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- PDB-4h8i: Structure of GluK2-LBD in complex with GluAzo -

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Basic information

Entry
Database: PDB / ID: 4h8i
TitleStructure of GluK2-LBD in complex with GluAzo
ComponentsGlutamate receptor, ionotropic kainate 2
KeywordsSIGNALING PROTEIN / membrane protein / glycoprotein / transmembrane protein / ligand-binding domain / ion transport / ion channel / ionotropic glutamate receptor / kainate receptor / GluAzo / PCL / photochromic ligand / MES / synapse / presynaptic cell membrane / postsynaptic cell membrane
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 / extracellularly glutamate-gated ion channel activity / regulation of JNK cascade / kainate selective glutamate receptor activity / ionotropic glutamate receptor complex / behavioral fear response / neuronal action potential / positive regulation of synaptic transmission / glutamate-gated receptor activity / glutamate-gated calcium ion channel activity / ligand-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / presynaptic modulation of chemical synaptic transmission / dendrite cytoplasm / hippocampal mossy fiber to CA3 synapse / regulation of membrane potential / SNARE binding / excitatory postsynaptic potential / synaptic transmission, glutamatergic / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / 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 / scaffold protein binding / chemical synaptic transmission / perikaryon / postsynaptic membrane / neuron apoptotic process / negative regulation of neuron apoptotic process / postsynaptic density / axon / neuronal cell body / glutamatergic synapse / dendrite / ubiquitin protein ligase binding / synapse / identical protein binding / membrane / 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-11W / Glutamate receptor ionotropic, kainate 2
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2 Å
AuthorsReiter, A. / Skerra, A. / Trauner, D. / Schiefner, A.
CitationJournal: Biochemistry / Year: 2013
Title: A photoswitchable neurotransmitter analogue bound to its receptor.
Authors: Reiter, A. / Skerra, A. / Trauner, D. / Schiefner, A.
History
DepositionSep 22, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 25, 2013Provider: repository / Type: Initial release
Revision 1.1Dec 24, 2014Group: Database references
Revision 1.2Jul 26, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 1.3Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Sep 20, 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_ncs_dom_lim / 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_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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)59,4376
Polymers58,7432
Non-polymers6944
Water8,521473
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2700 Å2
ΔGint-24 kcal/mol
Surface area24470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.609, 102.609, 282.513
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: GLY / Beg label comp-ID: GLY / End auth comp-ID: PRO / End label comp-ID: PRO / Refine code: 5 / Auth seq-ID: 254 - 258 / Label seq-ID: 254 - 258

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

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Protein , 1 types, 2 molecules AB

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


Mass: 29371.633 Da / Num. of mol.: 2 / Fragment: SEE REMARK 999
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Glur6, Grik2 / Plasmid: pET22b / Production host: Escherichia coli (E. coli) / Strain (production host): OrigamiB(DE3) / References: UniProt: P42260

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Non-polymers , 5 types, 477 molecules

#2: Chemical ChemComp-11W / (4R)-4-[(2E)-3-{4-[(E)-phenyldiazenyl]phenyl}prop-2-en-1-yl]-L-glutamic acid / trans-GluAzo


Type: L-peptide linking / Mass: 367.398 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H21N3O4
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 473 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsPROTEIN COMPRISES RESIDUES 429-544 AND RESIDUES 667-806 OF UNP P42260 SEPARATED BY A GT LINKER.

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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: 3.65 Å3/Da / Density % sol: 66.34 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 2.05 M lithium sulfate, 10 mM magnesium chloride, 50 mM MES sodium, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91841 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Apr 28, 2011
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 2→20 Å / Num. all: 60346 / Num. obs: 60248 / % possible obs: 99.8 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 10.6 % / Biso Wilson estimate: 34.3 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 27.54
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
2-2.10.6053.988461580421100
2.1-2.20.46.067073566451100
2.2-2.30.3077.925966255591100
2.3-2.50.21411.229414586881100
2.5-2.70.14816.076843663121100
2.7-30.09324.677149966041100
3-40.04152.03111192104341100
4-60.02578.385726955241100
6-80.02276.21397014051100
8-100.01595.3749775231100
10-200.01494.984438512184.5

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT3.11data extraction
MAR345data collection
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3G3F

3g3f


Resolution: 2→19.92 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.944 / WRfactor Rfree: 0.1857 / WRfactor Rwork: 0.158 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8846 / SU B: 5.078 / SU ML: 0.077 / SU R Cruickshank DPI: 0.1224 / SU Rfree: 0.1182 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.122 / ESU R Free: 0.118 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2039 3042 5 %RANDOM
Rwork0.1734 ---
obs0.175 60245 99.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 171.1 Å2 / Biso mean: 36.3453 Å2 / Biso min: 10.5 Å2
Baniso -1Baniso -2Baniso -3
1-0.49 Å20.25 Å20 Å2
2--0.49 Å20 Å2
3----0.74 Å2
Refinement stepCycle: LAST / Resolution: 2→19.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4082 0 45 473 4600
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0224251
X-RAY DIFFRACTIONr_angle_refined_deg1.5731.9785738
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9795520
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.47124.18189
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.26315786
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.1411527
X-RAY DIFFRACTIONr_chiral_restr0.1150.2628
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0213162
X-RAY DIFFRACTIONr_mcbond_it0.9771.52561
X-RAY DIFFRACTIONr_mcangle_it1.8332.54144
X-RAY DIFFRACTIONr_scbond_it3.733.51690
X-RAY DIFFRACTIONr_scangle_it6.217101592
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

NumberTypeRms dev position (Å)Weight position
20MEDIUM POSITIONAL0.410.5
9LOOSE POSITIONAL0.75
20MEDIUM THERMAL1.472
9LOOSE THERMAL1.0910
LS refinement shellResolution: 2→2.051 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.272 217 -
Rwork0.219 4115 -
all-4332 -
obs--99.98 %
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)
12.7922-1.07991.07671.5285-0.78492.041-0.0004-0.10680.17880.05770.0006-0.0272-0.21830.0135-0.00020.0618-0.0024-0.01780.0362-0.0270.04373.9782-27.994211.3932
22.28140.1805-0.86151.9226-0.60483.45410.1234-0.41830.01170.4273-0.06510.5008-0.2849-0.4733-0.05830.17390.00050.02710.2581-0.03910.223-12.7606-32.933517.3403
329.0816.195225.464322.603320.790325.52252.49422.16610.06540.212-2.4899-0.41531.43010.0789-0.00431.66930.0187-0.03181.4150.3141.2153-7.5665-52.753221.4856
42.4107-0.26720.7742.0014-0.22732.1275-0.01410.09470.1754-0.05740.050.0136-0.1583-0.0931-0.03590.04920.0317-0.01350.03010.00020.0283-18.1259-26.8693-15.2697
54.2261-0.17980.65783.19520.92682.00290.04220.175-0.43810.16610.0718-0.390.18750.2293-0.1140.07740.0304-0.0240.0872-0.01740.1019-19.1317-53.325-6.9438
63.13781.0924-0.15373.85690.14262.4361-0.0651-0.18890.27870.26870.08330.2839-0.0849-0.1477-0.01820.0750.0621-0.01430.0622-0.02910.0487-19.6263-27.2558-2.6111
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 107
2X-RAY DIFFRACTION2A108 - 253
3X-RAY DIFFRACTION3A254 - 258
4X-RAY DIFFRACTION4B3 - 109
5X-RAY DIFFRACTION5B110 - 213
6X-RAY DIFFRACTION6B214 - 258

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