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- PDB-5m2v: Structure of GluK1 ligand-binding domain (S1S2) in complex with (... -

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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


gamma-aminobutyric acid secretion / negative regulation of synaptic transmission, GABAergic / 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 / negative regulation of synaptic transmission, glutamatergic / regulation of short-term neuronal synaptic plasticity / inhibitory postsynaptic potential ...gamma-aminobutyric acid secretion / negative regulation of synaptic transmission, GABAergic / 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 / negative regulation of synaptic transmission, glutamatergic / regulation of short-term neuronal synaptic plasticity / inhibitory postsynaptic potential / synaptic transmission, GABAergic / glutamate binding / adult behavior / behavioral response to pain / modulation of excitatory postsynaptic potential / membrane depolarization / kainate selective glutamate receptor activity / ionotropic glutamate receptor complex / extracellularly glutamate-gated ion channel activity / glutamate-gated receptor 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 / excitatory postsynaptic potential / SNARE binding / synaptic transmission, glutamatergic / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / establishment of localization in cell / regulation of membrane potential / positive regulation of synaptic transmission, GABAergic / postsynaptic density membrane / modulation of chemical synaptic transmission / regulation of synaptic plasticity / terminal bouton / presynaptic membrane / nervous system development / scaffold protein binding / chemical synaptic transmission / postsynaptic density / receptor complex / neuronal cell body / glutamatergic synapse / synapse / dendrite / identical protein binding / membrane / 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-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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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

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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

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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: 2.63 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

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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 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

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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

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