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- PDB-3h6h: Crystal structure of the GluR6 amino terminal domain dimer assemb... -

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Basic information

Entry
Database: PDB / ID: 3h6h
TitleCrystal structure of the GluR6 amino terminal domain dimer assembly MPD form
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 / regulation of short-term neuronal synaptic plasticity / negative regulation of synaptic transmission, glutamatergic / 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 / regulation of short-term neuronal synaptic plasticity / negative regulation of synaptic transmission, glutamatergic / inhibitory postsynaptic potential / glutamate receptor activity / ubiquitin conjugating enzyme binding / regulation of JNK cascade / receptor clustering / modulation of excitatory postsynaptic potential / kainate selective glutamate receptor activity / ionotropic glutamate receptor complex / extracellularly glutamate-gated ion channel activity / behavioral fear response / positive regulation of synaptic transmission / neuronal action potential / glutamate-gated receptor activity / glutamate-gated calcium ion channel activity / ligand-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / dendrite cytoplasm / presynaptic modulation of chemical synaptic transmission / SNARE binding / hippocampal mossy fiber to CA3 synapse / regulation of membrane potential / excitatory postsynaptic potential / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / synaptic transmission, glutamatergic / PDZ domain binding / regulation of long-term neuronal synaptic plasticity / modulation of chemical synaptic transmission / postsynaptic density membrane / terminal bouton / intracellular calcium ion homeostasis / positive regulation of neuron apoptotic process / presynaptic membrane / scaffold protein binding / neuron apoptotic process / chemical synaptic transmission / perikaryon / negative regulation of neuron apoptotic process / postsynaptic membrane / postsynaptic density / axon / neuronal cell body / synapse / dendrite / ubiquitin protein ligase binding / glutamatergic synapse / identical protein binding / membrane / plasma membrane
Similarity search - Function
Response regulator / 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 ...Response regulator / 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 I / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Glutamate receptor ionotropic, kainate 2
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.901 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
Revision 1.5Nov 6, 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 2
B: Glutamate receptor, ionotropic kainate 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,35012
Polymers89,5002
Non-polymers1,85010
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5640 Å2
ΔGint-11 kcal/mol
Surface area32360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)177.253, 177.253, 81.173
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

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11THRTHRVALVALchain A and (resseq 2:14 or resseq 18:268 or resseq 278:384 ) and (not element H)AA2 - 142 - 14
12PROPROGLUGLUchain A and (resseq 2:14 or resseq 18:268 or resseq 278:384 ) and (not element H)AA18 - 26818 - 268
13SERSERGLUGLUchain A and (resseq 2:14 or resseq 18:268 or resseq 278:384 ) and (not element H)AA278 - 384278 - 384
21THRTHRVALVALchain B and (resseq 2:14 or resseq 18:268 or resseq 278:384 ) and (not element H)BB2 - 142 - 14
22PROPROGLUGLUchain B and (resseq 2:14 or resseq 18:268 or resseq 278:384 ) and (not element H)BB18 - 26818 - 268
23SERSERGLUGLUchain B and (resseq 2:14 or resseq 18:268 or resseq 278:384 ) and (not element H)BB278 - 384278 - 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


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-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
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: 4.11 Å3/Da / Density % sol: 70.09 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9
Details: 100 mM Bicine, 10% MPD, pH 9.0, 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: 2.9→50 Å / Num. all: 31930 / Num. obs: 31930 / % possible obs: 98.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 1 / Redundancy: 8.1 % / Biso Wilson estimate: 68.49 Å2 / Rmerge(I) obs: 0.089 / Net I/σ(I): 21
Reflection shellResolution: 2.9→3 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.763 / Mean I/σ(I) obs: 1.8 / % possible all: 92.6

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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 3H6G

