[English] 日本語
Yorodumi
- PDB-4nf8: Crystal structure of GluN1/GluN2A ligand-binding domain in comple... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4nf8
TitleCrystal structure of GluN1/GluN2A ligand-binding domain in complex with glycine and glutamate in PEG2000MME
Components
  • Glutamate receptor ionotropic, NMDA 1
  • Glutamate receptor ionotropic, NMDA 2A
Keywordstransport protein / receptor / glycine and glutamate
Function / homology
Function and homology information


regulation of response to alcohol / response to ammonium ion / response to environmental enrichment / neurotransmitter receptor transport, plasma membrane to endosome / receptor recycling / directional locomotion / auditory behavior / pons maturation / EPHB-mediated forward signaling / positive regulation of Schwann cell migration ...regulation of response to alcohol / response to ammonium ion / response to environmental enrichment / neurotransmitter receptor transport, plasma membrane to endosome / receptor recycling / directional locomotion / auditory behavior / pons maturation / EPHB-mediated forward signaling / positive regulation of Schwann cell migration / Assembly and cell surface presentation of NMDA receptors / regulation of cell communication / response to carbohydrate / suckling behavior / cellular response to magnesium ion / olfactory learning / response to other organism / response to methylmercury / response to hydrogen sulfide / protein localization to postsynaptic membrane / dendritic branch / conditioned taste aversion / sleep / regulation of ARF protein signal transduction / transmitter-gated monoatomic ion channel activity / response to manganese ion / serotonin metabolic process / response to glycoside / cellular response to dsRNA / regulation of respiratory gaseous exchange / cellular response to lipid / propylene metabolic process / response to glycine / dendritic spine organization / locomotion / regulation of NMDA receptor activity / neuromuscular process / RAF/MAP kinase cascade / positive regulation of inhibitory postsynaptic potential / neurotransmitter receptor complex / response to amine / Synaptic adhesion-like molecules / NMDA glutamate receptor activity / regulation of monoatomic cation transmembrane transport / cellular response to zinc ion / NMDA selective glutamate receptor complex / glutamate binding / voltage-gated monoatomic cation channel activity / regulation of axonogenesis / ligand-gated sodium channel activity / response to morphine / calcium ion transmembrane import into cytosol / regulation of synapse assembly / male mating behavior / positive regulation of reactive oxygen species biosynthetic process / startle response / protein heterotetramerization / regulation of dendrite morphogenesis / spinal cord development / dopamine metabolic process / glycine binding / response to lithium ion / parallel fiber to Purkinje cell synapse / positive regulation of calcium ion transport into cytosol / glutamate receptor signaling pathway / social behavior / regulation of neuronal synaptic plasticity / associative learning / regulation of postsynaptic membrane potential / action potential / neuron development / cellular response to glycine / multicellular organismal response to stress / response to light stimulus / modulation of excitatory postsynaptic potential / positive regulation of dendritic spine maintenance / monoatomic cation transmembrane transport / positive regulation of protein targeting to membrane / Unblocking of NMDA receptors, glutamate binding and activation / monoatomic cation transport / glutamate receptor binding / ligand-gated monoatomic ion channel activity / prepulse inhibition / conditioned place preference / long-term memory / calcium ion homeostasis / phosphatase binding / adult locomotory behavior / postsynaptic density, intracellular component / neurogenesis / synaptic cleft / response to fungicide / monoatomic cation channel activity / cellular response to manganese ion / glutamate-gated receptor activity / positive regulation of synaptic transmission, glutamatergic / sensory perception of pain / glutamate-gated calcium ion channel activity / presynaptic active zone membrane / cell adhesion molecule 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 / 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
GLUTAMIC ACID / 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: 1.856 Å
AuthorsJespersen, A. / Tajima, N. / Furukawa, H.
CitationJournal: Neuron / Year: 2014
Title: Structural Insights into Competitive Antagonism in NMDA Receptors.
Authors: Jespersen, A. / Tajima, N. / Fernandez-Cuervo, G. / Garnier-Amblard, E.C. / Furukawa, H.
History
DepositionOct 30, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 12, 2014Provider: repository / Type: Initial release
Revision 1.1Aug 9, 2017Group: Advisory / Refinement description / Source and taxonomy
Category: entity_src_gen / pdbx_unobs_or_zero_occ_atoms / software
Revision 1.2Oct 16, 2024Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms / 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, NMDA 1
B: Glutamate receptor ionotropic, NMDA 2A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,3484
Polymers65,1252
Non-polymers2222
Water10,683593
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2210 Å2
ΔGint-7 kcal/mol
Surface area25960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.377, 89.653, 125.414
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: Ligand-binding domain, unp residues 393-543; unp residues 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


Mass: 31785.299 Da / Num. of mol.: 1
Fragment: Ligand-binding domain; unp residues 402-539; unp residues 661-802
Mutation: S758T
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-GLU / GLUTAMIC ACID


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


Mass: 18.015 Da / Num. of mol.: 593 / 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: 2.35 Å3/Da / Density % sol: 47.59 %
Crystal growTemperature: 300 K / Method: vapor diffusion / pH: 7
Details: PEG2000MME and HEPES, pH 7, VAPOR DIFFUSION, temperature 300K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.85→50 Å / Num. obs: 51950 / % possible obs: 99.3 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2

-
Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine: 1.8.2_1309)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.856→19.857 Å / SU ML: 0.22 / σ(F): 1.34 / Phase error: 22.94 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2177 2649 5.1 %
Rwork0.1768 --
obs0.1789 51950 98.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.856→19.857 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4493 0 15 593 5101
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074677
X-RAY DIFFRACTIONf_angle_d1.0846328
X-RAY DIFFRACTIONf_dihedral_angle_d14.8391764
X-RAY DIFFRACTIONf_chiral_restr0.078702
X-RAY DIFFRACTIONf_plane_restr0.004816
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8561-1.88990.31491200.2722278X-RAY DIFFRACTION88
1.8899-1.92620.31131290.25252597X-RAY DIFFRACTION100
1.9262-1.96550.24931370.22482565X-RAY DIFFRACTION100
1.9655-2.00820.30051450.22122592X-RAY DIFFRACTION100
2.0082-2.05480.27351620.2162557X-RAY DIFFRACTION100
2.0548-2.10620.28411200.21472600X-RAY DIFFRACTION99
2.1062-2.1630.29551470.20512575X-RAY DIFFRACTION100
2.163-2.22660.26591260.20182582X-RAY DIFFRACTION100
2.2266-2.29840.22631340.19542628X-RAY DIFFRACTION100
2.2984-2.38040.27021250.18452620X-RAY DIFFRACTION100
2.3804-2.47550.23621530.18672610X-RAY DIFFRACTION100
2.4755-2.5880.26581320.18712612X-RAY DIFFRACTION100
2.588-2.72410.22481250.182638X-RAY DIFFRACTION100
2.7241-2.89430.22621310.18562592X-RAY DIFFRACTION99
2.8943-3.1170.22061490.18222625X-RAY DIFFRACTION100
3.117-3.42920.20721600.16582642X-RAY DIFFRACTION100
3.4292-3.92210.17351560.15012653X-RAY DIFFRACTION100
3.9221-4.92890.1731470.13772638X-RAY DIFFRACTION98
4.9289-19.85830.18841510.17182697X-RAY DIFFRACTION96

+
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