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- PDB-3olz: Crystal structure of the GluK3 (GluR7) ATD dimer at 2.75 Angstrom... -

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Basic information

Entry
Database: PDB / ID: 3olz
TitleCrystal structure of the GluK3 (GluR7) ATD dimer at 2.75 Angstrom resolution
ComponentsGlutamate receptor, ionotropic kainate 3
KeywordsMEMBRANE PROTEIN / Ion channel
Function / homology
Function and homology information


Presynaptic function of Kainate receptors / adenylate cyclase inhibiting G protein-coupled glutamate receptor activity / G protein-coupled glutamate receptor signaling pathway / kainate selective glutamate receptor complex / Activation of Ca-permeable Kainate Receptor / negative regulation of synaptic transmission, glutamatergic / glutamate receptor signaling pathway / glutamate receptor activity / kainate selective glutamate receptor activity / glutamate-gated receptor activity ...Presynaptic function of Kainate receptors / adenylate cyclase inhibiting G protein-coupled glutamate receptor activity / G protein-coupled glutamate receptor signaling pathway / kainate selective glutamate receptor complex / Activation of Ca-permeable Kainate Receptor / negative regulation of synaptic transmission, glutamatergic / glutamate receptor signaling pathway / glutamate receptor activity / kainate selective glutamate receptor activity / glutamate-gated receptor activity / ligand-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / dendrite cytoplasm / synaptic transmission, glutamatergic / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / regulation of membrane potential / postsynaptic density membrane / modulation of chemical synaptic transmission / terminal bouton / presynaptic membrane / chemical synaptic transmission / perikaryon / axon / glutamatergic synapse / dendrite / plasma membrane
Similarity search - Function
Response regulator / Ionotropic glutamate receptor, metazoa / Ligated ion channel L-glutamate- and glycine-binding site / : / Ligand-gated ion channel / Ionotropic glutamate receptor, L-glutamate and glycine-binding domain / Ligated ion channel L-glutamate- and glycine-binding site / Ionotropic glutamate receptor / Eukaryotic homologues of bacterial periplasmic substrate binding proteins. / Receptor, ligand binding region ...Response regulator / Ionotropic glutamate receptor, metazoa / Ligated ion channel L-glutamate- and glycine-binding site / : / Ligand-gated ion channel / Ionotropic glutamate receptor, L-glutamate and glycine-binding domain / Ligated ion channel L-glutamate- and glycine-binding site / Ionotropic glutamate receptor / Eukaryotic homologues of bacterial periplasmic substrate binding proteins. / Receptor, ligand binding region / Receptor family ligand binding region / Periplasmic binding protein-like I / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
: / Glutamate receptor ionotropic, kainate 3
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75 Å
AuthorsKumar, J. / Mayer, M.L.
CitationJournal: J.Mol.Biol. / Year: 2010
Title: Crystal Structures of the Glutamate Receptor Ion Channel GluK3 and GluK5 Amino-Terminal Domains.
Authors: Kumar, J. / Mayer, M.L.
History
DepositionAug 26, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 3, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Mar 31, 2021Group: Source and taxonomy / Structure summary / Category: chem_comp / entity_src_gen
Item: _chem_comp.pdbx_synonyms / _entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_strain
Revision 1.4Sep 6, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Glutamate receptor, ionotropic kainate 3
B: Glutamate receptor, ionotropic kainate 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,8819
Polymers90,7042
Non-polymers1,1777
Water25214
1
A: Glutamate receptor, ionotropic kainate 3
B: Glutamate receptor, ionotropic kainate 3
hetero molecules

A: Glutamate receptor, ionotropic kainate 3
B: Glutamate receptor, ionotropic kainate 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)183,76218
Polymers181,4084
Non-polymers2,35414
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555x-y,x,z+1/61
2


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3140 Å2
ΔGint-22 kcal/mol
Surface area31150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)171.211, 171.211, 68.234
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

#1: Protein Glutamate receptor, ionotropic kainate 3 / Glutamate receptor 7 / GluR-7 / GluR7


Mass: 45352.035 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Glur7, Grik3 / Plasmid: pRK-IRES-EGFP / Cell line (production host): HEK 293 GNTI(-) / Production host: Homo Sapiens (human) / References: UniProt: D3ZDH2, UniProt: P42264*PLUS
#2: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 14 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE SEQUENCE CORRESPONDS TO GLUTAMATE RECEPTOR SUBUNIT KAINATE SUBTYPE [RATTUS NORVEGICUS], GENE ...THE SEQUENCE CORRESPONDS TO GLUTAMATE RECEPTOR SUBUNIT KAINATE SUBTYPE [RATTUS NORVEGICUS], GENE BANK ID AAC80577.1

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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: 3.18 Å3/Da / Density % sol: 61.36 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.8
Details: 0.1 M MgCl2, 0.1 M MES, 10% Isopropanol, 5% PEG 4K, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.0332 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 24, 2009
RadiationMonochromator: Si(111) Double Crystal Monochrometer / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.75→45 Å / Num. all: 29967 / Num. obs: 29967 / % possible obs: 98 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 4.5 % / Biso Wilson estimate: 54.8 Å2 / Rmerge(I) obs: 0.091 / Net I/σ(I): 16
Reflection shellResolution: 2.75→2.85 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.64 / Mean I/σ(I) obs: 2.25 / Num. unique all: 2894 / % possible all: 97.3

