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- PDB-5nf5: Structure of GluK1 ligand-binding domain (S1S2) in complex with C... -

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Basic information

Entry
Database: PDB / ID: 5nf5
TitleStructure of GluK1 ligand-binding domain (S1S2) in complex with CIP-AS at 2.85 A resolution
ComponentsGlutamate receptor ionotropic, kainate 1,Glutamate receptor ionotropic, kainate 1
KeywordsMEMBRANE PROTEIN / IONOTROPIC GLUTAMATE RECEPTOR / KAINATE RECEPTOR / LIGAND-BINDING DOMAIN / GLUK1 / GLUR5 / AGONIST
Function / homology
Function and homology information


negative regulation of synaptic transmission, GABAergic / gamma-aminobutyric acid secretion / L-glutamate transmembrane transporter activity / positive regulation of gamma-aminobutyric acid secretion / Activation of Na-permeable kainate receptors / kainate selective glutamate receptor complex / Activation of Ca-permeable Kainate Receptor / regulation of short-term neuronal synaptic plasticity / negative regulation of synaptic transmission, glutamatergic / glutamate binding ...negative regulation of synaptic transmission, GABAergic / gamma-aminobutyric acid secretion / L-glutamate transmembrane transporter activity / positive regulation of gamma-aminobutyric acid secretion / Activation of Na-permeable kainate receptors / kainate selective glutamate receptor complex / Activation of Ca-permeable Kainate Receptor / regulation of short-term neuronal synaptic plasticity / negative regulation of synaptic transmission, glutamatergic / glutamate binding / inhibitory postsynaptic potential / synaptic transmission, GABAergic / adult behavior / behavioral response to pain / kainate selective glutamate receptor activity / modulation of excitatory postsynaptic potential / extracellularly glutamate-gated ion channel activity / ionotropic glutamate receptor complex / membrane depolarization / glutamate-gated receptor activity / glutamate-gated calcium ion channel activity / ligand-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / presynaptic modulation of chemical synaptic transmission / ionotropic glutamate receptor signaling pathway / SNARE binding / positive regulation of synaptic transmission, GABAergic / regulation of membrane potential / excitatory postsynaptic potential / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / synaptic transmission, glutamatergic / establishment of localization in cell / postsynaptic density membrane / modulation of chemical synaptic transmission / regulation of synaptic plasticity / terminal bouton / nervous system development / presynaptic membrane / scaffold protein binding / chemical synaptic transmission / postsynaptic membrane / receptor complex / postsynaptic density / neuronal cell body / synapse / dendrite / glutamatergic synapse / identical protein binding / membrane / plasma membrane
Similarity search - Function
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 ...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 II / Periplasmic binding protein-like I / D-Maltodextrin-Binding Protein; domain 2 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-8VN / Glutamate receptor ionotropic, kainate 1
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.85 Å
AuthorsFrydenvang, K. / Venskutonyte, R. / Thorsen, T.S. / Kastrup, J.S.
CitationJournal: ACS Chem Neurosci / Year: 2017
Title: Structure and Affinity of Two Bicyclic Glutamate Analogues at AMPA and Kainate Receptors.
Authors: Mllerud, S. / Pinto, A. / Marconi, L. / Frydenvang, K. / Thorsen, T.S. / Laulumaa, S. / Venskutonyte, R. / Winther, S. / Moral, A.M.C. / Tamborini, L. / Conti, P. / Pickering, D.S. / Kastrup, J.S.
History
DepositionMar 13, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 26, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2017Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.name
Revision 1.2Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: Glutamate receptor ionotropic, kainate 1,Glutamate receptor ionotropic, kainate 1
A: Glutamate receptor ionotropic, kainate 1,Glutamate receptor ionotropic, kainate 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,15311
Polymers58,2172
Non-polymers9369
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3800 Å2
ΔGint-49 kcal/mol
Surface area23410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.334, 70.334, 231.913
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111(CHAIN A AND ((RESID 5 AND (NAME N OR NAME...
211(CHAIN B AND ((RESID 5 AND (NAME N OR NAME...

NCS ensembles :
ID
1
2

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Components

#1: Protein Glutamate receptor ionotropic, kainate 1,Glutamate receptor ionotropic, kainate 1 / GluK1 / Glutamate receptor 5 / GluR5


Mass: 29108.453 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: THE DATABASE SEQUENCE IS P22756-2, ISOFORM GLUR5-2. THE PROTEIN CRYSTALLIZED IS THE EXTRACELLULAR LIGAND-BINDING DOMAIN OF GLUK1. TRANSMEMBRANE REGIONS WERE REPLACED WITH A GLY-THR LINKER ...Details: THE DATABASE SEQUENCE IS P22756-2, ISOFORM GLUR5-2. THE PROTEIN CRYSTALLIZED IS THE EXTRACELLULAR LIGAND-BINDING DOMAIN OF GLUK1. TRANSMEMBRANE REGIONS WERE REPLACED WITH A GLY-THR LINKER (RESIDUES 117-118). THE SEQUENCE MATCHES DISCONTINOUSLY WITH REFERENCE DATABASE (430-544, 667-805). THERE IS A SEQUENCE CONFLICT AT RESIDUE 34 (462) OF THE CRYSTALLIZED PROTEIN DUE TO DIFFERENCES IN DATABASE SEQUENCE (SEE GENBANK ACCESION NO.AAA02874). GLY1 IS A CLONING REMNANT.
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Grik1, Glur5 / Plasmid: pET28a+ / Production host: Escherichia coli (E. coli) / Variant (production host): Origami 2 / References: UniProt: P22756
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-8VN / (3~{a}~{S},4~{S},6~{a}~{R})-4,5,6,6~{a}-tetrahydro-3~{a}~{H}-pyrrolo[3,4-d][1,2]oxazole-3,4-dicarboxylic acid


