50.47520.70691.18420.22530.5512-0.10170.96311.7783-0.0122-0.16050.46320.86640.4842-0.979103.59250.221-0.1674-0.3293-0.39891.3405-41.3742-85.18254.5171
6-0.05740.4678-0.5495-0.9176-0.72513.2979-0.06080.1884-0.0243-0.07250.2777-0.1326-0.14490.329700.9124-0.13560.17961.1552-0.19270.8257-28.357739.4652-2.2584
70.0011-0.2078-0.15741.0012-0.216-0.0206-0.2344-0.43880.09980.4923-0.0843-0.43010.06080.301600.65850.0435-0.46460.96810.08631.796-12.463-19.016926.3056
8-0.4236-0.06240.36960.0956-0.9603-1.06781.6186-1.1581.18360.0769-0.64722.7261-0.40830.7827-03.0487-0.27870.15351.1870.30342.0933-35.7324-75.131537.9806
90.1445-0.3181-0.51540.5127-0.9285-0.91840.0951-0.2146-0.2974-0.0394-0.4320.6599-0.1920.248401.17580.1484-0.42821.21580.09891.5291-12.5256-34.912833.2487
10-1.1202-0.3917-0.86770.0253-0.0969-0.4525-1.17810.0954-0.5709-0.22310.11440.0584-1.2373-0.459-02.3157-0.2829-0.20041.63-0.1522.8166-21.8759-83.186830.0971
111.0867-0.7063-1.03511.75490.83671.70940.0443-0.4107-0.0809-0.42670.0466-0.1480.23180.0985-01.0937-0.03820.3251.2297-0.10831.0961-13.255736.472765.6308
12-1.38081.4695-0.0004-0.78230.2153-0.2111-0.1269-0.19130.49490.5521-0.27560.23260.36470.036301.74640.2841-0.67531.377-0.1751.2416-31.0677-19.962655.3556
13-0.37680.4732-0.98320.01310.2299-0.4910.4617-1.9352-0.8327-1.913-2.0738-0.3466-1.3932-0.10302.8454-0.314-0.52131.64240.09341.8375-53.6173-75.133732.6047
140.8482-0.5226-0.17180.3082-0.1863-0.8812-0.0155-0.3310.32460.3207-0.0531-0.20560.04040.1896-01.4570.0209-0.46361.4028-0.05741.3733-37.3836-30.700944.6285
151.1667-1.16250.28780.2434-0.1766-0.459-0.2321-0.3893-0.3293-0.02651.1587-0.53270.0072-0.0488-02.4458-0.2496-0.28191.8554-0.00781.9047-42.3805-74.742948.8301
160.6029-0.1022-0.4312-1.26170.86361.83320.0788-0.20010.2510.26620.12160.1953-0.0377-0.2843-01.28080.07470.19261.174-0.06660.8606-44.874542.770450.4638
171.1551-0.33050.20921.1440.0243-0.1613-0.1317-0.07320.0041-0.11670.41540.23140.47870.1459-00.77780.1358-0.23540.6672-0.06050.8634-72.2265-19.010817.0899
18-0.48420.86170.19420.38691.0613-0.38850.60450.5044-0.08380.6184-0.2286-0.4919-0.0439-0.4598-02.70750.2497-0.01891.1116-0.06272.0154-50.7762-77.333415.0309
19-0.0315-0.950.29820.2186-0.54230.47390.20530.0723-0.3862-0.12710.0461-0.00670.2091-0.144-00.86940.1737-0.23670.6495-0.03210.9705-72.9291-35.540713.0763
20-0.21750.2975-0.0588-0.12030.11440.13850.12670.062-0.58-0.20290.14070.7639-0.46120.071801.00350.28420.06230.9238-0.13912.2532-63.7339-79.758125.5162
210.39560.1279-0.47990.3230.3468-0.42290.0671-0.44070.37970.2682-0.3019-0.57570.10980.2311-00.77270.1435-0.17280.8472-0.0131.3801-48.9127-2.20137.8646
220.4107-0.631-0.23240.88930.09880.2354-0.18630.15490.08390.2560.138-0.43130.34740.3778-01.22890.113-0.5560.9409-0.18061.6337-35.3256-0.249232.7565
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 6:382 )A6 - 382
2X-RAY DIFFRACTION2( CHAIN A AND RESID 391:507 )A391 - 507
3X-RAY DIFFRACTION3( CHAIN A AND RESID 508:635 )A508 - 635
4X-RAY DIFFRACTION4( CHAIN A AND RESID 636:771 )A636 - 771
5X-RAY DIFFRACTION5( CHAIN A AND RESID 772:814 )A772 - 814
6X-RAY DIFFRACTION6( CHAIN B AND RESID 6:382 )B6 - 382
7X-RAY DIFFRACTION7( CHAIN B AND RESID 383:507 )B383 - 507
8X-RAY DIFFRACTION8( CHAIN B AND RESID 508:635 )B508 - 635
9X-RAY DIFFRACTION9( CHAIN B AND RESID 636:771 )B636 - 771
10X-RAY DIFFRACTION10( CHAIN B AND RESID 772:814 )B772 - 814
11X-RAY DIFFRACTION11( CHAIN C AND RESID 6:381 )C6 - 381
12X-RAY DIFFRACTION12( CHAIN C AND RESID 390:507 )C390 - 507
13X-RAY DIFFRACTION13( CHAIN C AND RESID 508:635 )C508 - 635
14X-RAY DIFFRACTION14( CHAIN C AND RESID 636:771 )C636 - 771
15X-RAY DIFFRACTION15( CHAIN C AND RESID 772:814 )C772 - 814
16X-RAY DIFFRACTION16( CHAIN D AND RESID 6:381 )D6 - 381
17X-RAY DIFFRACTION17( CHAIN D AND RESID 387:507 )D387 - 507
18X-RAY DIFFRACTION18( CHAIN D AND RESID 508:635 )D508 - 635
19X-RAY DIFFRACTION19( CHAIN D AND RESID 636:771 )D636 - 771
20X-RAY DIFFRACTION20( CHAIN D AND RESID 772:814 )D772 - 814
21X-RAY DIFFRACTION21( CHAIN E AND RESID 2:86 )E2 - 86
22X-RAY DIFFRACTION22( CHAIN F AND RESID 2:86 )F2 - 86

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