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- PDB-6jmv: Crystal structure of the GluK3 ligand binding domain complex with... -

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Basic information

Entry
Database: PDB / ID: 6jmv
TitleCrystal structure of the GluK3 ligand binding domain complex with SYM and zinc
ComponentsGlutamate receptor ionotropic, kainate 3
KeywordsMEMBRANE PROTEIN / Glutamate receptor / Kainate / SYM
Function / homology
Function and homology information


Presynaptic function of Kainate receptors / cochlear hair cell ribbon synapse / adenylate cyclase inhibiting G protein-coupled glutamate receptor activity / kainate selective glutamate receptor complex / Activation of Ca-permeable Kainate Receptor / G protein-coupled glutamate receptor signaling pathway / glutamate receptor activity / negative regulation of synaptic transmission, glutamatergic / glutamate receptor signaling pathway / kainate selective glutamate receptor activity ...Presynaptic function of Kainate receptors / cochlear hair cell ribbon synapse / adenylate cyclase inhibiting G protein-coupled glutamate receptor activity / kainate selective glutamate receptor complex / Activation of Ca-permeable Kainate Receptor / G protein-coupled glutamate receptor signaling pathway / glutamate receptor activity / negative regulation of synaptic transmission, glutamatergic / glutamate receptor signaling pathway / kainate selective glutamate receptor activity / 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 / regulation of membrane potential / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / synaptic transmission, glutamatergic / postsynaptic density membrane / modulation of chemical synaptic transmission / terminal bouton / presynaptic membrane / perikaryon / chemical synaptic transmission / postsynaptic membrane / axon / dendrite / glutamatergic synapse / 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
ACETATE ION / 2S,4R-4-METHYLGLUTAMATE / Glutamate receptor ionotropic, kainate 3
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.832 Å
AuthorsKumari, J. / Kumar, J.
Funding support India, 1items
OrganizationGrant numberCountry
Wellcome TrustIA/I/13/2/501023 India
CitationJournal: Sci Rep / Year: 2019
Title: Structural and Functional Insights into GluK3-kainate Receptor Desensitization and Recovery.
Authors: Jyoti Kumari / Rajesh Vinnakota / Janesh Kumar /
Abstract: GluK3-kainate receptors are atypical members of the iGluR family that reside at both the pre- and postsynapse and play a vital role in the regulation of synaptic transmission. For a better ...GluK3-kainate receptors are atypical members of the iGluR family that reside at both the pre- and postsynapse and play a vital role in the regulation of synaptic transmission. For a better understanding of structural changes that underlie receptor functions, GluK3 receptors were trapped in desensitized and resting/closed states and structures analyzed using single particle cryo-electron microscopy. While the desensitized GluK3 has domain organization as seen earlier for another kainate receptor-GluK2, antagonist bound GluK3 trapped a resting state with only two LBD domains in dimeric arrangement necessary for receptor activation. Using structures as a guide, we show that the N-linked glycans at the interface of GluK3 ATD and LBD likely mediate inter-domain interactions and attune receptor-gating properties. The mutational analysis also identified putative N-glycan interacting residues. Our results provide a molecular framework for understanding gating properties unique to GluK3 and exploring the role of N-linked glycosylation in their modulation.
History
DepositionMar 13, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 24, 2019Provider: repository / Type: Initial release
Revision 1.1Jul 31, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Nov 22, 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 / 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.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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.ptnr3_symmetry / _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.ptnr1_symmetry / _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
Revision 1.3Oct 16, 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
A: Glutamate receptor ionotropic, kainate 3
B: Glutamate receptor ionotropic, kainate 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,69125
Polymers58,1072
Non-polymers1,58423
Water5,945330
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A: Glutamate receptor ionotropic, kainate 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,6499
Polymers29,0531
Non-polymers5968
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Glutamate receptor ionotropic, kainate 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,04216
Polymers29,0531
Non-polymers98915
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)56.460, 88.030, 130.470
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number17
Space group name H-MP2212
Components on special symmetry positions
IDModelComponents
11B-303-

