[English] 日本語
Yorodumi
- PDB-2a5s: Crystal Structure Of The NR2A Ligand Binding Core In Complex With... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2a5s
TitleCrystal Structure Of The NR2A Ligand Binding Core In Complex With Glutamate
ComponentsN-methyl-D-aspartate receptor NMDAR2A subunit
KeywordsMETAL TRANSPORT / MEMBRANE PROTEIN / Protein-ligand complex
Function / homology
Function and homology information


neurotransmitter receptor transport, plasma membrane to endosome / regulation of response to alcohol / response to ammonium ion / receptor recycling / directional locomotion / response to environmental enrichment / auditory behavior / Assembly and cell surface presentation of NMDA receptors / serotonin metabolic process / response to hydrogen sulfide ...neurotransmitter receptor transport, plasma membrane to endosome / regulation of response to alcohol / response to ammonium ion / receptor recycling / directional locomotion / response to environmental enrichment / auditory behavior / Assembly and cell surface presentation of NMDA receptors / serotonin metabolic process / response to hydrogen sulfide / response to other organism / positive regulation of inhibitory postsynaptic potential / protein localization to postsynaptic membrane / cellular response to magnesium ion / regulation of ARF protein signal transduction / response to methylmercury / conditioned place preference / locomotion / dendritic spine organization / response to carbohydrate / regulation of NMDA receptor activity / sleep / cellular response to dsRNA / cellular response to lipid / Synaptic adhesion-like molecules / regulation of monoatomic cation transmembrane transport / NMDA glutamate receptor activity / voltage-gated monoatomic cation channel activity / response to manganese ion / NMDA selective glutamate receptor complex / cellular response to zinc ion / calcium ion transmembrane import into cytosol / glutamate receptor signaling pathway / glutamate binding / spinal cord development / parallel fiber to Purkinje cell synapse / regulation of postsynaptic membrane potential / response to amine / startle response / dopamine metabolic process / monoatomic cation transmembrane transport / response to lithium ion / modulation of excitatory postsynaptic potential / regulation of neuronal synaptic plasticity / action potential / cellular response to glycine / positive regulation of excitatory postsynaptic potential / response to light stimulus / positive regulation of protein targeting to membrane / Unblocking of NMDA receptors, glutamate binding and activation / cellular response to manganese ion / postsynaptic density, intracellular component / glutamate receptor binding / neuron development / multicellular organismal response to stress / monoatomic cation channel activity / glutamate-gated receptor activity / response to fungicide / cell adhesion molecule binding / glutamate-gated calcium ion channel activity / neurogenesis / ligand-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / dendrite membrane / sensory perception of pain / sodium ion transmembrane transport / response to amphetamine / ionotropic glutamate receptor signaling pathway / cytoplasmic vesicle membrane / positive regulation of synaptic transmission, glutamatergic / protein tyrosine kinase binding / hippocampus development / learning / regulation of membrane potential / excitatory postsynaptic potential / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / synaptic transmission, glutamatergic / cellular response to amino acid stimulus / response to nicotine / response to cocaine / synaptic membrane / modulation of chemical synaptic transmission / regulation of long-term neuronal synaptic plasticity / response to lead ion / protein catabolic process / postsynaptic density membrane / : / terminal bouton / visual learning / cellular response to growth factor stimulus / negative regulation of protein catabolic process / calcium ion transmembrane transport / cerebral cortex development / regulation of synaptic plasticity / calcium channel activity / memory / response to wounding / long-term synaptic potentiation / response to calcium ion / calcium ion transport / calcium-dependent protein binding
Similarity search - Function
Glutamate [NMDA] receptor, epsilon subunit, C-terminal / N-methyl D-aspartate receptor 2B3 C-terminus / 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. ...Glutamate [NMDA] receptor, epsilon subunit, C-terminal / N-methyl D-aspartate receptor 2B3 C-terminus / 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
GLUTAMIC ACID / : / Glutamate receptor ionotropic, NMDA 2A
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Combination of molecular replacement, SAD / Resolution: 1.7 Å
AuthorsFurukawa, H. / Singh, S.K. / Mancusso, R. / Gouaux, E.
CitationJournal: Nature / Year: 2005
Title: Subunit arrangement and function in NMDA receptors
Authors: Furukawa, H. / Singh, S.K. / Mancusso, R. / Gouaux, E.
History
DepositionJun 30, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 15, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 26, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 1.4Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: N-methyl-D-aspartate receptor NMDAR2A subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,0002
Polymers31,8521
Non-polymers1471
Water5,693316
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
A: N-methyl-D-aspartate receptor NMDAR2A subunit
hetero molecules

