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- PDB-3fv1: Crystal Structure of the human glutamate receptor, GluR5, ligand-... -

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Basic information

Entry
Database: PDB / ID: 3fv1
TitleCrystal Structure of the human glutamate receptor, GluR5, ligand-binding core in complex with dysiherbaine in space group P1
ComponentsGlutamate receptor, ionotropic kainate 1
KeywordsMEMBRANE PROTEIN / Natural compound / glutamate receptor / ligand
Function / homology
Function and homology information


Activation of Na-permeable kainate receptors / kainate selective glutamate receptor complex / glutamate receptor signaling pathway / Activation of Ca-permeable Kainate Receptor / kainate selective glutamate receptor activity / glutamate-gated receptor activity / glutamate-gated calcium ion channel activity / regulation of synaptic transmission, glutamatergic / synaptic transmission, glutamatergic / central nervous system development ...Activation of Na-permeable kainate receptors / kainate selective glutamate receptor complex / glutamate receptor signaling pathway / Activation of Ca-permeable Kainate Receptor / kainate selective glutamate receptor activity / glutamate-gated receptor activity / glutamate-gated calcium ion channel activity / regulation of synaptic transmission, glutamatergic / synaptic transmission, glutamatergic / central nervous system development / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / postsynaptic density membrane / modulation of chemical synaptic transmission / presynaptic membrane / nervous system development / chemical synaptic transmission / intracellular membrane-bounded organelle / 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-DYH / Glutamate receptor ionotropic, kainate 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsUnno, M. / Sasaki, M. / Ikeda-Saito, M.
CitationJournal: J.Mol.Biol. / Year: 2011
Title: Binding and Selectivity of the Marine Toxin Neodysiherbaine A and Its Synthetic Analogues to GluK1 and GluK2 Kainate Receptors.
Authors: Unno, M. / Shinohara, M. / Takayama, K. / Tanaka, H. / Teruya, K. / Doh-Ura, K. / Sakai, R. / Sasaki, M. / Ikeda-Saito, M.
History
DepositionJan 15, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 19, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 26, 2011Group: Database references
Revision 1.3Aug 16, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software / Item: _software.classification
Revision 1.4Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)59,55212
Polymers58,1872
Non-polymers1,36510
Water8,323462
1
A: Glutamate receptor, ionotropic kainate 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,7826
Polymers29,0931
Non-polymers6895
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Glutamate receptor, ionotropic kainate 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,7706
Polymers29,0931
Non-polymers6775
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3030 Å2
ΔGint-60 kcal/mol
Surface area23700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.486, 50.740, 63.252
Angle α, β, γ (deg.)80.08, 84.18, 62.06
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Glutamate receptor, ionotropic kainate 1 / Glutamate receptor 5 / GluR-5 / GluR5 / Excitatory amino acid receptor 3 / EAA3


Mass: 29093.441 Da / Num. of mol.: 2
Fragment: ligand-binding domain, UNP residues 445-559, 682-820
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Genus: GRIK1, GLUR5 / Plasmid: pCold-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P39086
#2: Chemical ChemComp-DYH / (2R,3aR,6S,7R,7aR)-2-[(2S)-2-amino-2-carboxyethyl]-6-hydroxy-7-(methylamino)hexahydro-2H-furo[3,2-b]pyran-2-carboxylic acid


Mass: 304.296 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H20N2O7
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 462 / Source method: isolated from a natural source / Formula: H2O

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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: 2.28 Å3/Da / Density % sol: 46.02 %
Crystal growTemperature: 303 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 35% PEG3350, 0.3M LiSO4, 5mM dysiherbaine, pH5.5, VAPOR DIFFUSION, HANGING DROP, temperature 303K

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 0.9 Å
DetectorType: RIGAKU JUPITER 210 / Detector: CCD / Date: Oct 20, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.5→50 Å / Num. obs: 79411 / % possible obs: 97 % / Redundancy: 3.8 % / Rsym value: 0.049 / Net I/σ(I): 29.6
Reflection shellResolution: 1.5→1.55 Å / Redundancy: 3.7 % / Mean I/σ(I) obs: 3.8 / Num. unique all: 7741 / Rsym value: 0.193 / % possible all: 95.1

