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- PDB-7z2r: Differences between the GluD1 and GluD2 receptors revealed by Glu... -

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Basic information

Entry
Database: PDB / ID: 7z2r
TitleDifferences between the GluD1 and GluD2 receptors revealed by GluD1 X-ray crystallography, binding studies and molecular dynamics
ComponentsGlutamate receptor ionotropic, delta-1
KeywordsMEMBRANE PROTEIN / GLUD1 / IONOTROPIC GLUTAMATE RECEPTOR / LIGAND-BINDING DOMAIN / SIGNALLING PROTEIN / DELTA-1 / APO / STRUCTURAL PROTEIN
Function / homology
Function and homology information


GABA receptor activity / trans-synaptic protein complex / negative regulation of synaptic plasticity / G protein-coupled receptor activity involved in regulation of postsynaptic membrane potential / synaptic signaling via neuropeptide / regulation of postsynapse organization / AMPA glutamate receptor activity / AMPA glutamate receptor complex / social behavior / regulation of postsynaptic membrane neurotransmitter receptor levels ...GABA receptor activity / trans-synaptic protein complex / negative regulation of synaptic plasticity / G protein-coupled receptor activity involved in regulation of postsynaptic membrane potential / synaptic signaling via neuropeptide / regulation of postsynapse organization / AMPA glutamate receptor activity / AMPA glutamate receptor complex / social behavior / regulation of postsynaptic membrane neurotransmitter receptor levels / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / synaptic transmission, glutamatergic / postsynaptic density membrane / modulation of chemical synaptic transmission / GABA-ergic synapse / phospholipase C-activating G protein-coupled receptor signaling pathway / dendritic spine / postsynaptic membrane / glutamatergic synapse / metal ion binding / identical protein binding / 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
Glutamate receptor ionotropic, delta-1
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.574 Å
AuthorsMasternak, M. / Laulumaa, S. / Kastrup, J.S.
Funding support Denmark, 1items
OrganizationGrant numberCountry
Danish Council for Independent Research Denmark
CitationJournal: Febs J. / Year: 2023
Title: Differences between the GluD1 and GluD2 receptors revealed by GluD1 X-ray crystallography, binding studies and molecular dynamics.
Authors: Masternak, M. / Koch, A. / Laulumaa, S. / Tapken, D. / Hollmann, M. / Jorgensen, F.S. / Kastrup, J.S.
History
DepositionFeb 28, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 11, 2023Provider: repository / Type: Initial release
Revision 1.1Aug 16, 2023Group: Database references / Refinement description / Category: citation / citation_author / struct_ncs_dom_lim
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.identifier_ORCID / _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 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)59,8557
Polymers59,3752
Non-polymers4805
Water1,69394
1
A: Glutamate receptor ionotropic, delta-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,9764
Polymers29,6881
Non-polymers2883
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Glutamate receptor ionotropic, delta-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,8803
Polymers29,6881
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)33.310, 136.440, 54.610
Angle α, β, γ (deg.)90.000, 96.980, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resseq 1 or (resid 2 and (name...
21(chain B and (resseq 1 or (resid 2 and (name...

NCS domain segments:

Ens-ID: 1 / Beg auth comp-ID: GLY / Beg label comp-ID: GLY

Dom-IDComponent-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLYGLY(chain A and (resseq 1 or (resid 2 and (name...AA11
12GLYGLY(chain A and (resseq 1 or (resid 2 and (name...AA22
13PROPRO(chain A and (resseq 1 or (resid 2 and (name...AA1 - 2581 - 258
14PROPRO(chain A and (resseq 1 or (resid 2 and (name...AA1 - 2581 - 258
15PROPRO(chain A and (resseq 1 or (resid 2 and (name...AA1 - 2581 - 258
16PROPRO(chain A and (resseq 1 or (resid 2 and (name...AA1 - 2581 - 258
17PROPRO(chain A and (resseq 1 or (resid 2 and (name...AA1 - 2581 - 258
21GLYGLY(chain B and (resseq 1 or (resid 2 and (name...BB11
22GLYGLY(chain B and (resseq 1 or (resid 2 and (name...BB22
23HISHIS(chain B and (resseq 1 or (resid 2 and (name...BB1 - 2591 - 259
24HISHIS(chain B and (resseq 1 or (resid 2 and (name...BB1 - 2591 - 259
25HISHIS(chain B and (resseq 1 or (resid 2 and (name...BB1 - 2591 - 259

