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- PDB-3h6g: Crystal structure of the GluR6 amino terminal domain dimer assembly -

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Basic information

Entry
Database: PDB / ID: 3h6g
TitleCrystal structure of the GluR6 amino terminal domain dimer assembly
ComponentsGlutamate receptor, ionotropic kainate 2
KeywordsMEMBRANE PROTEIN / MEMBRANE PROTEIN GLYCOPROTEIN / Cell junction / Cell membrane / Glycoprotein / Ion transport / Ionic channel / Isopeptide bond / Membrane / Postsynaptic cell membrane / Receptor / RNA editing / Synapse / Transmembrane / Transport
Function / homology
Function and homology information


mossy fiber rosette / detection of cold stimulus involved in thermoception / Activation of Na-permeable kainate receptors / kainate selective glutamate receptor complex / Activation of Ca-permeable Kainate Receptor / negative regulation of synaptic transmission, glutamatergic / regulation of short-term neuronal synaptic plasticity / inhibitory postsynaptic potential / glutamate receptor activity / ubiquitin conjugating enzyme binding ...mossy fiber rosette / detection of cold stimulus involved in thermoception / Activation of Na-permeable kainate receptors / kainate selective glutamate receptor complex / Activation of Ca-permeable Kainate Receptor / negative regulation of synaptic transmission, glutamatergic / regulation of short-term neuronal synaptic plasticity / inhibitory postsynaptic potential / glutamate receptor activity / ubiquitin conjugating enzyme binding / receptor clustering / modulation of excitatory postsynaptic potential / neuronal action potential / regulation of JNK cascade / kainate selective glutamate receptor activity / ionotropic glutamate receptor complex / extracellularly glutamate-gated ion channel activity / behavioral fear response / positive regulation of synaptic transmission / glutamate-gated receptor activity / ligand-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / excitatory postsynaptic potential / hippocampal mossy fiber to CA3 synapse / presynaptic modulation of chemical synaptic transmission / dendrite cytoplasm / regulation of membrane potential / SNARE binding / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / synaptic transmission, glutamatergic / PDZ domain binding / postsynaptic density membrane / regulation of long-term neuronal synaptic plasticity / modulation of chemical synaptic transmission / terminal bouton / intracellular calcium ion homeostasis / positive regulation of neuron apoptotic process / presynaptic membrane / perikaryon / chemical synaptic transmission / postsynaptic membrane / scaffold protein binding / neuron apoptotic process / negative regulation of neuron apoptotic process / postsynaptic density / axon / dendrite / neuronal cell body / glutamatergic synapse / synapse / ubiquitin protein ligase binding / membrane / identical protein binding / plasma membrane
Similarity search - Function
Ionotropic glutamate receptor, metazoa / Ligated ion channel L-glutamate- and glycine-binding site / : / Response regulator / 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 ...Ionotropic glutamate receptor, metazoa / Ligated ion channel L-glutamate- and glycine-binding site / : / Response regulator / 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
L(+)-TARTARIC ACID / Glutamate receptor ionotropic, kainate 2
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.697 Å
AuthorsKumar, J. / Mayer, M.L.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2009
Title: The N-terminal domain of GluR6-subtype glutamate receptor ion channels.
Authors: Kumar, J. / Schuck, P. / Jin, R. / Mayer, M.L.
History
DepositionApr 23, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 26, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Jul 29, 2020Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / database_PDB_caveat ...chem_comp / database_PDB_caveat / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_conn_type / 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.conn_type_id / _struct_conn.id / _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_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn_type.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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Glutamate receptor, ionotropic kainate 2
B: Glutamate receptor, ionotropic kainate 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,65014
Polymers89,5002
Non-polymers2,15012
Water79344
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6140 Å2
ΔGint-9 kcal/mol
Surface area32470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)172.074, 172.074, 111.547
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Ens-ID: 1 / End auth comp-ID: GLU / End label comp-ID: GLU

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11THRTHRchain A and (resseq 2:268 or resseq 275:384 ) and (not element H)AA2 - 2682 - 268
12LYSLYSchain A and (resseq 2:268 or resseq 275:384 ) and (not element H)AA275 - 384275 - 384
21THRTHRchain B and (resseq 2:268 or resseq 275:384 ) and (not element H)BB2 - 2682 - 268
22LYSLYSchain B and (resseq 2:268 or resseq 275:384 ) and (not element H)BB275 - 384275 - 384

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Components

#1: Protein Glutamate receptor, ionotropic kainate 2 / / Glutamate receptor 6 / GluR-6 / GluR6


Mass: 44750.121 Da / Num. of mol.: 2 / Fragment: UNP residues 32-420
Source method: isolated from a genetically manipulated source
Details: The last six amino acids are vector encoded. The protein is a secreted product in which the 31 amino acid signal peptide was cleaved by the expression system between residues 31 and 32 and ...Details: The last six amino acids are vector encoded. The protein is a secreted product in which the 31 amino acid signal peptide was cleaved by the expression system between residues 31 and 32 and verified by N-terminal sequencing.
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Glur6, Grik2 / Plasmid: pRK8 / Cell line (production host): HEK-293 / Production host: Homo Sapiens (human) / References: UniProt: P42260
#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 / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 8
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-TLA / L(+)-TARTARIC ACID / Tartaric acid


