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

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Basic information

Entry
Database: PDB / ID: 3fvn
TitleCrystal structure of the human glutamate receptor, GluR5, ligand-binding core in complex with 9-deoxy-neodysiherbaine A in space group P1
ComponentsGlutamate receptor, ionotropic kainate 1
KeywordsMEMBRANE PROTEIN / glutamate receptor / ligand-binding domain / 9-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 / glutamate-gated receptor activity / regulation of synaptic transmission, glutamatergic / glutamate-gated calcium ion channel activity / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / central nervous system development ...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 / glutamate-gated receptor activity / regulation of synaptic transmission, glutamatergic / glutamate-gated calcium ion channel activity / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / central nervous system development / synaptic transmission, glutamatergic / modulation of chemical synaptic transmission / postsynaptic density membrane / 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-9DX / 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 16, 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
Revision 1.5Nov 6, 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
Water8,071448
1
A: Glutamate receptor, ionotropic kainate 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,8337
Polymers29,0931
Non-polymers7406
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Glutamate receptor, ionotropic kainate 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,9298
Polymers29,0931
Non-polymers8367
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4440 Å2
ΔGint-47.5 kcal/mol
Surface area22690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.550, 50.814, 63.037
Angle α, β, γ (deg.)80.38, 84.37, 62.09
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-9DX / (2R,3aR,7R,7aR)-2-[(2S)-2-amino-3-hydroxy-3-oxo-propyl]-7-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.: 448 / 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: 2.28 Å3/Da / Density % sol: 46.05 %
Crystal growTemperature: 303 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 35% PEG3350, 0.3M LiSO4, 5mM 9-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: 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: 77805 / % possible obs: 95.4 % / Redundancy: 2.9 % / Rsym value: 0.041 / Net I/σ(I): 26
Reflection shellResolution: 1.5→1.55 Å / Redundancy: 2.7 % / Mean I/σ(I) obs: 2.7 / Num. unique all: 7485 / Rsym value: 0.212 / % possible all: 92

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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 ENATRY 2ZNT

2znt


Resolution: 1.5→30 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.953 / SU B: 2.172 / SU ML: 0.042 / Cross valid method: THROUGHOUT / ESU R: 0.077 / ESU R Free: 0.074 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18966 3928 5 %RANDOM
Rwork0.17159 ---
obs0.17251 73871 95.12 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 11.05 Å2
Baniso -1Baniso -2Baniso -3
1--0.07 Å20.08 Å20.04 Å2
2---0.24 Å2-0.09 Å2
3---0.26 Å2
Refinement stepCycle: LAST / Resolution: 1.5→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4012 0 101 448 4561
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0224292
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2872.0435822
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5495526
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.37924.057175
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.89215769
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.2331525
X-RAY DIFFRACTIONr_chiral_restr0.0850.2661
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.023103
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1940.22050
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3090.23034
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1010.2419
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1740.262
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1180.220
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7331.52656
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.08724169
X-RAY DIFFRACTIONr_scbond_it1.71431881
X-RAY DIFFRACTIONr_scangle_it2.4914.51645
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.503→1.542 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.252 256 -
Rwork0.208 5052 -
obs--87.92 %
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)
10.49060.04950.02560.86430.12740.7459-0.0389-0.03950.0109-0.00080.0145-0.02090.02590.05970.0244-0.03320.01340.004-0.02130.0089-0.0170.8324.91418.28
20.65940.1874-0.01170.84650.26910.751-0.04790.06760.0028-0.02240.02330.0054-0.05410.0640.0245-0.0283-0.01610.0043-0.02190.0142-0.02090.87613.685-10.829
31.3934-0.1085-0.18961.5193-0.01630.490.0073-0.09460.0280.07510.0120.0357-0.0619-0.0804-0.0192-0.0240.0326-0.0043-0.01530.0084-0.0295-16.2621.73621.237
40.91650.03990.05961.2562-0.04980.73670.00480.03210.01-0.05780.00010.07770.0805-0.1215-0.0049-0.0214-0.02950.0096-0.01070.0077-0.0241-16.204-3.126-13.943
50.1111-0.11050.2973.77860.06650.8295-0.0516-0.0902-0.03820.20840.0250.1344-0.0625-0.12910.0266-0.01510.01540.0057-0.00580.0011-0.007-7.5289.6511.096
60.12230.26220.33050.85490.42261.173-0.09320.08610.0266-0.1620.04910.1413-0.0189-0.10510.0441-0.0002-0.00720.0099-0.0033-0.00050.0101-7.559.226-3.642
725.66844.3215-9.83629.831-1.445711.75130.0514-0.1023-0.06830.0318-0.00780.1992-0.0589-0.0028-0.0436-0.01580.0165-0.0144-0.03050.0123-0.0096-7.6315.13119.932
820.8276-9.96348.454410.6352-0.6376.15550.00830.3497-0.1519-0.1691-0.0190.2946-0.14840.10230.0107-0.0113-0.01250.0123-0.02250.0112-0.0055-7.6253.689-12.465
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 103
2X-RAY DIFFRACTION1A216 - 256
3X-RAY DIFFRACTION2B1 - 103
4X-RAY DIFFRACTION2B216 - 256
5X-RAY DIFFRACTION3A108 - 212
6X-RAY DIFFRACTION4B108 - 212
7X-RAY DIFFRACTION5A104 - 107
8X-RAY DIFFRACTION5A213 - 215
9X-RAY DIFFRACTION6B104 - 107
10X-RAY DIFFRACTION6B213 - 215
11X-RAY DIFFRACTION7A1
12X-RAY DIFFRACTION8B2

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