[English] 日本語
Yorodumi
- PDB-7z2r: Differences between the GluD1 and GluD2 receptors revealed by Glu... -

+
Open data


ID or keywords:

Loading...

-
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


glutamate receptor activity / regulation of postsynapse organization / regulation of postsynaptic membrane neurotransmitter receptor levels / social behavior / GABA-ergic synapse / synaptic transmission, glutamatergic / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / postsynaptic density membrane / modulation of chemical synaptic transmission / postsynaptic membrane ...glutamate receptor activity / regulation of postsynapse organization / regulation of postsynaptic membrane neurotransmitter receptor levels / social behavior / GABA-ergic synapse / synaptic transmission, glutamatergic / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / postsynaptic density membrane / modulation of chemical synaptic transmission / postsynaptic membrane / glutamatergic synapse / 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 / Periplasmic binding protein-like I
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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more