Mass: 200.149 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H8N2O5
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
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: 2.47 Å3/Da / Density % sol: 50.29 %
Crystal growTemperature: 279 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 24.4% PEG4000, 0.3 M lithium sulfate, 0.1 M cacodylate buffer pH 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I911-3 / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 18, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.85→48.63 Å / Num. obs: 14455 / % possible obs: 100 % / Redundancy: 10.7 % / Biso Wilson estimate: 40.1 Å2 / Rsym value: 0.118 / Net I/σ(I): 19.4
Reflection shellResolution: 2.85→3 Å / Redundancy: 11.1 % / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 1.6 / Rsym value: 0.48 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIXrefinement
SCALA3.3.20data scaling
PDB_EXTRACT3.22data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4E0X

4e0x


Resolution: 2.85→45.71 Å / SU ML: 0.36 / Cross valid method: THROUGHOUT / σ(F): 1.39 / Phase error: 23.44
RfactorNum. reflection% reflection
Rfree0.261 723 5.03 %
Rwork0.21 --
obs0.213 14388 100 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 40.7 Å2
Refinement stepCycle: LAST / Resolution: 2.85→45.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4058 0 59 0 4117
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0034192
X-RAY DIFFRACTIONf_angle_d0.6155653
X-RAY DIFFRACTIONf_dihedral_angle_d12.5252525
X-RAY DIFFRACTIONf_chiral_restr0.041623
X-RAY DIFFRACTIONf_plane_restr0.004710
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDType
11A2778X-RAY DIFFRACTIONPOSITIONAL
12B2778X-RAY DIFFRACTIONPOSITIONAL
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8503-3.07030.34961480.26532644X-RAY DIFFRACTION100
3.0703-3.37920.29511570.23412648X-RAY DIFFRACTION100
3.3792-3.86790.26181380.21272704X-RAY DIFFRACTION100
3.8679-4.87230.22631340.17512733X-RAY DIFFRACTION100
4.8723-45.71290.23521460.20812936X-RAY DIFFRACTION100
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)
11.81971.05990.17032.34340.26953.7936-0.01180.1515-0.09-0.17990.0140.0963-0.0499-0.4299-0.00460.14220.0217-0.02470.304-0.02040.2282-15.2374-34.9146-20.7924
23.4147-2.3037-0.28083.33480.27891.5605-0.1126-0.2720.0627-0.03740.166-0.0779-0.1274-0.0157-0.02050.22-0.044-0.03020.16650.00610.13982.881-29.9093-15.7191
33.49440.3144-0.84175.24322.13722.7633-0.01370.31010.6263-0.94450.23580.1006-0.3310.1532-0.11550.4124-0.1031-0.06730.25340.1110.414213.6334-32.3729-22.3264
44.1463-1.0422-2.60041.92321.0531.9435-0.11130.1246-0.2703-0.0068-0.02560.07970.28510.38660.2180.3748-0.0425-0.11980.2337-0.00120.24156.2894-42.415-15.5696
52.44212.3187-1.72733.7168-4.59597.09560.0161-0.22160.15330.0947-0.17910.24750.0999-0.67620.19560.24350.0483-0.0070.3391-0.07270.2043-13.8268-28.5235-5.2158
68.32950.5495-0.50151.8925-1.77883.5508-0.0789-0.4425-1.387-0.3333-0.21330.51550.29840.30350.1720.2821-0.0866-0.05970.29090.12830.5815-7.0245-48.3759-10.9959
71.88610.51180.50730.97321.79743.4291-0.15440.10290.14870.06360.2441-0.1675-0.14710.37-0.05110.2462-0.0019-0.10560.2492-0.03270.33128.2615-20.8315.3062
81.2972-0.89820.52663.8793-1.09061.2337-0.0685-0.1362-0.0360.02770.16070.10230.0567-0.1734-0.05820.2429-0.01540.00070.2817-0.03360.141-5.0813-33.452711.9351
94.0505-0.47861.7963.9301-2.81192.7907-0.1652-0.27760.0478-0.02320.18840.35320.0167-0.2035-0.0380.33110.04850.01570.2569-0.06550.2661-2.4462-45.950214.5751
100.21650.3432-0.57092.23260.54013.54110.01820.1990.1093-0.1987-0.1404-0.2588-0.23110.41840.20970.2004-0.032-0.02720.20410.02380.29716.189-26.04442.8008
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN 'A' AND (RESID 4 THROUGH 65 )
2X-RAY DIFFRACTION2CHAIN 'A' AND (RESID 66 THROUGH 132 )
3X-RAY DIFFRACTION3CHAIN 'A' AND (RESID 133 THROUGH 184 )
4X-RAY DIFFRACTION4CHAIN 'A' AND (RESID 185 THROUGH 216 )
5X-RAY DIFFRACTION5CHAIN 'A' AND (RESID 217 THROUGH 239 )
6X-RAY DIFFRACTION6CHAIN 'A' AND (RESID 240 THROUGH 257 )
7X-RAY DIFFRACTION7CHAIN 'B' AND (RESID 4 THROUGH 47 )
8X-RAY DIFFRACTION8CHAIN 'B' AND (RESID 48 THROUGH 132 )
9X-RAY DIFFRACTION9CHAIN 'B' AND (RESID 133 THROUGH 216 )
10X-RAY DIFFRACTION10CHAIN 'B' AND (RESID 217 THROUGH 257 )

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