[English] 日本語
Yorodumi
- PDB-5dex: Crystal structure of GluN1/GluN2A NMDA receptor agonist binding d... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5dex
TitleCrystal structure of GluN1/GluN2A NMDA receptor agonist binding domains with glycine and antagonist, phenyl-ACEPC
Components
  • Glutamate receptor ionotropic, NMDA 1
  • Glutamate receptor ionotropic, NMDA 2A
KeywordsTRANSPORT PROTEIN / RECEPTOR
Function / homology
Function and homology information


regulation of response to alcohol / response to ammonium ion / neurotransmitter receptor transport, plasma membrane to endosome / receptor recycling / response to environmental enrichment / directional locomotion / pons maturation / EPHB-mediated forward signaling / Assembly and cell surface presentation of NMDA receptors / regulation of cell communication ...regulation of response to alcohol / response to ammonium ion / neurotransmitter receptor transport, plasma membrane to endosome / receptor recycling / response to environmental enrichment / directional locomotion / pons maturation / EPHB-mediated forward signaling / Assembly and cell surface presentation of NMDA receptors / regulation of cell communication / auditory behavior / positive regulation of Schwann cell migration / olfactory learning / response to hydrogen sulfide / response to other organism / cellular response to magnesium ion / dendritic branch / conditioned taste aversion / response to methylmercury / protein localization to postsynaptic membrane / serotonin metabolic process / regulation of ARF protein signal transduction / regulation of respiratory gaseous exchange / response to manganese ion / transmitter-gated monoatomic ion channel activity / suckling behavior / sleep / positive regulation of inhibitory postsynaptic potential / response to carbohydrate / cellular response to dsRNA / cellular response to lipid / propylene metabolic process / response to glycine / regulation of NMDA receptor activity / dendritic spine organization / RAF/MAP kinase cascade / locomotion / response to amine / neurotransmitter receptor complex / Synaptic adhesion-like molecules / response to glycoside / regulation of monoatomic cation transmembrane transport / NMDA glutamate receptor activity / voltage-gated monoatomic cation channel activity / NMDA selective glutamate receptor complex / glutamate binding / ligand-gated sodium channel activity / glutamate receptor signaling pathway / neuromuscular process / regulation of axonogenesis / calcium ion transmembrane import into cytosol / response to morphine / regulation of dendrite morphogenesis / male mating behavior / protein heterotetramerization / regulation of synapse assembly / spinal cord development / glycine binding / startle response / positive regulation of reactive oxygen species biosynthetic process / dopamine metabolic process / response to lithium ion / cellular response to zinc ion / parallel fiber to Purkinje cell synapse / monoatomic ion channel complex / regulation of postsynaptic membrane potential / monoatomic cation transmembrane transport / action potential / positive regulation of calcium ion transport into cytosol / cellular response to glycine / associative learning / positive regulation of dendritic spine maintenance / modulation of excitatory postsynaptic potential / response to light stimulus / Unblocking of NMDA receptors, glutamate binding and activation / regulation of neuronal synaptic plasticity / positive regulation of protein targeting to membrane / monoatomic cation transport / glutamate receptor binding / conditioned place preference / prepulse inhibition / social behavior / ligand-gated monoatomic ion channel activity / neuron development / multicellular organismal response to stress / long-term memory / phosphatase binding / postsynaptic density, intracellular component / response to fungicide / monoatomic cation channel activity / synaptic cleft / calcium ion homeostasis / positive regulation of synaptic transmission, glutamatergic / cellular response to manganese ion / glutamate-gated receptor activity / glutamate-gated calcium ion channel activity / presynaptic active zone membrane / excitatory synapse / cell adhesion molecule binding / sensory perception of pain
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 / Ligand-gated ion channel / Ionotropic glutamate receptor, L-glutamate and glycine-binding domain / Ligated ion channel L-glutamate- and glycine-binding site / : ...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 / 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. / Periplasmic binding protein-like II / Receptor, ligand binding region / Receptor family ligand binding region / D-Maltodextrin-Binding Protein; domain 2 / Periplasmic binding protein-like I / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-5E0 / GLYCINE / Glutamate receptor ionotropic, NMDA 1 / Glutamate receptor ionotropic, NMDA 2A
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsMou, T.-C. / Conti, P. / Pinto, A. / Tamborini, L. / Sprang, S.R. / Hansen, K.B.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P20GM103546 United States
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2017
Title: Structural basis of subunit selectivity for competitive NMDA receptor antagonists with preference for GluN2A over GluN2B subunits.
Authors: Lind, G.E. / Mou, T.C. / Tamborini, L. / Pomper, M.G. / De Micheli, C. / Conti, P. / Pinto, A. / Hansen, K.B.
History
DepositionAug 26, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 14, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 2, 2017Group: Database references / Derived calculations
Category: citation / citation_author / pdbx_struct_oper_list
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Aug 23, 2017Group: Author supporting evidence / Database references / Category: citation / citation_author / pdbx_audit_support
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed ..._citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name / _pdbx_audit_support.funding_organization
Revision 1.3Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Sep 27, 2023Group: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.5Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Glutamate receptor ionotropic, NMDA 1
B: Glutamate receptor ionotropic, NMDA 2A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,4764
Polymers65,1252
Non-polymers3502
Water2,684149
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2330 Å2
ΔGint-4 kcal/mol
Surface area25230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.629, 87.302, 122.572
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Glutamate receptor ionotropic, NMDA 1 / GluN1 / Glutamate [NMDA] receptor subunit zeta-1 / N-methyl-D-aspartate receptor subunit NR1 / NMD-R1


