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- PDB-5neb: Structure of GluK1 ligand-binding domain (S1S2) in complex with L... -

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Basic information

Entry
Database: PDB / ID: 5neb
TitleStructure of GluK1 ligand-binding domain (S1S2) in complex with LM-12b at 2.05 A resolution
ComponentsGlutamate receptor ionotropic, kainate 1
KeywordsMEMBRANE PROTEIN / IONOTROPIC GLUTAMATE RECEPTOR / KAINATE RECEPTOR / LIGAND-BINDING DOMAIN / GLUK1 / GLUR5 / AGONIST
Function / homology
Function and homology information


negative regulation of synaptic transmission, GABAergic / gamma-aminobutyric acid secretion / L-glutamate transmembrane transporter activity / positive regulation of gamma-aminobutyric acid secretion / 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 / glutamate binding ...negative regulation of synaptic transmission, GABAergic / gamma-aminobutyric acid secretion / L-glutamate transmembrane transporter activity / positive regulation of gamma-aminobutyric acid secretion / 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 / glutamate binding / inhibitory postsynaptic potential / synaptic transmission, GABAergic / adult behavior / behavioral response to pain / kainate selective glutamate receptor activity / modulation of excitatory postsynaptic potential / extracellularly glutamate-gated ion channel activity / ionotropic glutamate receptor complex / membrane depolarization / 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 / ionotropic glutamate receptor signaling pathway / SNARE binding / positive regulation of synaptic transmission, GABAergic / regulation of membrane potential / excitatory postsynaptic potential / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / synaptic transmission, glutamatergic / establishment of localization in cell / postsynaptic density membrane / modulation of chemical synaptic transmission / regulation of synaptic plasticity / terminal bouton / nervous system development / presynaptic membrane / scaffold protein binding / chemical synaptic transmission / postsynaptic membrane / receptor complex / postsynaptic density / neuronal cell body / synapse / dendrite / glutamatergic 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-8VE / ACETATE ION / Glutamate receptor ionotropic, kainate 1
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsMoellerud, S. / Frydenvang, K. / Laulumaa, S. / Kastrup, J.S.
CitationJournal: ACS Chem Neurosci / Year: 2017
Title: Structure and Affinity of Two Bicyclic Glutamate Analogues at AMPA and Kainate Receptors.
Authors: Mllerud, S. / Pinto, A. / Marconi, L. / Frydenvang, K. / Thorsen, T.S. / Laulumaa, S. / Venskutonyte, R. / Winther, S. / Moral, A.M.C. / Tamborini, L. / Conti, P. / Pickering, D.S. / Kastrup, J.S.
History
DepositionMar 10, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 26, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2017Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.name
Revision 1.2Mar 7, 2018Group: Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_variant
Revision 1.3Jan 17, 2024Group: 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
Revision 1.4Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Glutamate receptor ionotropic, kainate 1
A: Glutamate receptor ionotropic, kainate 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,79719
Polymers58,2172
Non-polymers1,58017
Water2,540141
1
A: Glutamate receptor ionotropic, kainate 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,7738
Polymers29,1081
Non-polymers6647
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Glutamate receptor ionotropic, kainate 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,02411
Polymers29,1081
Non-polymers91610
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)51.862, 57.839, 89.302
Angle α, β, γ (deg.)90.00, 102.41, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111(CHAIN A AND (RESSEQ 1:15 OR (RESID 16 AND (NAME...
211(CHAIN B AND (RESSEQ 1:15 OR (RESID 16 AND (NAME...

NCS ensembles :
ID
1
2

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Components

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Protein , 1 types, 2 molecules BA

#1: Protein Glutamate receptor ionotropic, kainate 1 / GluK1 / Glutamate receptor 5 / GluR5


Mass: 29108.453 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: THE DATABASE SEQUENCE IS P22756-2, ISOFORM GLUR5-2. THE PROTEIN CRYSTALLIZED IS THE EXTRACELLULAR LIGAND-BINDING DOMAIN OF GLUK1. TRANSMEMBRANE REGIONS WERE REPLACED WITH A GLY-THR LINKER ...Details: THE DATABASE SEQUENCE IS P22756-2, ISOFORM GLUR5-2. THE PROTEIN CRYSTALLIZED IS THE EXTRACELLULAR LIGAND-BINDING DOMAIN OF GLUK1. TRANSMEMBRANE REGIONS WERE REPLACED WITH A GLY-THR LINKER (RESIDUES 117-118). THE SEQUENCE MATCHES DISCONTINOUSLY WITH REFERENCE DATABASE (430-544, 667-805). THERE IS A SEQUENCE CONFLICT AT RESIDUE 34 (462) OF THE CRYSTALLIZED PROTEIN DUE TO DIFFERENCES IN DATABASE SEQUENCE (SEE GENBANK ACCESION NO.AAA02874). GLY1 IS A CLONING REMNANT.
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Grik1, Glur5 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Origami 2 / References: UniProt: P22756

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Non-polymers , 6 types, 158 molecules

#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-8VE / (3~{a}~{R},4~{S},6~{a}~{R})-1-methyl-4,5,6,6~{a}-tetrahydro-3~{a}~{H}-pyrrolo[3,4-c]pyrazole-3,4-dicarboxylic acid


