[English] 日本語
Yorodumi
- PDB-6uz6: Crystal structure of GLUN1/GLUN2A-4M mutant ligand-binding domain... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6uz6
TitleCrystal structure of GLUN1/GLUN2A-4M mutant ligand-binding domain in complex with glycine and glutamate
Components
  • Glutamate receptor ionotropic, NMDA 1
  • Glutamate receptor ionotropic, NMDA 2A
KeywordsMEMBRANE PROTEIN / NMDAR / ligand-binding domain / agonist
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 / pons maturation / regulation of cell communication / positive regulation of Schwann cell migration / response to environmental enrichment / EPHB-mediated forward signaling ...neurotransmitter receptor transport, plasma membrane to endosome / regulation of response to alcohol / response to ammonium ion / receptor recycling / directional locomotion / pons maturation / regulation of cell communication / positive regulation of Schwann cell migration / response to environmental enrichment / EPHB-mediated forward signaling / Assembly and cell surface presentation of NMDA receptors / response to hydrogen sulfide / olfactory learning / serotonin metabolic process / conditioned place preference / conditioned taste aversion / dendritic branch / regulation of respiratory gaseous exchange / protein localization to postsynaptic membrane / response to other organism / positive regulation of inhibitory postsynaptic potential / propylene metabolic process / response to glycine / regulation of ARF protein signal transduction / cellular response to magnesium ion / response to methylmercury / voltage-gated monoatomic cation channel activity / sleep / cellular response to dsRNA / dendritic spine organization / response to carbohydrate / regulation of monoatomic cation transmembrane transport / cellular response to lipid / locomotion / response to morphine / NMDA glutamate receptor activity / Synaptic adhesion-like molecules / regulation of NMDA receptor activity / NMDA selective glutamate receptor complex / RAF/MAP kinase cascade / glutamate-gated calcium ion channel activity / parallel fiber to Purkinje cell synapse / response to manganese ion / calcium ion transmembrane import into cytosol / protein heterotetramerization / glutamate binding / neuromuscular process / cellular response to zinc ion / positive regulation of reactive oxygen species biosynthetic process / regulation of synapse assembly / action potential / glycine binding / positive regulation of calcium ion transport into cytosol / regulation of dendrite morphogenesis / regulation of axonogenesis / male mating behavior / spinal cord development / dopamine metabolic process / suckling behavior / startle response / response to amine / monoatomic cation transmembrane transport / monoatomic cation transport / regulation of neuronal synaptic plasticity / modulation of excitatory postsynaptic potential / response to lithium ion / associative learning / positive regulation of excitatory postsynaptic potential / social behavior / ligand-gated monoatomic ion channel activity / cellular response to glycine / excitatory synapse / positive regulation of dendritic spine maintenance / response to light stimulus / neuron development / positive regulation of protein targeting to membrane / Unblocking of NMDA receptors, glutamate binding and activation / phosphatase binding / regulation of postsynaptic membrane potential / postsynaptic density, intracellular component / cellular response to manganese ion / calcium ion homeostasis / glutamate receptor binding / prepulse inhibition / multicellular organismal response to stress / monoatomic cation channel activity / long-term memory / regulation of neuron apoptotic process / synaptic cleft / glutamate-gated receptor activity / presynaptic active zone membrane / response to fungicide / sensory perception of pain / cell adhesion molecule binding / dendrite membrane / ligand-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / response to amphetamine / ionotropic glutamate receptor signaling pathway / excitatory postsynaptic potential / hippocampal mossy fiber to CA3 synapse
Similarity search - Function
Glutamate [NMDA] receptor, epsilon subunit, C-terminal / N-methyl D-aspartate receptor 2B3 C-terminus / : / : / 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 ...Glutamate [NMDA] receptor, epsilon subunit, C-terminal / N-methyl D-aspartate receptor 2B3 C-terminus / : / : / 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
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: 1.66 Å
AuthorsWang, J.X. / Furukawa, H.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)NS111745 United States
National Institutes of Health/National Institute of Mental Health (NIH/NIMH)MH085926 United States
CitationJournal: Nat Commun / Year: 2020
Title: Structural basis of subtype-selective competitive antagonism for GluN2C/2D-containing NMDA receptors.
Authors: Wang, J.X. / Irvine, M.W. / Burnell, E.S. / Sapkota, K. / Thatcher, R.J. / Li, M. / Simorowski, N. / Volianskis, A. / Collingridge, G.L. / Monaghan, D.T. / Jane, D.E. / Furukawa, H.
History
DepositionNov 14, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 29, 2020Provider: repository / Type: Initial release
Revision 1.1Feb 5, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 11, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms / software
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _software.name