Mass: 150.087 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H6O6
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 44 / Source method: isolated from a natural source / Formula: H2O

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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: 5.33 Å3/Da / Density % sol: 76.91 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 600 mM NaKTartrate, 200 mM NaCl, 20 mM NaAcetate, 1 mM EDTA, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 6, 2008
RadiationMonochromator: Si(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.69→50 Å / Num. all: 50708 / Num. obs: 50708 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 1 / Redundancy: 4.4 % / Biso Wilson estimate: 68.93 Å2 / Rmerge(I) obs: 0.073 / Net I/σ(I): 14
Reflection shellResolution: 2.69→2.74 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.63 / Mean I/σ(I) obs: 2.1 / % possible all: 99.4

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Processing

Software
NameClassification
HKL-2000data collection
PHASERphasing
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3H5V

3h5v


Resolution: 2.697→46.8 Å / SU ML: 0.31 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2271 2571 5.07 %Throughout
Rwork0.2038 ---
obs0.2049 50708 97.86 %-
all-50708 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 54.644 Å2 / ksol: 0.371 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--11.6145 Å2--
2---11.6145 Å2-
3---23.229 Å2
Refinement stepCycle: LAST / Resolution: 2.697→46.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6055 0 134 44 6233
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONf_bond_d0.009
X-RAY DIFFRACTIONf_angle_deg0.841
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A3004X-RAY DIFFRACTIONPOSITIONAL0.03
12B3004X-RAY DIFFRACTIONPOSITIONAL0.03
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.697-2.74850.3002930.28351869X-RAY DIFFRACTION70
2.7485-2.80460.36311290.29992735X-RAY DIFFRACTION99
2.8046-2.86560.3121440.28992741X-RAY DIFFRACTION100
2.8656-2.93220.32791670.27382698X-RAY DIFFRACTION100
2.9322-3.00560.24311430.2512695X-RAY DIFFRACTION100
3.0056-3.08680.2911520.23482716X-RAY DIFFRACTION100
3.0868-3.17760.27051690.23132677X-RAY DIFFRACTION100
3.1776-3.28020.21041610.20312727X-RAY DIFFRACTION100
3.2802-3.39740.20881260.20492722X-RAY DIFFRACTION100
3.3974-3.53330.25081440.19642716X-RAY DIFFRACTION100
3.5333-3.69410.19281310.20412747X-RAY DIFFRACTION100
3.6941-3.88880.20881400.18272711X-RAY DIFFRACTION100
3.8888-4.13230.21631530.16712723X-RAY DIFFRACTION100
4.1323-4.45110.18591380.15562728X-RAY DIFFRACTION100
4.4511-4.89860.18191400.15252741X-RAY DIFFRACTION99
4.8986-5.60640.18371570.16072697X-RAY DIFFRACTION99
5.6064-7.05960.22951400.19182750X-RAY DIFFRACTION99
7.0596-46.80730.17241440.19462744X-RAY DIFFRACTION98
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)
11.4228-0.78131.55282.5370.2049-1.9213-0.03310.2416-0.2945-0.3241-0.13870.28110.0618-0.230.11160.44760.06360.0370.4928-0.00680.241-80.696428.59416.6412
20.4214-0.3301-1.0740.56760.2812.5218-0.03110.00660.5729-0.15990.0448-0.5215-0.2436-0.00350.01970.5073-0.0531-0.07070.32260.07140.7739-54.22210.31789.4732
30.9741-0.92280.23852.63450.51822.259-0.1629-0.2594-0.08190.77650.1751-0.38660.0833-0.27590.00380.5455-0.0332-0.0550.36530.05710.408-69.060223.369624.2822
42.4774-0.0324-1.42551.94090.7363-1.3338-0.3161-0.21510.1610.17670.039-0.27620.0979-0.2410.13580.45630.0106-0.10680.61670.04780.3141-76.503638.7077-12.6766
52.69791.61690.44880.3748-0.31472.13590.0794-0.0183-0.8634-0.0736-0.0812-0.01470.1189-0.11240.0030.4228-0.08330.05120.30650.00540.7537-45.048431.926-6.7014
64.6197-0.0922-0.1361.02670.37852.0381-0.22250.8636-0.291-0.21650.1365-0.1915-0.0304-0.20350.07870.5488-0.09850.02150.4753-0.00470.4503-65.180535.0122-20.756
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 2:120) or (chain C and resid 1:2)A2 - 120
2X-RAY DIFFRACTION1(chain A and resid 2:120) or (chain C and resid 1:2)A1 - 397
3X-RAY DIFFRACTION2(chain A and resid 121:242)A121 - 242
4X-RAY DIFFRACTION3(chain A and resid 243:384) or (chain C and resid 3:5)A243 - 384
5X-RAY DIFFRACTION3(chain A and resid 243:384) or (chain C and resid 3:5)A3 - 400
6X-RAY DIFFRACTION4(chain B and resid 2:121) or (chain C and resid 6)B2 - 121
7X-RAY DIFFRACTION4(chain B and resid 2:121) or (chain C and resid 6)B6 - 396
8X-RAY DIFFRACTION5(chain B and resid 122:242)B122 - 242
9X-RAY DIFFRACTION6(chain B and resid 243:384) or (chain C and resid 8:9)B243 - 384
10X-RAY DIFFRACTION6(chain B and resid 243:384) or (chain C and resid 8:9)B8 - 398

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