ZN

21A-544-

HOH

31A-593-

HOH

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Glutamate receptor ionotropic, kainate 3 / GluK3 / Glutamate receptor 7 / GluR7


Mass: 29053.371 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: GluK3 ligand binding domain, residues 433-546 and 669-807 from P42264 (GRIK3_RAT) linked with linker residues GT.
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Grik3, Glur7 / Production host: Escherichia coli (E. coli) / Strain (production host): Origami B / References: UniProt: P42264

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Non-polymers , 7 types, 353 molecules

#2: Chemical ChemComp-SYM / 2S,4R-4-METHYLGLUTAMATE


Mass: 160.148 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H10NO4
#3: Chemical
ChemComp-CL / CHLORIDE ION


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


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H3O2
#7: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 330 / 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: 2.8 Å3/Da / Density % sol: 56.11 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 50mM HEPES, pH 7.0, 4% PEG 8000, 100mM NaCl

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97242 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 11, 2018
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97242 Å / Relative weight: 1
ReflectionResolution: 1.83→88.03 Å / Num. obs: 57772 / % possible obs: 99.7 % / Redundancy: 4.7 % / CC1/2: 0.995 / Rmerge(I) obs: 0.095 / Rpim(I) all: 0.072 / Rrim(I) all: 0.12 / Net I/σ(I): 7.9
Reflection shellResolution: 1.83→1.87 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.5088 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 3540 / CC1/2: 0.165 / Rpim(I) all: 0.735 / Rrim(I) all: 0.7196 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
PDB_EXTRACT3.24data extraction
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3U93