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Processing

Software
NameVersionClassification
CNSrefinement
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2ZNT

2znt


Resolution: 1.5→30 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.955 / SU B: 2.2 / SU ML: 0.042 / Cross valid method: THROUGHOUT / ESU R: 0.076 / ESU R Free: 0.073 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18895 4011 5.1 %RANDOM
Rwork0.1706 ---
obs0.17154 75397 96.82 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 12.771 Å2
Baniso -1Baniso -2Baniso -3
1--0.11 Å20.16 Å2-0.02 Å2
2---0.25 Å2-0.04 Å2
3---0.23 Å2
Refinement stepCycle: LAST / Resolution: 1.5→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4154 0 85 462 4701
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_refined_d0.009
X-RAY DIFFRACTIONr_angle_refined_deg1.27
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.563
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.695
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.71
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.997
X-RAY DIFFRACTIONr_chiral_restr0.084
X-RAY DIFFRACTIONr_gen_planes_refined0.005
X-RAY DIFFRACTIONr_nbd_refined0.195
X-RAY DIFFRACTIONr_nbtor_refined0.309
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.115
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.161
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.124
X-RAY DIFFRACTIONr_mcbond_it0.924
X-RAY DIFFRACTIONr_mcangle_it1.08
X-RAY DIFFRACTIONr_scbond_it1.767
X-RAY DIFFRACTIONr_scangle_it2.682
LS refinement shellResolution: 1.501→1.54 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.232 273 -
Rwork0.196 5336 -
obs--92.41 %
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)
10.54620.0178-0.01030.96420.03240.9239-0.0415-0.0494-0.005-0.01770.0225-0.00610.03950.06680.0189-0.04360.01740.0037-0.03520.0149-0.00370.4075.14218.383
20.74670.1759-0.011.07170.31080.8613-0.07660.09210.0193-0.01150.04280.0568-0.05070.07730.0338-0.0485-0.01930.0018-0.03230.0255-0.00210.51713.645-11.019
31.396-0.2585-0.13321.5068-0.11490.75410.023-0.05980.03830.04650.00770.0525-0.069-0.1118-0.0307-0.03280.0302-0.0026-0.02890.0175-0.0137-16.47322.09421.305
41.0134-0.06650.05921.5025-0.04210.74630.01560.02850.016-0.08250.00770.04150.0672-0.1251-0.0233-0.0436-0.03050.0141-0.02030.02-0.0087-16.43-3.093-14.205
51.469-0.9857-1.12193.25220.08151.0308-0.028-0.09460.05160.11040.00340.1303-0.0241-0.04480.0246-0.0170.0194-0.0154-0.0196-0.00210.0236-7.8529.80211.247
60.65120.98830.884.50020.85141.2674-0.02670.08330.0810.00630.00050.29580.0055-0.13770.0263-0.0229-0.02150.0178-0.0199-0.0110.0432-7.8739.281-4.011
79.56345.7366-4.47583.5753-2.04625.1335-0.1995-0.13250.0421-0.09110.21040.0029-0.04390.0121-0.0109-0.0310.03870.0051-0.03480.01480.0241-7.98515.01320.008
817.2639-6.38197.23343.2028-2.84745.8994-0.00620.2116-0.19240.17960.06880.01250.08120.0855-0.0625-0.0531-0.03370.0221-0.02720.00470.0317-8.0293.986-12.764
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A415 - 517
2X-RAY DIFFRACTION1A750 - 790
3X-RAY DIFFRACTION2B415 - 517
4X-RAY DIFFRACTION2B750 - 790
5X-RAY DIFFRACTION3A522 - 746
6X-RAY DIFFRACTION4B522 - 746
7X-RAY DIFFRACTION5A518 - 521
8X-RAY DIFFRACTION5A747 - 749
9X-RAY DIFFRACTION6B518 - 521
10X-RAY DIFFRACTION6B747 - 749
11X-RAY DIFFRACTION7A1
12X-RAY DIFFRACTION8B2

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