[English] 日本語
Yorodumi
- PDB-1pbq: CRYSTAL STRUCTURE OF THE NR1 LIGAND BINDING CORE IN COMPLEX WITH ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1pbq
TitleCRYSTAL STRUCTURE OF THE NR1 LIGAND BINDING CORE IN COMPLEX WITH 5,7-DICHLOROKYNURENIC ACID (DCKA) AT 1.90 ANGSTROMS RESOLUTION
ComponentsN-methyl-D-aspartate Receptor Subunit 1NMDA receptor
KeywordsLIGAND BINDING PROTEIN / Ligand binding receptor / rat / NR1
Function / homology
Function and homology information


pons maturation / regulation of cell communication / positive regulation of Schwann cell migration / EPHB-mediated forward signaling / Assembly and cell surface presentation of NMDA receptors / olfactory learning / conditioned taste aversion / protein localization to postsynaptic membrane / dendritic branch / regulation of respiratory gaseous exchange ...pons maturation / regulation of cell communication / positive regulation of Schwann cell migration / EPHB-mediated forward signaling / Assembly and cell surface presentation of NMDA receptors / olfactory learning / conditioned taste aversion / protein localization to postsynaptic membrane / dendritic branch / regulation of respiratory gaseous exchange / propylene metabolic process / response to glycine / voltage-gated monoatomic cation channel activity / response to morphine / glutamate-gated calcium ion channel activity / regulation of monoatomic cation transmembrane transport / NMDA glutamate receptor activity / NMDA selective glutamate receptor complex / RAF/MAP kinase cascade / Synaptic adhesion-like molecules / parallel fiber to Purkinje cell synapse / calcium ion transmembrane import into cytosol / protein heterotetramerization / glutamate binding / positive regulation of reactive oxygen species biosynthetic process / neuromuscular process / regulation of synapse assembly / glycine binding / positive regulation of calcium ion transport into cytosol / male mating behavior / regulation of neuronal synaptic plasticity / regulation of dendrite morphogenesis / regulation of axonogenesis / suckling behavior / startle response / response to amine / monoatomic cation transmembrane transport / social behavior / positive regulation of excitatory postsynaptic potential / ligand-gated monoatomic ion channel activity / associative learning / monoatomic cation transport / excitatory synapse / positive regulation of dendritic spine maintenance / Unblocking of NMDA receptors, glutamate binding and activation / long-term memory / glutamate receptor binding / phosphatase binding / calcium ion homeostasis / synaptic cleft / cellular response to manganese ion / prepulse inhibition / regulation of neuron apoptotic process / glutamate-gated receptor activity / presynaptic active zone membrane / response to fungicide / monoatomic cation channel activity / sensory perception of pain / dendrite membrane / ligand-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / response to amphetamine / excitatory postsynaptic potential / hippocampal mossy fiber to CA3 synapse / ionotropic glutamate receptor signaling pathway / regulation of membrane potential / positive regulation of synaptic transmission, glutamatergic / adult locomotory behavior / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / synaptic membrane / learning / synaptic transmission, glutamatergic / postsynaptic density membrane / regulation of long-term neuronal synaptic plasticity / regulation of synaptic plasticity / calcium channel activity / visual learning / terminal bouton / intracellular calcium ion homeostasis / synaptic vesicle membrane / response to organic cyclic compound / cerebral cortex development / memory / neuron cellular homeostasis / response to calcium ion / rhythmic process / calcium ion transport / synaptic vesicle / signaling receptor activity / presynaptic membrane / amyloid-beta binding / chemical synaptic transmission / postsynaptic membrane / protein-containing complex assembly / response to ethanol / negative regulation of neuron apoptotic process / dendritic spine / postsynaptic density / transcription by RNA polymerase II / learning or memory / calmodulin binding
Similarity search - Function
Bacterial extracellular solute-binding proteins, family 3 / Solute-binding protein family 3/N-terminal domain of MltF / 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. ...Bacterial extracellular solute-binding proteins, family 3 / Solute-binding protein family 3/N-terminal domain of MltF / 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
5,7-DICHLORO-4-HYDROXYQUINOLINE-2-CARBOXYLIC ACID / Glutamate receptor ionotropic, NMDA 1
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsFurukawa, H. / Gouaux, E.
CitationJournal: Embo J. / Year: 2003
Title: Mechanisms of activation, inhibition and specificity: crystal structures of the NMDA receptor NR1 ligand-binding core
Authors: Furukawa, H. / Gouaux, E.
History
DepositionMay 14, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 29, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 16, 2017Group: Source and taxonomy / Category: entity_src_gen
Revision 1.4Jul 15, 2020Group: Advisory / Database references ...Advisory / Database references / Derived calculations / Structure summary
Category: chem_comp / pdbx_distant_solvent_atoms ...chem_comp / pdbx_distant_solvent_atoms / pdbx_struct_assembly / pdbx_struct_assembly_gen / struct_ref_seq_dif
Item: _chem_comp.pdbx_synonyms / _struct_ref_seq_dif.details
Remark 999SEQUENCE THE FIRST RESIDUE IN THE SEQUENCE, GLY, IS A CLONING ARTIFACT. RESIDUES 153 AND 154, GLY ...SEQUENCE THE FIRST RESIDUE IN THE SEQUENCE, GLY, IS A CLONING ARTIFACT. RESIDUES 153 AND 154, GLY AND THR, ARE INSERTED AS A LINK REPLACING RESIDUES 545 -- 662 OF THE PROTEIN FROM THE GB SEQUENCE ENTRY AAB50932 475566.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: N-methyl-D-aspartate Receptor Subunit 1
B: N-methyl-D-aspartate Receptor Subunit 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,1964
Polymers66,6802
Non-polymers5162
Water9,206511
1
A: N-methyl-D-aspartate Receptor Subunit 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,5982
Polymers33,3401
Non-polymers2581
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: N-methyl-D-aspartate Receptor Subunit 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,5982
Polymers33,3401
Non-polymers2581
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)85.700, 65.300, 124.300
Angle α, β, γ (deg.)90.00, 98.10, 90.00
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein N-methyl-D-aspartate Receptor Subunit 1 / NMDA receptor