3u93


Resolution: 1.832→72.973 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 28.08
RfactorNum. reflection% reflectionSelection details
Rfree0.2424 2925 5.07 %Random
Rwork0.2032 ---
obs0.2052 57704 99.46 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.832→72.973 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4039 0 86 330 4455
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.014190
X-RAY DIFFRACTIONf_angle_d0.9975627
X-RAY DIFFRACTIONf_dihedral_angle_d6.5173009
X-RAY DIFFRACTIONf_chiral_restr0.051619
X-RAY DIFFRACTIONf_plane_restr0.006710
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.832-1.86210.46821510.4152549X-RAY DIFFRACTION100
1.8621-1.89420.42821260.39332593X-RAY DIFFRACTION100
1.8942-1.92860.42361270.39672573X-RAY DIFFRACTION100
1.9286-1.96570.38061290.34152607X-RAY DIFFRACTION100
1.9657-2.00580.31041480.29172572X-RAY DIFFRACTION100
2.0058-2.04950.29281510.28082547X-RAY DIFFRACTION100
2.0495-2.09710.31341410.27752571X-RAY DIFFRACTION98
2.0971-2.14960.30591470.24252538X-RAY DIFFRACTION100
2.1496-2.20770.28811170.22862603X-RAY DIFFRACTION100
2.2077-2.27270.33671390.23042612X-RAY DIFFRACTION100
2.2727-2.3460.23121540.20292576X-RAY DIFFRACTION100
2.346-2.42990.24791260.2062627X-RAY DIFFRACTION100
2.4299-2.52720.26141360.18472556X-RAY DIFFRACTION99
2.5272-2.64220.26061330.18742586X-RAY DIFFRACTION99
2.6422-2.78150.22981240.19122645X-RAY DIFFRACTION100
2.7815-2.95580.25191400.17792625X-RAY DIFFRACTION100
2.9558-3.1840.19811460.16542623X-RAY DIFFRACTION100
3.184-3.50440.20191460.16182625X-RAY DIFFRACTION99
3.5044-4.01150.1911410.15582657X-RAY DIFFRACTION100
4.0115-5.05390.18231530.14912663X-RAY DIFFRACTION99
5.0539-73.03130.24941500.23212831X-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)
10.05530.00450.00610.14530.07890.05420.00080.27470.0798-0.21680.08880.2379-0.0981-0.24080.0020.30960.0356-0.09530.48820.03360.3676-22.783310.185114.3958
20.2079-0.1520.05830.3237-0.26720.4557-0.08280.08430.03590.07130.00670.0362-0.10650.0054-0.03260.20150.0512-0.03870.25880.0410.2426-10.562515.723523.6772
30.1487-0.0453-0.37830.29840.04480.978-0.13040.01490.14180.02-0.2394-0.2452-0.6746-0.0425-1.63390.46050.0332-0.12360.22170.09970.31120.696423.264815.8874
40.1321-0.03220.00870.1024-0.08510.0729-0.06620.0565-0.0538-0.00080.0461-0.0540.014-0.1445-00.21860.03650.01920.28430.01940.2303-10.51582.193722.366
50.07950.04230.00390.0275-0.00940.0610.1158-0.1453-0.13120.2860.03680.1265-0.03420.065-0.00010.2763-0.0063-0.00280.2477-0.02230.31076.75149.825557.5579
60.1096-0.0792-0.00680.2434-0.0070.06090.131-0.1388-0.08510.11650.149-0.27430.16390.65590.05530.2680.0167-0.03390.5217-0.11160.3421.594512.094650.8578
70.1595-0.01770.0760.3534-0.47390.65240.13490.0260.2291-0.02350.10730.1038-0.1911-0.10960.73430.5426-0.01030.24030.19160.00760.349411.291637.508841.907
80.05610.05680.1090.08850.12090.21560.12150.07950.17380.07180.1124-0.2558-0.21330.14990.06410.5759-0.27040.17920.4835-0.10530.521923.652335.112244.0049
90.01630.01340.00030.0141-0.00480.00830.1738-0.0440.02640.178-0.00140.069-0.25620.1670.00010.6077-0.14650.11450.3675-0.08060.383615.807735.429455.5127
100.0149-0.00650.00080.009-0.00070.02640.0850.08670.1102-0.1724-0.0454-0.0315-0.34150.03520.01350.59350.02780.08640.23610.03830.30197.648431.148646.1293
110.0193-0.0013-0.00720.00850.01640.03240.00360.1415-0.1444-0.02280.1477-0.0735-0.18360.21980.00030.25260.0413-0.03120.4231-0.07980.368418.31597.922344.8616
120.00080.0007-0.0020.00120.00070.01720.07510.0439-0.024-0.14360.0327-0.02650.11190.1534-00.24890.0831-0.04480.3466-0.09540.29648.91684.375739.2946
130.09370.117-0.15220.1487-0.18660.25270.0575-0.0421-0.08170.12830.14530.4084-0.151-0.10210.05330.25080.1367-0.00440.4009-0.06320.3724-2.059217.631246.1127
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 34 )
2X-RAY DIFFRACTION2chain 'A' and (resid 35 through 128 )
3X-RAY DIFFRACTION3chain 'A' and (resid 129 through 215 )
4X-RAY DIFFRACTION4chain 'A' and (resid 216 through 256 )
5X-RAY DIFFRACTION5chain 'B' and (resid 3 through 47 )
6X-RAY DIFFRACTION6chain 'B' and (resid 48 through 105 )
7X-RAY DIFFRACTION7chain 'B' and (resid 106 through 128 )
8X-RAY DIFFRACTION8chain 'B' and (resid 129 through 163 )
9X-RAY DIFFRACTION9chain 'B' and (resid 164 through 183 )
10X-RAY DIFFRACTION10chain 'B' and (resid 184 through 212 )
11X-RAY DIFFRACTION11chain 'B' and (resid 213 through 225 )
12X-RAY DIFFRACTION12chain 'B' and (resid 226 through 238 )
13X-RAY DIFFRACTION13chain 'B' and (resid 239 through 255 )

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