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

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Basic information

Entry
Database: PDB / ID: 3fvg
TitleCrystal structure of the human glutamate receptor, GluR5, ligand-binding core in complex with MSVIII-19 in space group P1
ComponentsGlutamate receptor, ionotropic kainate 1
KeywordsMEMBRANE PROTEIN / glutamate receptor / dysiherbaine analogue / ligand-binding domain
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-MS8 / 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)59,82616
Polymers58,1872
Non-polymers1,64014
Water6,684371
1
A: Glutamate receptor, ionotropic kainate 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,8217
Polymers29,0931
Non-polymers7286
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Glutamate receptor, ionotropic kainate 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,0059
Polymers29,0931
Non-polymers9128
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4630 Å2
ΔGint-58.8 kcal/mol
Surface area22430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.627, 50.860, 62.931
Angle α, β, γ (deg.)80.41, 84.16, 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-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-MS8 / (2R,3aR,7aR)-2-[(2S)-2-amino-3-hydroxy-3-oxo-propyl]-3,3a,5,6,7,7a-hexahydrofuro[4,5-b]pyran-2-carboxylic acid


Mass: 259.256 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H17NO6
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / 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: 2.28 Å3/Da / Density % sol: 46.08 %
Crystal growTemperature: 303 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 35% PEG3350, 0.3M LiSO4, 5mM MSVIII-19, 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. all: 79952 / Num. obs: 79952 / % possible obs: 96.9 % / Redundancy: 3.9 % / Rsym value: 0.04 / Net I/σ(I): 32
Reflection shellResolution: 1.5→1.55 Å / Redundancy: 3.5 % / Mean I/σ(I) obs: 4.54 / Num. unique all: 7699 / Rsym value: 0.265 / % possible all: 93.8

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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 3FVN

3fvn


Resolution: 1.5→27.24 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.951 / SU B: 2.16 / SU ML: 0.042 / Cross valid method: THROUGHOUT / ESU R: 0.073 / ESU R Free: 0.073 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19184 4002 5 %RANDOM
Rwork0.16802 ---
obs0.16925 75825 96.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 13.632 Å2
Baniso -1Baniso -2Baniso -3
1-0.05 Å2-0.02 Å20.1 Å2
2---0.31 Å2-0.07 Å2
3---0.28 Å2
Refinement stepCycle: LAST / Resolution: 1.5→27.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4103 0 104 371 4578
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0224293
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2661.9985829
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5625541
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.09324.35177
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.37215767
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.9311523
X-RAY DIFFRACTIONr_chiral_restr0.0840.2655
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023141
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1970.21980
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3080.23037
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1040.2368
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1730.260
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1230.212
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7651.52675
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.11724207
X-RAY DIFFRACTIONr_scbond_it1.79331861
X-RAY DIFFRACTIONr_scangle_it2.7024.51606
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
Rfree0.239 303 -
Rwork0.198 5408 -
obs--93.49 %
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)
10.5660.09830.04440.8750.09240.7033-0.0551-0.05480.01960.01240.0276-0.03270.02860.04670.0275-0.03290.0232-0.0013-0.028-0.0018-0.01480.7664.77318.227
20.57660.11910.02520.87580.25370.6889-0.06850.07180.0049-0.03290.03680.0193-0.05360.06980.0317-0.0303-0.0182-0.0024-0.02580.0077-0.01010.75913.813-10.774
31.5411-0.0997-0.17371.6474-0.07920.5489-0.0222-0.10650.05330.0720.05640.051-0.0855-0.0843-0.0342-0.02760.0453-0.0077-0.0243-0.0046-0.0215-16.37421.78321.099
40.9129-0.03810.04111.2968-0.05490.59130.01230.0278-0.0037-0.05180.0050.06960.0931-0.1075-0.0173-0.0212-0.03270.0086-0.015-0.0034-0.0169-16.271-3.19-13.888
50.251-0.26130.16133.89371.55580.924-0.0766-0.1313-0.02360.22720.02160.1971-0.0393-0.13490.0549-0.01350.02130.0002-0.0088-0.00220.004-7.5699.58811.039
60.41290.66320.3581.92341.4511.2046-0.11670.1615-0.0049-0.20470.06470.16610.0438-0.09440.0521-0.0186-0.01070.0023-0.0129-0.00430.0083-7.69.122-3.652
721.20082.8554-6.92655.84283.45275.7868-0.0622-0.0509-0.1659-0.0593-0.04580.09490.05290.02430.1079-0.02090.0218-0.0227-0.0146-0.00130.0047-7.31314.753319.7361
813.6462-4.75516.96493.4775-0.09376.54520.02620.0216-0.00920.0643-0.08870.0716-0.1138-0.00570.0625-0.0149-0.0110.0197-0.0204-0.00330.0134-7.32433.96-12.3182
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 DIFFRACTION7A901
12X-RAY DIFFRACTION8B902

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