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- PDB-5nf6: Structure of GluK3 ligand-binding domain (S1S2) in complex with C... -

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Basic information

Entry
Database: PDB / ID: 5nf6
TitleStructure of GluK3 ligand-binding domain (S1S2) in complex with CIP-AS at 2.55 A resolution
ComponentsGlutamate receptor ionotropic, kainate 3,Glutamate receptor ionotropic, kainate 3
KeywordsMEMBRANE PROTEIN / IONOTROPIC GLUTAMATE RECEPTOR / KAINATE RECEPTOR / LIGAND-BINDING DOMAIN / GLUK3 / GLUR7 / AGONIST
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
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 ...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 II / Periplasmic binding protein-like I / D-Maltodextrin-Binding Protein; domain 2 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-8VN / ACETATE ION / Glutamate receptor ionotropic, kainate 3
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.55 Å
AuthorsFrydenvang, K. / Venskutonyte, R. / Thorsen, T.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 13, 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 1.2Jan 17, 2024Group: 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 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)59,25614
Polymers58,1852
Non-polymers1,07112
Water1,56787
1
A: Glutamate receptor ionotropic, kainate 3,Glutamate receptor ionotropic, kainate 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,4895
Polymers29,0921
Non-polymers3964
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Glutamate receptor ionotropic, kainate 3,Glutamate receptor ionotropic, kainate 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,7689
Polymers29,0921
Non-polymers6758
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)130.138, 56.071, 87.516
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number17
Space group name H-MP2221
Components on special symmetry positions
IDModelComponents
11B-303-

ZN

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111(CHAIN A AND (RESSEQ 5:8 OR (RESID 9 AND (NAME...
211(CHAIN B AND (RESSEQ 5:8 OR (RESID 9 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 3,Glutamate receptor ionotropic, kainate 3 / GluK3 / Glutamate receptor 7 / GluR7


Mass: 29092.453 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: THE PROTEIN CRYSTALLIZED IS THE EXTRACELLULAR LIGAND-BINDING DOMAIN OF GLUK3. TRANSMEMBRANE REGIONS WERE REPLACED WITH A GLY-THR LINKER (RESIDUES 117-118). THE SEQUENCE MATCHES ...Details: THE PROTEIN CRYSTALLIZED IS THE EXTRACELLULAR LIGAND-BINDING DOMAIN OF GLUK3. TRANSMEMBRANE REGIONS WERE REPLACED WITH A GLY-THR LINKER (RESIDUES 117-118). THE SEQUENCE MATCHES DISCONTINOUSLY WITH REFERENCE DATABASE (432-546, 669-806). THE FIRST THREE RESIDUES GLY-PRO-GLY ARE CLONING REMNANTS.
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Grik3, Glur7 / Plasmid: POPINJ / Production host: Escherichia coli (E. coli) / Variant (production host): Origami 2 / References: UniProt: P42264

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Non-polymers , 6 types, 99 molecules

#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-8VN / (3~{a}~{S},4~{S},6~{a}~{R})-4,5,6,6~{a}-tetrahydro-3~{a}~{H}-pyrrolo[3,4-d][1,2]oxazole-3,4-dicarboxylic acid


Mass: 200.149 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H8N2O5
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 87 / 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: 2.77 Å3/Da / Density % sol: 55.65 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 20% PEG8000, 5 mM Zinc Acetate, 0.1 M Tris pH 8.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I911-3 / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 21, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.55→47.21 Å / Num. obs: 21596 / % possible obs: 100 % / Redundancy: 6.1 % / Biso Wilson estimate: 38.96 Å2 / Rsym value: 0.076 / Net I/σ(I): 20
Reflection shellResolution: 2.55→2.69 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.484 / Mean I/σ(I) obs: 1.6 / Rsym value: 0.484 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIXrefinement
SCALA3.3.22data scaling
PDB_EXTRACT3.22data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3U92

