[English] 日本語
Yorodumi
- PDB-4dld: Crystal structure of the GluK1 ligand-binding domain (S1S2) in co... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4dld
TitleCrystal structure of the GluK1 ligand-binding domain (S1S2) in complex with the antagonist (S)-2-amino-3-(2-(2-carboxyethyl)-5-chloro-4-nitrophenyl)propionic acid at 2.0 A resolution
ComponentsGlutamate receptor, ionotropic kainate 1
KeywordsMEMBRANE PROTEIN / ionotropic glutamate receptor / glutamate / membrane
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-TZG / Glutamate receptor ionotropic, kainate 1
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2 Å
AuthorsVenskutonyte, R. / Frydenvang, K. / Kastrup, J.S.
Citation
Journal: Chemmedchem / Year: 2012
Title: Structural and pharmacological characterization of phenylalanine-based AMPA receptor antagonists at kainate receptors
Authors: Venskutonyte, R. / Frydenvang, K. / Valades, E.A. / Szymanska, E. / Johansen, T.N. / Kastrup, J.S. / Pickering, D.S.
#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
DepositionFeb 6, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 10, 2012Provider: repository / Type: Initial release
Revision 1.1Aug 16, 2017Group: Data collection / Refinement description / Source and taxonomy
Category: diffrn_source / entity_src_gen / software / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.2Nov 8, 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 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

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


Theoretical massNumber of molelcules
Total (without water)59,0747
Polymers58,2172
Non-polymers8575
Water9,026501
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2520 Å2
ΔGint-29 kcal/mol
Surface area23900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.320, 69.320, 234.970
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

-
Components

-
Protein , 1 types, 2 molecules AB

#1: Protein Glutamate receptor, ionotropic kainate 1 / Glutamate receptor 5 / GluR-5 / GluR5


Mass: 29108.453 Da / Num. of mol.: 2 / Fragment: GluK1 Ligand binding domain (GluK1-S1S2)
Source method: isolated from a genetically manipulated source
Details: The protein crystallized is the extracellular ligand binding domain of GluK1. Transmembrane regions were genetically removed and replaced with a Gly-Thr linker.
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Grik1 / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): Origami 2 / References: UniProt: P22756

-
Non-polymers , 5 types, 506 molecules

#2: Chemical ChemComp-TZG / (S)-2-amino-3-(2-(2-carboxyethyl)-5-chloro-4-nitrophenyl)propionic acid


Mass: 316.694 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H13ClN2O6
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 501 / Source method: isolated from a natural source / Formula: H2O

-
Details

Sequence detailsTHE SEQUENCE DATABASE IS P22756-2, ISOFORM GLUR5-2. THE CRYSTALLIZED PROTEIN CONSISTS OF GLY ...THE SEQUENCE DATABASE IS P22756-2, ISOFORM GLUR5-2. THE CRYSTALLIZED PROTEIN CONSISTS OF GLY RESIDUE FOLLOWED BY RESIDUE 430-544 AND 667-805 FROM THE INTACT RECEPTOR LINKED BY A GLY-THR DIPEPTIDE. THERE IS A SEQUENCE CONFLICT AT RESIDUE 34 OF THE CRYSTALLIZED PROTEIN DUE TO DIFFERENCES IN DATABASE SEQUENCE (SEE GENBANK ACCESION NO.AAA02874).

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.42 Å3/Da / Density % sol: 49.26 % / Mosaicity: 0.69 °
Crystal growTemperature: 279 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 17 % PEG4000, 0.1M cacodylic acid, 0.3M lithium sulfate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 279K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I911-2 / Wavelength: 1.038 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Mar 19, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.038 Å / Relative weight: 1
ReflectionResolution: 2→25.877 Å / Num. all: 39813 / Num. obs: 39813 / % possible obs: 99.9 % / Redundancy: 7.9 % / Biso Wilson estimate: 21.09 Å2 / Rsym value: 0.081 / Net I/σ(I): 6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) allRmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRrim(I) allRsym valueNet I/σ(I) obs% possible all
2-2.1180.340.3181.84537256960.1190.340.3186.3100
2.11-2.2480.2430.2271.54334354330.0840.2430.2278.8100
2.24-2.3980.1910.1783.24068150970.0660.1910.17810.9100
2.39-2.5880.1420.1334.23795947620.0490.1420.13313.8100
2.58-2.8380.1080.1016.43490943860.0380.1080.10117.2100
2.83-3.167.90.0770.0726.93204340370.0270.0770.07222.5100
3.16-3.657.90.0560.05312.22813335630.020.0560.05328.8100
3.65-4.477.80.0570.053112380630430.020.0570.05333.799.8
4.47-6.327.70.0630.0598.81851724080.0220.0630.05939.199.5
6.32-25.8777.10.0430.0413.9986813880.0160.0430.0443.197

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.3.9data scaling
PHASERphasing
PHENIX1.7.1_743refinement
PDB_EXTRACT3.1data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2PBW chain A

2pbw


Resolution: 2→25.877 Å / Occupancy max: 1 / Occupancy min: 0.35 / FOM work R set: 0.8385 / SU ML: 0.57 / Isotropic thermal model: Restrained / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 22.61 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.246 1997 5.02 %Random
Rwork0.1864 ---
obs0.1894 39768 99.83 %-
Solvent computationShrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40.268 Å2 / ksol: 0.347 e/Å3
Displacement parametersBiso max: 81.67 Å2 / Biso mean: 24.6097 Å2 / Biso min: 7.05 Å2
Baniso -1Baniso -2Baniso -3
1-2.019 Å20 Å2-0 Å2
2--2.019 Å2-0 Å2
3----4.038 Å2
Refinement stepCycle: LAST / Resolution: 2→25.877 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4058 0 54 501 4613
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074252
X-RAY DIFFRACTIONf_angle_d1.0355744
X-RAY DIFFRACTIONf_chiral_restr0.069629
X-RAY DIFFRACTIONf_plane_restr0.005727
X-RAY DIFFRACTIONf_dihedral_angle_d14.3841632
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection allNum. reflection obs% reflection obs (%)
2-2.050.29431390.2213265627952656100
2.05-2.10540.2791420.2016262227642622100
2.1054-2.16740.26541450.1953266228072662100
2.1674-2.23730.24271270.1804267127982671100
2.2373-2.31720.25611090.192267127802671100
2.3172-2.40990.2751570.1952263927962639100
2.4099-2.51950.28061520.1995264627982646100
2.5195-2.65220.28011600.1975268428442684100
2.6522-2.81820.26611330.205268528182685100
2.8182-3.03550.24751230.198272328462723100
3.0355-3.34040.23691450.1878270028452700100
3.3404-3.82240.25031570.1774272628832726100
3.8224-4.81080.2021630.1507275729202757100
4.8108-25.87960.221450.190729293074292998

+
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://pdbjlvh1.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