A: N-methyl-D-aspartate receptor NMDAR2A subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,9994
Polymers63,7052
Non-polymers2942
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_665-y+1,-x+1,-z+1/21
Buried area2790 Å2
ΔGint-11 kcal/mol
Surface area25990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.106, 52.106, 198.675
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Cell settingtetragonal
Space group name H-MP41212

-
Components

#1: Protein N-methyl-D-aspartate receptor NMDAR2A subunit / NMDA receptor NR2A subunit / NMDA receptor NMDAR2A subunit / glutamate receptor / ionotropic / N- ...NMDA receptor NR2A subunit / NMDA receptor NMDAR2A subunit / glutamate receptor / ionotropic / N-methyl D-aspartate 2A


Mass: 31852.391 Da / Num. of mol.: 1 / Fragment: S1S2 ligand-binding core
Source method: isolated from a genetically manipulated source
Details: construct of residues 401-539 and 661-802 of GB AAB58801
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Plasmid: pET22b / Production host: Escherichia coli (E. coli) / Strain (production host): OrigamiB (DE3) / References: UniProt: Q00959, GenBank: 2155310
#2: Chemical ChemComp-GLU / GLUTAMIC ACID


Type: L-peptide linking / Mass: 147.129 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H9NO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 316 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.117 Å3/Da / Density % sol: 42 %
Crystal growTemperature: 277 K / Method: evaporation / pH: 7
Details: PEG 8000, HEPES, calcium acetate, pH 7, EVAPORATION, temperature 277K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 9, 2003
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.7→20 Å / Num. all: 30942 / Num. obs: 30725 / % possible obs: 99.3 % / Biso Wilson estimate: 17.5 Å2

-
Processing

Software
NameVersionClassification
HKL-2000data collection
SCALEPACKdata scaling
SOLVEphasing
CNS1.1refinement
HKL-2000data reduction
RefinementMethod to determine structure: Combination of molecular replacement, SAD
Resolution: 1.7→19.19 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 1859072.89 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.223 3074 10 %RANDOM
Rwork0.196 ---
obs0.1961 30942 98.4 %-
all-30942 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 52.0422 Å2 / ksol: 0.409777 e/Å3
Displacement parametersBiso mean: 19.1 Å2
Baniso -1Baniso -2Baniso -3
1-0.9 Å20 Å20 Å2
2--0.9 Å20 Å2
3----1.8 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.21 Å0.19 Å
Luzzati d res low-5 Å
Luzzati sigma a0.11 Å0.08 Å
Refinement stepCycle: LAST / Resolution: 1.7→19.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2175 0 10 316 2501
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d23
X-RAY DIFFRACTIONc_improper_angle_d0.74
X-RAY DIFFRACTIONc_mcbond_it1.221.5
X-RAY DIFFRACTIONc_mcangle_it1.842
X-RAY DIFFRACTIONc_scbond_it2.192
X-RAY DIFFRACTIONc_scangle_it3.272.5
LS refinement shellResolution: 1.7→1.81 Å / Rfactor Rfree error: 0.011 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.244 458 9.7 %
Rwork0.215 4249 -
obs--92.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2glut.paramglut.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