3h6g


Resolution: 2.901→44.313 Å / SU ML: 0.32 / Cross valid method: THROUGHOUT / σ(F): 1.35 / σ(I): 1 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2542 1623 5.08 %RANDOM
Rwork0.2105 ---
obs0.2127 31930 98.57 %-
all-31930 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 49.483 Å2 / ksol: 0.339 e/Å3
Refinement stepCycle: LAST / Resolution: 2.901→44.313 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6072 0 114 0 6186
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONf_bond_d0.004
X-RAY DIFFRACTIONf_angle_deg0.753
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A2961X-RAY DIFFRACTIONPOSITIONAL0.062
12B2961X-RAY DIFFRACTIONPOSITIONAL0.062
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.901-2.98640.39541110.33982334X-RAY DIFFRACTION92
2.9864-3.08280.33281210.28692432X-RAY DIFFRACTION95
3.0828-3.19290.34251330.2662461X-RAY DIFFRACTION97
3.1929-3.32070.33111300.23952512X-RAY DIFFRACTION99
3.3207-3.47180.28251330.22312573X-RAY DIFFRACTION100
3.4718-3.65470.24631480.20072539X-RAY DIFFRACTION100
3.6547-3.88360.25821450.18552547X-RAY DIFFRACTION100
3.8836-4.18320.19741340.17982555X-RAY DIFFRACTION100
4.1832-4.60380.21071430.162559X-RAY DIFFRACTION100
4.6038-5.26910.19311500.16272567X-RAY DIFFRACTION100
5.2691-6.63490.25891410.19942586X-RAY DIFFRACTION100
6.6349-44.31840.2461340.20542642X-RAY DIFFRACTION100
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)
11.26310.27550.33521.0011-0.34820.96170.1749-0.2116-0.0083-0.0422-0.22550.52490.1232-0.37350.02390.378-0.01040.16510.37690.04811.2632-54.3025-66.14872.8603
20.7839-2.38720.45041.5712-1.46171.2209-0.01580.2159-0.44290.12230.02060.4715-0.2395-0.1466-0.00110.27330.09240.09680.38170.01681.0391-32.0893-44.2868-7.2989
30.96320.4166-0.05730.4195-0.32341.2608-0.1406-0.3521-0.18070.11250.08290.34630.0973-0.09160.03720.25230.10270.13130.2453-0.02011.0107-39.4191-57.6937.0957
40.2426-0.39170.26890.535-0.2481-0.0696-0.1666-0.1254-0.035-0.0147-0.12040.23110.0282-0.21210.27860.32860.0539-0.09170.4975-0.13881.3953-64.4131-57.5623-25.2813
52.0932-1.87420.5041.96160.21022.3280.06590.0718-0.51390.18840.0480.25170.04110.074-0.10140.20850.0653-0.01520.169-0.09570.9053-47.4274-30.9309-18.6967
60.08511.49830.18230.93491.16771.12580.10170.0174-0.2081-0.5673-0.06850.4515-0.184-0.119-0.03390.38920.1841-0.20930.3842-0.05071.2453-57.2514-48.193-33.7011
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 2:125) or (chain C and resid 1)A2 - 125
2X-RAY DIFFRACTION1(chain A and resid 2:125) or (chain C and resid 1)C1
3X-RAY DIFFRACTION2(chain A and resid 126:191)A126 - 191
4X-RAY DIFFRACTION3(chain A and resid 192:384) or (chain C and resid 3:5)A192 - 384
5X-RAY DIFFRACTION3(chain A and resid 192:384) or (chain C and resid 3:5)C3 - 5
6X-RAY DIFFRACTION4(chain B and resid 1:124) or (chain C and resid 6)B1 - 124
7X-RAY DIFFRACTION4(chain B and resid 1:124) or (chain C and resid 6)C6
8X-RAY DIFFRACTION5(chain B and resid 125:241)B125 - 241
9X-RAY DIFFRACTION6(chain B and resid 242:384) or (chain C and resid 8:10)B242 - 384
10X-RAY DIFFRACTION6(chain B and resid 242:384) or (chain C and resid 8:10)C8 - 10

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