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine: 1.6.4_486)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3H6G

3h6g


Resolution: 2.75→43.307 Å / SU ML: 0.35 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2525 1493 5.09 %Random
Rwork0.1949 ---
all0.1978 29345 --
obs0.1978 29345 98.02 %-
Solvent computationShrinkage radii: 0.77 Å / VDW probe radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 49.177 Å2 / ksol: 0.406 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.9174 Å20 Å20 Å2
2---0.9174 Å2-0 Å2
3---1.8348 Å2
Refinement stepCycle: LAST / Resolution: 2.75→43.307 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5975 0 72 14 6061
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0076188
X-RAY DIFFRACTIONf_angle_d0.9568381
X-RAY DIFFRACTIONf_dihedral_angle_d13.8412282
X-RAY DIFFRACTIONf_chiral_restr0.053934
X-RAY DIFFRACTIONf_plane_restr0.0041068
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.75-2.84840.34651440.24652746X-RAY DIFFRACTION97
2.8484-2.96240.2841400.23512773X-RAY DIFFRACTION98
2.9624-3.09720.32431410.22172754X-RAY DIFFRACTION98
3.0972-3.26040.31121610.22562756X-RAY DIFFRACTION98
3.2604-3.46460.30291340.20552794X-RAY DIFFRACTION99
3.4646-3.7320.2561790.19612765X-RAY DIFFRACTION99
3.732-4.10730.22131470.1642806X-RAY DIFFRACTION98
4.1073-4.7010.19921490.15582784X-RAY DIFFRACTION98
4.701-5.92030.22541570.18572820X-RAY DIFFRACTION98
5.9203-43.31270.25111410.21212854X-RAY DIFFRACTION97
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)
11.38220.16430.11352.87341.84061.1225-0.26210.00090.04630.21820.2079-0.23610.1214-0.2167-0.02750.2268-0.011-0.01960.33110.08860.195233.93883.29812.2517
20.4980.9655-0.02772.97520.55280.2906-0.1005-0.25930.14960.30240.09360.7857-0.02630.00880.00130.17590.07790.04160.36660.04830.302218.334675.64394.4263
32.2127-1.63310.13641.333-0.68821.5991-0.18860.22490.10220.02390.1562-0.0150.0385-0.06970.00510.04640.02970.04890.1852-0.03390.227126.862249.93028.7642
4-0.0363-0.3110.13582.9845-0.14620.9513-0.0663-0.0903-0.0008-0.3957-0.08890.08750.0725-0.06660.10950.11980.05150.01220.32460.03170.131426.316572.8689-6.6007
52.5925-0.5922-0.83452.2224-1.10951.2933-0.10680.23820.4295-0.00530.04470.1519-0.1606-0.47630.03380.23810.0940.01960.3217-0.08960.262510.774789.575330.5896
60.94750.8861-0.27842.0668-0.2028-0.02290.41580.0220.0195-0.2339-0.3626-0.2164-0.03460.03390.01380.24150.1402-0.03390.36770.00640.277918.797971.85427.1007
70.89680.3694-0.14270.29540.63462.2989-0.19-0.1067-0.0239-0.07510.0328-0.41390.0881-0.01760.12220.13440.01780.07720.38910.14120.46790.142256.701421.0458
81.02340.883-0.59431.12590.17070.90320.2066-0.2289-0.01230.3253-0.18480.0972-0.0216-0.06040.0110.08320.0759-0.03450.36650.02940.096512.615674.761238.6426
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 3:90) or (chain E and resid 1)A3 - 90
2X-RAY DIFFRACTION1(chain A and resid 3:90) or (chain E and resid 1)E1
3X-RAY DIFFRACTION2(chain A and resid 91:130)A91 - 130
4X-RAY DIFFRACTION3(chain A and resid 131:252) or (chain E and resid 2)A131 - 252
5X-RAY DIFFRACTION3(chain A and resid 131:252) or (chain E and resid 2)E2
6X-RAY DIFFRACTION4(chain A and resid 253:385) or (chain E and resid 3)A253 - 385
7X-RAY DIFFRACTION4(chain A and resid 253:385) or (chain E and resid 3)E3
8X-RAY DIFFRACTION5(chain B and resid 3:81)B3 - 81
9X-RAY DIFFRACTION6(chain B and resid 82:139)B82 - 139
10X-RAY DIFFRACTION7(chain B and resid 140:249) or (chain F and resid 1)B140 - 249
11X-RAY DIFFRACTION7(chain B and resid 140:249) or (chain F and resid 1)F1
12X-RAY DIFFRACTION8(chain B and resid 250:385) or (chain F and resid 2)B250 - 385
13X-RAY DIFFRACTION8(chain B and resid 250:385) or (chain F and resid 2)F2

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