[English] 日本語
Yorodumi
- PDB-5m2v: Structure of GluK1 ligand-binding domain (S1S2) in complex with (... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5m2v
TitleStructure of GluK1 ligand-binding domain (S1S2) in complex with (2S,4R)-4-(2-carboxyphenoxy)pyrrolidine-2-carboxylic acid at 3.18 A resolution
ComponentsGlutamate receptor ionotropic, kainate 1,Glutamate receptor ionotropic, kainate 1
KeywordsMEMBRANE PROTEIN / Kainate receptor ligand-binding domain / GluK1-LBD / GluK1-S1S2 / antagonist
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 / regulation of synaptic plasticity / modulation of chemical synaptic transmission / 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-7E5 / Glutamate receptor ionotropic, kainate 1
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.18 Å
AuthorsFrydenvang, K. / Kastrup, J.S. / Kristensen, C.M.
Citation
Journal: J. Med. Chem. / Year: 2017
Title: Design and Synthesis of a Series of l-trans-4-Substituted Prolines as Selective Antagonists for the Ionotropic Glutamate Receptors Including Functional and X-ray Crystallographic Studies of ...Title: Design and Synthesis of a Series of l-trans-4-Substituted Prolines as Selective Antagonists for the Ionotropic Glutamate Receptors Including Functional and X-ray Crystallographic Studies of New Subtype Selective Kainic Acid Receptor Subtype 1 (GluK1) Antagonist (2S,4R)-4-(2-Carboxyphenoxy)pyrrolidine-2-carboxylic Acid.
Authors: Krogsgaard-Larsen, N. / Delgar, C.G. / Koch, K. / Brown, P.M. / Moller, C. / Han, L. / Huynh, T.H. / Hansen, S.W. / Nielsen, B. / Bowie, D. / Pickering, D.S. / Kastrup, J.S. / Frydenvang, K. / Bunch, L.
#1: Journal: FEBS Lett. / Year: 2005
Title: Crystal structure of the kainate receptor GluR5 ligand-binding core in complex with (S)-glutamate.
Authors: Naur, P. / Vestergaard, B. / Skov, L.K. / Egebjerg, J. / Gajhede, M. / Kastrup, J.S.
History
DepositionOct 13, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 11, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 25, 2017Group: Database references
Revision 1.2Aug 9, 2017Group: Data collection / Database references / Category: citation_author / diffrn_source
Item: _citation_author.name / _diffrn_source.pdbx_synchrotron_site
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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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 1.4Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

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


Theoretical massNumber of molelcules
Total (without water)59,36712
Polymers58,2172
Non-polymers1,15010
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3080 Å2
ΔGint-86 kcal/mol
Surface area24210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.986, 71.986, 233.363
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and ((resid 5 and (name N or name...
21(chain B and ((resid 5 and (name O or name...

NCS domain segments:

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

Dom-IDComponent-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11THRTHR(chain A and ((resid 5 and (name N or name...AA55
12PROPRO(chain A and ((resid 5 and (name N or name...AA5 - 2575 - 257
13PROPRO(chain A and ((resid 5 and (name N or name...AA5 - 2575 - 257
14PROPRO(chain A and ((resid 5 and (name N or name...AA5 - 2575 - 257
15PROPRO(chain A and ((resid 5 and (name N or name...AA5 - 2575 - 257
16PROPRO(chain A and ((resid 5 and (name N or name...AA5 - 2575 - 257
21THRTHR(chain B and ((resid 5 and (name O or name...BB55
22PROPRO(chain B and ((resid 5 and (name O or name...BB5 - 2575 - 257
23PROPRO(chain B and ((resid 5 and (name O or name...BB5 - 2575 - 257
24PROPRO(chain B and ((resid 5 and (name O or name...BB5 - 2575 - 257
25PROPRO(chain B and ((resid 5 and (name O or name...BB5 - 2575 - 257
26PROPRO(chain B and ((resid 5 and (name O or name...BB5 - 2575 - 257

-
Components

#1: Protein Glutamate receptor ionotropic, kainate 1,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: Native GluK1 is a membrane protein. The protein crystallized is the extracellular ligand-binding domain of GluK1. Transmembrane regions were genetically removed and replaced with a Gly-Thr ...Details: Native GluK1 is a membrane protein. The protein crystallized is the extracellular ligand-binding domain of GluK1. Transmembrane regions were genetically removed and replaced with a Gly-Thr linker (residue 117-118). The sequence matches discontinously with reference database (430-544, 667-805). Gly1 is a cloning remnance. isoform GluR5-2. The conflict of Gly34 is refered to Ala - Gly sequence conflict at residue 462 in UNP database
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
#2: Chemical ChemComp-7E5 / (2~{S},4~{R})-4-(2-carboxyphenoxy)pyrrolidine-2-carboxylic acid


Mass: 251.235 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H13NO5
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.63 Å3/Da / Density % sol: 53.28 %
Crystal growTemperature: 280 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 15.2% PEG4000, 0.3 M lithium sulfate, 0.1 M cacodylate buffer pH 6.5

-
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 11, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.18→29.75 Å / Num. obs: 11055 / % possible obs: 99.8 % / Redundancy: 6.5 % / Biso Wilson estimate: 55.42 Å2 / Rsym value: 0.14 / Net I/av σ(I): 4.353 / Net I/σ(I): 10.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
3.18-3.356.70.4061.91100
3.35-3.566.70.2862.71100
3.56-3.86.70.2712.61100
3.8-4.116.70.1495.11100
4.11-4.56.60.1096.51100
4.5-5.036.50.09871100
5.03-5.816.40.1026.71100
5.81-7.116.30.0996.61100
7.11-10.065.90.0687.71100
10.06-29.175.20.0695.9194.2

-
Processing

Software
NameVersionClassification
SCALA3.3.16data scaling
PHENIX1.10_2155refinement
PDB_EXTRACT3.2data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1VSO

1vso


Resolution: 3.18→29.17 Å / SU ML: 0.47 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 27.1
RfactorNum. reflection% reflectionSelection details
Rfree0.2714 524 4.77 %Random selection
Rwork0.2188 ---
obs0.2214 10984 99.8 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 134.13 Å2 / Biso mean: 50.3727 Å2 / Biso min: 18.1 Å2
Refinement stepCycle: final / Resolution: 3.18→29.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4016 0 68 0 4084
Biso mean--70.32 --
Num. residues----504
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0024157
X-RAY DIFFRACTIONf_angle_d0.4695613
X-RAY DIFFRACTIONf_chiral_restr0.041617
X-RAY DIFFRACTIONf_plane_restr0.005700
X-RAY DIFFRACTIONf_dihedral_angle_d9.9462489
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2390X-RAY DIFFRACTION4.343TORSIONAL
12B2390X-RAY DIFFRACTION4.343TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 4 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
3.18-3.49960.3761080.272825602668
3.4996-4.00490.33461440.278725502694
4.0049-5.04150.25061310.187925902721
5.0415-29.17160.20591410.18427602901

+
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