Mass: 33340.031 Da / Num. of mol.: 2 / Fragment: Ligand Binding Core
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: GRIN1 OR NMDAR1 / Organ: forebrain / Plasmid: pET22b(+) / Production host: Escherichia coli (E. coli) / Strain (production host): OrigamiB (DE3) / References: UniProt: P35439
#2: Chemical ChemComp-DK1 / 5,7-DICHLORO-4-HYDROXYQUINOLINE-2-CARBOXYLIC ACID / DCKA / 5,7-DICHLOROKYNURENIC ACID / 5,7-Dichlorokynurenic acid


Mass: 258.058 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H5Cl2NO3 / Comment: antagonist*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 511 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.58 Å3/Da / Density % sol: 52.34 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7
Details: PEG2000, HEPES, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K

-
Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.9202 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 4, 2002 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9202 Å / Relative weight: 1
ReflectionResolution: 1.9→20 Å / Num. all: 53903 / Num. obs: 47403 / % possible obs: 88 % / Observed criterion σ(F): 3.25 / Observed criterion σ(I): 12.79 / Biso Wilson estimate: 15.3 Å2
Reflection shellResolution: 1.9→1.97 Å / % possible all: 47.7

-
Processing

Software
NameVersionClassification
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→9.99 Å / Rfactor Rfree error: 0.004 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.27 4694 10.1 %RANDOM
Rwork0.231 ---
obs0.231 46652 87.4 %-
all-47357 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 81.3132 Å2 / ksol: 0.465878 e/Å3
Displacement parametersBiso mean: 28.3 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyzeLuzzati coordinate error free: 0.32 Å / Luzzati sigma a free: 0.27 Å
Refinement stepCycle: LAST / Resolution: 1.9→9.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4072 0 32 511 4615
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d22.1
X-RAY DIFFRACTIONc_improper_angle_d0.78
LS refinement shellResolution: 1.9→2.02 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.35 444 10 %
Rwork0.27 4016 -
obs-4016 50.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2DCKA.PARAMDCKA.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP

+
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