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- PDB-3fvk: Crystal structure of the human glutamate receptor, GluR5, ligand-... -

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Basic information

Entry
Database: PDB / ID: 3fvk
TitleCrystal structure of the human glutamate receptor, GluR5, ligand-binding core in complex with 8-deoxy-neodysiherbaine A in space group P1
ComponentsGlutamate receptor, ionotropic kainate 1
KeywordsMEMBRANE PROTEIN / glutamate receptor / ligand-binding core / 8-deoxy-neodysiherbaine
Function / homology
Function and homology information


Activation of Na-permeable kainate receptors / kainate selective glutamate receptor complex / Activation of Ca-permeable Kainate Receptor / glutamate receptor signaling pathway / kainate selective glutamate receptor activity / regulation of synaptic transmission, glutamatergic / glutamate-gated receptor activity / glutamate-gated calcium ion channel activity / central nervous system development / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential ...Activation of Na-permeable kainate receptors / kainate selective glutamate receptor complex / Activation of Ca-permeable Kainate Receptor / glutamate receptor signaling pathway / kainate selective glutamate receptor activity / regulation of synaptic transmission, glutamatergic / glutamate-gated receptor activity / glutamate-gated calcium ion channel activity / central nervous system development / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / synaptic transmission, glutamatergic / postsynaptic density membrane / modulation of chemical synaptic transmission / nervous system development / presynaptic membrane / 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-8DX / 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: Data collection / Refinement description / Source and taxonomy
Category: diffrn_detector / entity_src_gen / software / Item: _diffrn_detector.detector / _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
Revision 1.5Oct 30, 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, ionotropic kainate 1
B: Glutamate receptor, ionotropic kainate 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,76215
Polymers58,1872
Non-polymers1,57513
Water6,684371
1
A: Glutamate receptor, ionotropic kainate 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,9258
Polymers29,0931
Non-polymers8327
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Glutamate receptor, ionotropic kainate 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,8377
Polymers29,0931
Non-polymers7446
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4420 Å2
ΔGint-49.2 kcal/mol
Surface area22760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.508, 50.787, 62.644
Angle α, β, γ (deg.)80.43, 84.41, 62.10
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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-8DX / (2R,3aR,6S,7aR)-2-[(2S)-2-amino-3-hydroxy-3-oxo-propyl]-6-hydroxy-3,3a,5,6,7,7a-hexahydrofuro[4,5-b]pyran-2-carboxylic acid


Mass: 275.255 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H17NO7
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 371 / Source method: isolated from a natural source / Formula: H2O
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: 2.26 Å3/Da / Density % sol: 45.65 %
Crystal growTemperature: 303 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 35% PEG3350, 0.3M LiSO4, 5mM 8-deoxy-neodysiherbaine, 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: BL26B2 / Wavelength: 0.9 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Nov 25, 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: 78332 / % possible obs: 96 % / Redundancy: 3.8 % / Rsym value: 0.036 / Net I/σ(I): 35.9
Reflection shellResolution: 1.5→1.55 Å / Redundancy: 3.2 % / Mean I/σ(I) obs: 3.2 / Num. unique all: 7117 / Rsym value: 0.261 / % possible all: 87.4

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
CNSrefinement
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3FVN

3fvn


Resolution: 1.5→30 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.957 / SU B: 2.296 / SU ML: 0.044 / Cross valid method: THROUGHOUT / ESU R: 0.074 / ESU R Free: 0.074 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19148 3918 5 %RANDOM
Rwork0.16594 ---
obs0.16727 74370 95.86 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.303 Å2
Baniso -1Baniso -2Baniso -3
1--0.22 Å20.15 Å2-0.01 Å2
2---0.54 Å20.14 Å2
3---0.57 Å2
Refinement stepCycle: LAST / Resolution: 1.5→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4035 0 101 371 4507
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0224316
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2421.9995837
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4765524
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.10124.208183
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.12915797
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.8291526
X-RAY DIFFRACTIONr_chiral_restr0.0880.2653
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023136
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1960.22056
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3080.23041
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.110.2382
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1810.261
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1240.221
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7811.52659
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.18824184
X-RAY DIFFRACTIONr_scbond_it1.8531899
X-RAY DIFFRACTIONr_scangle_it2.7774.51647
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.5→1.539 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.243 255 -
Rwork0.205 4860 -
obs--84.77 %
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)
10.6239-0.0721-0.05131.05110.11890.9673-0.0683-0.07740.02370.00830.0409-0.03630.04790.06590.0274-0.0410.01890.004-0.0310.01-0.01630.6974.83418.297
20.70960.19970.07511.0670.30150.7687-0.06980.09110.0165-0.02630.04870.0092-0.06420.08810.0211-0.0359-0.02180.0094-0.02950.0194-0.01250.77113.878-10.736
31.8341-0.0092-0.28061.9301-0.06230.62640.0074-0.14080.06350.08770.03770.0765-0.0965-0.1126-0.0451-0.03390.0413-0.0007-0.02290.0141-0.0309-16.28221.75121.237
41.1315-0.04380.04631.66090.00470.88670.01510.0507-0.0147-0.07730.01080.07090.0997-0.1443-0.0259-0.0326-0.03550.0159-0.01580.0127-0.0266-16.253-3.096-13.795
50.1714-0.641-0.05365.23011.56690.6757-0.1008-0.1799-0.11080.25380.05550.3156-0.0203-0.16690.0453-0.01330.0180.014-0.01080.01030.0161-7.5959.59511.052
60.68672.27880.62527.61372.12520.6188-0.13360.21330.0005-0.2390.03280.20980.0033-0.10710.1008-0.0241-0.01080.0079-0.0030.00790.0081-7.5859.181-3.535
758.34752.2779-4.688710.0683-0.963714.1036-0.2264-0.9951-0.3422-0.06040.15620.15550.0716-0.23540.0703-0.05240.0226-0.0135-0.02420.0195-0.0182-7.6614.91119.946
841.3889-9.54731.07884.7706-0.51947.66040.35530.7320.08240.1229-0.20920.12690.1161-0.1615-0.1461-0.0431-0.01460.0304-0.01810.01880.0063-7.633.889-12.361
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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