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

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Basic information

Entry
Database: PDB / ID: 3fuz
TitleCrystal structure of the human glutamate receptor, GluR5, ligand-binding core in complex with L-glutamate in space group P1
ComponentsGlutamate receptor, ionotropic kainate 1
KeywordsMEMBRANE PROTEIN / human glutamate receptor / ligand-binding core
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
GLUTAMIC ACID / Glutamate receptor ionotropic, kainate 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 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
Revision 1.5Oct 30, 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
A: Glutamate receptor, ionotropic kainate 1
B: Glutamate receptor, ionotropic kainate 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,7697
Polymers58,1872
Non-polymers5825
Water7,855436
1
A: Glutamate receptor, ionotropic kainate 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,4334
Polymers29,0931
Non-polymers3393
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Glutamate receptor, ionotropic kainate 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,3373
Polymers29,0931
Non-polymers2432
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2070 Å2
ΔGint-36 kcal/mol
Surface area23740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.617, 50.724, 63.254
Angle α, β, γ (deg.)93.52, 96.41, 117.86
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-GLU / GLUTAMIC ACID


Type: L-peptide linking / Mass: 147.129 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H9NO4
#3: Chemical ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 436 / 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: 2.29 Å3/Da / Density % sol: 46.23 %
Crystal growTemperature: 303 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 35% PEG3350, 0.3M LiSO4, pH5.5, VAPOR DIFFUSION, HANGING DROP, temperature 303K

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A
DetectorType: ADSC QUANTUM 270 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.65→50 Å / Num. all: 59662 / Num. obs: 59662 / % possible obs: 96.3 % / Redundancy: 3.9 % / Rsym value: 0.074 / Net I/σ(I): 19
Reflection shellResolution: 1.65→1.71 Å / Redundancy: 3.6 % / Mean I/σ(I) obs: 2 / Num. unique all: 5634 / Rsym value: 0.378 / % possible all: 91.3

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Processing

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

2znt


Resolution: 1.65→30 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.938 / SU B: 3.784 / SU ML: 0.067 / Cross valid method: THROUGHOUT / ESU R: 0.111 / ESU R Free: 0.106 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21936 3010 5 %RANDOM
Rwork0.18866 ---
obs0.19023 56612 96.14 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 13.107 Å2
Baniso -1Baniso -2Baniso -3
1--0.45 Å2-0.19 Å20.17 Å2
2---0.57 Å20.06 Å2
3---0.89 Å2
Refinement stepCycle: LAST / Resolution: 1.65→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4082 0 35 436 4553
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0224192
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3131.9815664
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7295510
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.05424.045178
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.24915780
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.9441526
X-RAY DIFFRACTIONr_chiral_restr0.0930.2634
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023076
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2030.22017
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3070.22933
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1210.2390
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1830.246
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1150.218
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.841.52634
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.2424129
X-RAY DIFFRACTIONr_scbond_it2.14131801
X-RAY DIFFRACTIONr_scangle_it3.2324.51535
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.65→1.693 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.348 218 -
Rwork0.265 3862 -
obs--88.7 %
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)
10.49590.0526-0.0951.0264-0.18410.8056-0.0269-0.04560.0146-0.02580.01140.0162-0.0283-0.04080.0155-0.03650.00950.0016-0.0298-0.0123-0.0168-0.895-5.30118.82
20.54810.0270.17591.2718-0.36960.8044-0.02960.0701-0.0083-0.0064-0.0099-0.00050.0736-0.04550.0394-0.0324-0.010.0067-0.0242-0.0106-0.029-0.549-14.17-10.426
31.5985-0.14170.01821.34980.11470.5934-0.0007-0.0675-0.0320.03450.0040.0050.05840.0956-0.0033-0.03930.02570.0108-0.0194-0.0002-0.026116.133-22.02721.731
41.1336-0.02760.13561.6190.05930.7957-0.00980.0229-0.0116-0.0747-0.0017-0.0985-0.0830.11640.0115-0.0428-0.0311-0.0046-0.0164-0.0044-0.017916.2972.675-13.433
50.3165-0.93760.3633.1139-1.0280.4233-0.0697-0.1228-0.05950.24110.0643-0.25420.0645-0.0610.0054-0.00480.01570.0051-0.0042-0.00830.00357.573-9.79911.735
60.96250.0528-1.59141.29230.19312.6923-0.0940.04640.045-0.18110.096-0.1568-0.03490.186-0.002-0.0122-0.0245-0.01240.00760.0180.00967.744-9.47-3.274
725.7143-10.8071-17.10955.99867.263511.3878-1.32330.1902-0.26490.61090.9065-0.1770.1742-0.12720.4169-0.03260.026-0.0222-0.05290.00970.05456.05-15.89419.455
830.988-1.555315.01298.93917.297514.5885-1.0082-0.4440.1479-0.30430.55870.0482-0.2804-0.04430.4495-0.0381-0.0127-0.0076-0.02590.02110.04066.214-3.438-10.984
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 DIFFRACTION7A301
12X-RAY DIFFRACTION8B302

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