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Components

#1: Protein Glutamate receptor ionotropic, delta-1 / GluD1 / GluR delta-1 subunit


Mass: 29687.586 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Native GluD1 is a membrane protein. The crystallized protein is a ligand-binding domain of GluD1. Transmembrane regions are replaced with Gly-Thr linker (residues 114-115). Gly1 is a cloning ...Details: Native GluD1 is a membrane protein. The crystallized protein is a ligand-binding domain of GluD1. Transmembrane regions are replaced with Gly-Thr linker (residues 114-115). Gly1 is a cloning remnant. The sequence matches discontinuously with the reference database (436-547 and 664-814).
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Grid1 / Plasmid: pET 22b(+) / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Origami B (DE3) / References: UniProt: Q62640
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 94 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.13 Å3/Da / Density % sol: 42.2 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 24.4% PEG 4000, 0.1M ammonium sulfate, 0.1 cacodylate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: MAX IV / Beamline: BioMAX / Wavelength: 0.79 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 20, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.79 Å / Relative weight: 1
ReflectionResolution: 2.57→68.22 Å / Num. obs: 15301 / % possible obs: 99.8 % / Redundancy: 3.936 % / Biso Wilson estimate: 35.31 Å2 / CC1/2: 0.993 / Rmerge(I) obs: 0.127 / Rrim(I) all: 0.146 / Χ2: 0.932 / Net I/σ(I): 8.73 / Num. measured all: 60218 / Scaling rejects: 4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
2.57-2.643.950.612.114380110711090.7270.705100
2.64-2.713.9520.5462.344363110311040.7590.631100
2.71-2.793.9090.4582.784198108110740.8240.52999.4
2.79-2.883.9080.3953.24099105510490.8550.45999.4
2.88-2.973.8870.3193.9638259859840.9140.36999.9
2.97-3.083.9230.2734.6538689919860.9290.31799.5
3.08-3.193.8920.2135.8636869489470.9590.24799.9
3.19-3.323.8310.1687.1234829089090.980.196100
3.32-3.473.9140.1488.1633508628560.9810.17299.3
3.47-3.644.0180.12210.0234118488490.9850.141100
3.64-3.844.0620.111.9431367747720.990.11599.7
3.84-4.074.0090.08913.4530317587560.9920.10399.7
4.07-4.353.9680.07415.3927667006970.9960.08599.6
4.35-4.73.9070.06517.126106666680.9950.076100
4.7-5.153.9850.07216.4123796005970.9930.08499.5
5.15-5.753.920.08214.1421565525500.9930.09599.6
5.75-6.643.9450.07514.619454944930.9950.08799.8
6.64-8.143.9980.05818.6616234074060.9960.06699.8
8.14-11.514.0220.03725.2412953233220.9990.04399.7
11.51-68.223.5550.03525.366151751730.9980.0498.9

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Processing

Software
NameVersionClassification
PHENIX1.10_2155refinement
PDB_EXTRACT3.24data extraction
AutoProcessdata processing
XSCALEdata scaling
PHASERphasing
TRUNCATEdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2V3T