Mass: 213.191 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H11N3O4
#6: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 141 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.25 Å3/Da / Density % sol: 45.44 %
Crystal growTemperature: 279 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 20% PEG4000, 0.3 M lithium sulfate, 0.1 M phosphate-citrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.9751 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Sep 2, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9751 Å / Relative weight: 1
ReflectionResolution: 2.05→87.216 Å / Num. obs: 32564 / % possible obs: 99.7 % / Redundancy: 3.4 % / Biso Wilson estimate: 32.68 Å2 / Rsym value: 0.067 / Net I/σ(I): 10.9
Reflection shellResolution: 2.05→2.16 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.487 / Mean I/σ(I) obs: 1.5 / Rsym value: 0.487 / % possible all: 99.3

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Processing

Software
NameVersionClassification
PHENIXrefinement
SCALA3.3.20data scaling
PDB_EXTRACT3.22data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4E0X

4e0x


Resolution: 2.05→50.65 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 22.85
RfactorNum. reflection% reflection
Rfree0.214 1652 5.08 %
Rwork0.194 --
obs0.195 32547 99.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 48.7 Å2
Refinement stepCycle: LAST / Resolution: 2.05→50.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4035 0 90 141 4266
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0024206
X-RAY DIFFRACTIONf_angle_d0.5285682
X-RAY DIFFRACTIONf_dihedral_angle_d9.6742514
X-RAY DIFFRACTIONf_chiral_restr0.042627
X-RAY DIFFRACTIONf_plane_restr0.003708
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDType
11A2702X-RAY DIFFRACTIONPOSITIONAL
12B2702X-RAY DIFFRACTIONPOSITIONAL
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.05-2.11030.29631380.27042545X-RAY DIFFRACTION99
2.1103-2.17840.3331180.26152575X-RAY DIFFRACTION99
2.1784-2.25630.2691300.25432544X-RAY DIFFRACTION99
2.2563-2.34660.25951430.23992569X-RAY DIFFRACTION100
2.3466-2.45340.27381250.23232540X-RAY DIFFRACTION100
2.4534-2.58280.23731460.23152592X-RAY DIFFRACTION100
2.5828-2.74460.24071470.22632557X-RAY DIFFRACTION100
2.7446-2.95650.23471410.21562562X-RAY DIFFRACTION100
2.9565-3.2540.23021270.19622586X-RAY DIFFRACTION100
3.254-3.72470.19521560.18092577X-RAY DIFFRACTION100
3.7247-4.69220.16031350.15042599X-RAY DIFFRACTION100
4.6922-50.66590.18961460.16212649X-RAY DIFFRACTION99
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)
13.8365-1.5114-0.96952.94180.77421.45820.46040.3230.0921-0.6111-0.51970.4864-0.3344-0.7042-0.01330.40520.1673-0.11870.6026-0.1030.3652-21.22271.8489-7.7018
24.1525-0.81220.40583.13661.69364.1666-0.004-0.1668-0.1276-0.43250.03140.0541-0.4425-0.1745-0.01380.2259-0.02840.02830.19630.00370.1997-4.872-6.5426-7.439
35.7955-0.45460.01723.8534-0.89114.40950.1351-0.50350.4114-0.05770.1002-0.6398-0.71540.6567-0.1290.2956-0.10980.0520.313-0.08610.31937.9652-1.8074-6.4178
44.2885-0.09-0.61724.3016-0.77131.57890.15660.4060.4537-1.17070.0093-0.1758-1.153-0.3293-0.13140.8934-0.00410.12840.20040.01690.2631-0.65662.3793-17.8835
53.0089-0.0265-0.69535.0582.11533.24460.29110.0018-0.3201-0.6477-0.66340.8107-0.1706-0.89190.17390.32180.0578-0.13450.5323-0.10150.4078-20.8056-10.7164-14.8925
65.04640.71030.45922.5591-0.35893.95840.29130.4511-0.2971-0.2575-0.1541-0.2216-0.18870.7524-0.11230.2459-0.01360.04160.3686-0.05050.26548.9002-27.848-35.0018
75.8897-0.64351.80261.5279-0.03022.97120.0796-0.2594-0.3828-0.09760.00130.1951-0.147-0.2734-0.07040.2164-0.03830.00930.1880.00380.1902-10.5822-27.2696-27.7151
85.13420.24950.36252.1434-0.29373.08790.0150.29970.1134-0.1444-0.07260.0943-0.3918-0.23950.03460.27660.05-0.00540.2277-0.02430.2167-14.7148-21.5838-35.2659
93.77991.1261.08162.51460.87413.04980.1883-0.65370.33890.1836-0.1752-0.1409-0.63390.41670.02850.3376-0.14750.08980.4244-0.0470.27547.6252-18.2642-24.6681
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN 'A' AND (RESID 1 THROUGH 65 )
2X-RAY DIFFRACTION2CHAIN 'A' AND (RESID 66 THROUGH 128 )
3X-RAY DIFFRACTION3CHAIN 'A' AND (RESID 129 THROUGH 172 )
4X-RAY DIFFRACTION4CHAIN 'A' AND (RESID 173 THROUGH 216 )
5X-RAY DIFFRACTION5CHAIN 'A' AND (RESID 217 THROUGH 251 )
6X-RAY DIFFRACTION6CHAIN 'B' AND (RESID 1 THROUGH 65 )
7X-RAY DIFFRACTION7CHAIN 'B' AND (RESID 66 THROUGH 151 )
8X-RAY DIFFRACTION8CHAIN 'B' AND (RESID 152 THROUGH 216 )
9X-RAY DIFFRACTION9CHAIN 'B' AND (RESID 217 THROUGH 251 )

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