3u92


Resolution: 2.55→42.48 Å / SU ML: 0.32 / Cross valid method: THROUGHOUT / σ(F): 1.29 / Phase error: 24.75
RfactorNum. reflection% reflection
Rfree0.246 1106 5.13 %
Rwork0.2 --
obs0.202 21573 100 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 55.8 Å2
Refinement stepCycle: LAST / Resolution: 2.55→42.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4022 0 51 87 4160
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0024154
X-RAY DIFFRACTIONf_angle_d0.5285595
X-RAY DIFFRACTIONf_dihedral_angle_d11.6252503
X-RAY DIFFRACTIONf_chiral_restr0.039619
X-RAY DIFFRACTIONf_plane_restr0.003705
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDType
11A2429X-RAY DIFFRACTIONPOSITIONAL
12B2429X-RAY DIFFRACTIONPOSITIONAL
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.55-2.66610.321320.25352513X-RAY DIFFRACTION100
2.6661-2.80660.281230.24352517X-RAY DIFFRACTION100
2.8066-2.98240.31021240.24142520X-RAY DIFFRACTION100
2.9824-3.21260.2931400.23752518X-RAY DIFFRACTION100
3.2126-3.53580.23731370.21422555X-RAY DIFFRACTION100
3.5358-4.0470.23481540.19332534X-RAY DIFFRACTION100
4.047-5.09750.19671470.15552596X-RAY DIFFRACTION100
5.0975-42.4820.2351490.18122714X-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)
15.6877-0.65-0.36953.5722-0.03781.9667-0.25170.5256-0.00060.01170.1129-0.2081-0.03310.37160.13870.3216-0.0852-0.00750.3197-0.07120.168357.40276.777397.8277
24.0633-0.6783-0.46092.26720.41244.0112-0.3143-0.03740.75270.11550.1611-0.0381-0.59360.15770.12720.3939-0.021-0.10070.2586-0.07810.308448.747618.9116104.8737
33.5016-0.3463-0.41911.56710.17753.0282-0.3564-0.89990.51360.47180.14390.0144-0.1779-0.05710.17970.42470.0656-0.0440.4852-0.17330.309145.524615.6072116.0349
45.60232.2715-1.237.4315.34936.3401-0.2182-0.4625-0.264-0.0299-0.4441-0.17241.0664-0.37850.34330.3769-0.07790.07230.2238-0.04510.301745.7982-1.798105.1776
51.58140.82410.59811.6561-0.44823.5162-0.120.2997-1.2022-0.06010.10140.96370.6988-0.4510.17440.4248-0.11260.04490.3832-0.15780.934215.1685-20.665495.2045
64.3934-0.5072-1.1832.080.1292.78790.1628-0.7742-0.25040.64080.01050.36990.11680.12360.01360.3965-0.09730.17030.31940.0010.309523.3745-7.9041106.5355
74.742-0.9741-1.56222.2482-0.03182.28650.3008-0.65860.14460.3765-0.09730.5311-0.3830.1086-0.1440.4129-0.11550.17510.3623-0.03210.4319.5405-2.4016106.2381
80.02820.09080.19293.491-0.72854.43370.85930.8148-0.8756-0.1356-0.39381.3395-0.7902-1.0180.18210.26870.1505-0.02550.6787-0.08690.636612.0138-5.288.3385
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN 'B' AND (RESID 4 THROUGH 47 )
2X-RAY DIFFRACTION2CHAIN 'B' AND (RESID 48 THROUGH 122 )
3X-RAY DIFFRACTION3CHAIN 'B' AND (RESID 123 THROUGH 238 )
4X-RAY DIFFRACTION4CHAIN 'B' AND (RESID 239 THROUGH 255 )
5X-RAY DIFFRACTION5CHAIN 'A' AND (RESID 3 THROUGH 47 )
6X-RAY DIFFRACTION6CHAIN 'A' AND (RESID 48 THROUGH 132 )
7X-RAY DIFFRACTION7CHAIN 'A' AND (RESID 133 THROUGH 238 )
8X-RAY DIFFRACTION8CHAIN 'A' AND (RESID 239 THROUGH 256 )

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