2v3t


Resolution: 2.574→68.22 Å / SU ML: 0.32 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 25.17
RfactorNum. reflection% reflection
Rfree0.2515 759 4.96 %
Rwork0.2148 --
obs0.2166 15291 99.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 85.59 Å2 / Biso mean: 38.5737 Å2 / Biso min: 23.8 Å2
Refinement stepCycle: final / Resolution: 2.574→68.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4068 0 25 94 4187
Biso mean--44.87 35.62 -
Num. residues----517
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0024175
X-RAY DIFFRACTIONf_angle_d0.5755655
X-RAY DIFFRACTIONf_chiral_restr0.043617
X-RAY DIFFRACTIONf_plane_restr0.004720
X-RAY DIFFRACTIONf_dihedral_angle_d12.9772469
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2649X-RAY DIFFRACTION7.746TORSIONAL
12B2649X-RAY DIFFRACTION7.746TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
2.574-2.77220.31251570.28142906
2.7722-3.05120.3281600.25962878
3.0512-3.49270.25511540.22852873
3.4927-4.40040.23081500.18772909
4.4004-68.220.21241380.19212966
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)
12.8162-0.57680.23582.55330.57781.6847-0.0205-0.2475-0.03790.0556-0.0504-0.15560.03910.17260.06230.18310.0196-0.01110.21680.01790.200629.96283.99221.4002
21.7063-0.2587-1.62020.46580.15065.18990.0473-0.07670.2324-0.08890.08790.22330.0208-0.2047-0.15090.215-0.004-0.01960.29010.01220.229527.600385.3996-0.6925
32.89331.04480.75015.30413.26864.7849-0.18650.119-0.1190.01240.1418-0.47990.14650.5241-0.01960.3090.06650.00330.36380.09140.306736.016377.5612-7.7708
40.99190.592-0.89513.39382.43824.16560.0586-0.45950.2514-0.14790.1967-0.232-0.55150.7947-0.20750.3803-0.0731-0.00240.59690.07540.354438.720791.4136-0.5498
54.03021.2828-3.00492.7733-2.18855.34380.10810.6546-0.2325-0.33530.15840.0714-0.1611-0.4561-0.19620.28130.0055-0.05750.34680.0050.320320.500491.053812.8964
62.08020.1466-0.63641.8456-0.33312.4163-0.0794-0.1049-0.0376-0.01530.02510.3502-0.0805-0.21940.07740.21420.0202-0.02390.235-0.05180.327715.970651.610936.1554
72.0991-0.7082-0.5051.0644-0.23012.60620.16310.559-0.3694-0.36120.01340.0199-0.0035-0.08260.07630.3537-0.0323-0.05420.2325-0.02220.338315.873850.212112.6452
87.9502-1.47550.5779.01171.23595.51190.03490.75710.0194-0.64850.1099-0.20950.08460.1524-0.09630.3931-0.0313-0.01620.321-0.08410.389212.924761.98397.0225
91.35-0.79530.75812.4618-1.57891.87130.237-0.0982-0.7543-0.00640.10981.27130.1145-0.3567-0.26510.2329-0.0065-0.06460.2946-0.05150.49514.055353.267713.8543
101.8925-0.70390.76522.5157-0.13344.02950.08620.3069-0.0898-0.5156-0.01390.05880.17910.3391-0.00740.3108-0.04080.02440.33070.03680.423222.120946.319625.1566
114.4453-1.36763.14252.2066-1.73075.25181.05641.1741-0.4611-0.9587-0.31550.37481.08730.3954-0.19710.38560.0343-0.08370.323-0.00660.458617.491336.031823.5606
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 89 )A1 - 89
2X-RAY DIFFRACTION2chain 'A' and (resid 90 through 125 )A90 - 125
3X-RAY DIFFRACTION3chain 'A' and (resid 126 through 188 )A126 - 188
4X-RAY DIFFRACTION4chain 'A' and (resid 189 through 213 )A189 - 213
5X-RAY DIFFRACTION5chain 'A' and (resid 214 through 258 )A214 - 258
6X-RAY DIFFRACTION6chain 'B' and (resid 1 through 94 )B1 - 94
7X-RAY DIFFRACTION7chain 'B' and (resid 95 through 125 )B95 - 125
8X-RAY DIFFRACTION8chain 'B' and (resid 126 through 164 )B126 - 164
9X-RAY DIFFRACTION9chain 'B' and (resid 165 through 203 )B165 - 203
10X-RAY DIFFRACTION10chain 'B' and (resid 204 through 246 )B204 - 246
11X-RAY DIFFRACTION11chain 'B' and (resid 247 through 259 )B247 - 259

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