Mass: 33340.031 Da / Num. of mol.: 1 / Fragment: UNP residues 394-544, 663-800
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Grin1, Nmdar1 / Production host: Escherichia coli (E. coli) / References: UniProt: P35439
#2: Protein Glutamate receptor ionotropic, NMDA 2A / GluN2A / Glutamate [NMDA] receptor subunit epsilon-1 / N-methyl D-aspartate receptor subtype 2A / NR2A


Mass: 31785.299 Da / Num. of mol.: 1 / Fragment: UNP residues 402-539, 661-802
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Grin2a / Production host: Escherichia coli (E. coli) / References: UniProt: Q00959
#3: Chemical ChemComp-GLY / GLYCINE


Type: peptide linking / Mass: 75.067 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H5NO2
#4: Chemical ChemComp-5E0 / 5-[(2R)-2-amino-2-carboxyethyl]-1-phenyl-1H-pyrazole-3-carboxylic acid


Mass: 275.260 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H13N3O4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 149 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsAUTHORS STATE THAT THIS SEQUENCE CORRESPONDS TO THE NCBI REFERENCE SEQUENCE NP_036705.3 FOR GLUN2A. ...AUTHORS STATE THAT THIS SEQUENCE CORRESPONDS TO THE NCBI REFERENCE SEQUENCE NP_036705.3 FOR GLUN2A. RESIDUE THR 758 IN THIS SEQUENCE IS A SER758 IN UNP Q00959.

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.24 Å3/Da / Density % sol: 45.19 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: AMMONIUM ACETATE, PEG 4000

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9794 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 12, 2015
RadiationMonochromator: sI (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2.4→20 Å / Num. obs: 25970 / % possible obs: 97.7 % / Redundancy: 4.4 % / Net I/σ(I): 6.69
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 3 % / Mean I/σ(I) obs: 1.37 / % possible all: 90.6

-
Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4NF8

4nf8


Resolution: 2.4→14.969 Å / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 28.01 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2854 1783 7.7 %
Rwork0.2067 --
obs0.2129 23150 98.46 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.4→14.969 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4361 0 25 149 4535
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0134479
X-RAY DIFFRACTIONf_angle_d1.1846047
X-RAY DIFFRACTIONf_dihedral_angle_d16.3032688
X-RAY DIFFRACTIONf_chiral_restr0.063669
X-RAY DIFFRACTIONf_plane_restr0.008772
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.46460.37071310.30221555X-RAY DIFFRACTION95
2.4646-2.53680.37581310.28551571X-RAY DIFFRACTION96
2.5368-2.61830.35321290.28051573X-RAY DIFFRACTION96
2.6183-2.71130.34771350.28411605X-RAY DIFFRACTION97
2.7113-2.81920.35151350.25931621X-RAY DIFFRACTION99
2.8192-2.94660.34151380.2411643X-RAY DIFFRACTION99
2.9466-3.10060.31611370.24321653X-RAY DIFFRACTION100
3.1006-3.2930.29471360.2251634X-RAY DIFFRACTION99
3.293-3.54410.2911390.20381659X-RAY DIFFRACTION100
3.5441-3.89510.26511400.18161680X-RAY DIFFRACTION100
3.8951-4.44570.2351400.15511683X-RAY DIFFRACTION100
4.4457-5.55320.22231430.15351710X-RAY DIFFRACTION100
5.5532-14.96930.25031490.17471780X-RAY DIFFRACTION100

+
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