-
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)65,1684
Polymers64,9462
Non-polymers2222
Water10,935607
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: Full-length NMDAR available, showed the same assembly of LBD dimers (dimer of dimer structure)
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2180 Å2
ΔGint-5 kcal/mol
Surface area26050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.635, 90.063, 125.151
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

-
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 415-565,684-821)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Grin1, Nmdar1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): OrigamiB (DE3) / 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: 31606.236 Da / Num. of mol.: 1
Fragment: ligand-binding domain (UNP residues 402-539,661-800)
Mutation: A414R, K738M, G740R, R741K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Grin2a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): OrigamiB (DE3) / References: UniProt: Q00959
#3: Chemical ChemComp-GLY / GLYCINE


Type: peptide linking / Mass: 75.067 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C2H5NO2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-GLU / GLUTAMIC ACID


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


Mass: 18.015 Da / Num. of mol.: 607 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.37 Å3/Da / Density % sol: 48.01 % / Description: long rod-shaped crystals
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 100 mM HEPES, pH 7.0, 75 mM sodium chloride, 18% PEG2000 MME

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.92013 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Apr 18, 2018
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92013 Å / Relative weight: 1
ReflectionResolution: 1.66→73.1 Å / Num. obs: 71406 / % possible obs: 96.4 % / Redundancy: 6.3 % / Biso Wilson estimate: 22.21 Å2 / Rmerge(I) obs: 0.073 / Net I/σ(I): 14.3
Reflection shellResolution: 1.66→1.69 Å / Redundancy: 3.9 % / Num. unique obs: 5481 / CC1/2: 0.515

-
Processing

Software
NameVersionClassification
autoPROCdata collection
XDSdata reduction
PHENIX1.13_2998refinement
Aimlessdata scaling
pointlessdata scaling
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 4NF8

4nf8


Resolution: 1.66→50.07 Å / SU ML: 0.1746 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 21.333
RfactorNum. reflection% reflection
Rfree0.2118 3628 5.08 %
Rwork0.1794 --
obs0.1811 71406 96.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 30.05 Å2
Refinement stepCycle: LAST / Resolution: 1.66→50.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4497 0 15 607 5119
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00924676
X-RAY DIFFRACTIONf_angle_d0.99686335
X-RAY DIFFRACTIONf_chiral_restr0.0664701
X-RAY DIFFRACTIONf_plane_restr0.0068815
X-RAY DIFFRACTIONf_dihedral_angle_d13.89752854
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.66-1.680.23871060.20191915X-RAY DIFFRACTION72.08
1.68-1.70.2391980.20972049X-RAY DIFFRACTION75.33
1.7-1.730.25621080.20072131X-RAY DIFFRACTION80.6
1.73-1.750.21781150.20582322X-RAY DIFFRACTION86.3
1.75-1.780.2171320.20292515X-RAY DIFFRACTION94.4
1.78-1.810.25251570.21472613X-RAY DIFFRACTION98.58
1.81-1.840.2521290.1952662X-RAY DIFFRACTION98.83
1.84-1.870.24471530.19832656X-RAY DIFFRACTION100
1.87-1.910.22131460.18742682X-RAY DIFFRACTION99.96
1.91-1.950.19691280.17912707X-RAY DIFFRACTION99.96
1.95-1.990.22551450.18872655X-RAY DIFFRACTION100
1.99-2.040.20881550.18352658X-RAY DIFFRACTION100
2.04-2.090.23981520.1862696X-RAY DIFFRACTION100
2.09-2.140.22861390.18692690X-RAY DIFFRACTION100
2.14-2.210.22341500.18242702X-RAY DIFFRACTION100
2.21-2.280.20591460.18642675X-RAY DIFFRACTION100
2.28-2.360.25291170.18332720X-RAY DIFFRACTION100
2.36-2.460.22961620.18442673X-RAY DIFFRACTION99.96
2.46-2.570.23961330.19412729X-RAY DIFFRACTION99.97
2.57-2.70.23211210.19432716X-RAY DIFFRACTION99.86
2.7-2.870.22731450.18842734X-RAY DIFFRACTION100
2.87-3.090.21811490.19712721X-RAY DIFFRACTION100
3.09-3.40.2191650.1792726X-RAY DIFFRACTION100
3.4-3.90.18881550.16362752X-RAY DIFFRACTION99.97
3.9-4.910.17341560.13972769X-RAY DIFFRACTION99.86
4.91-50.070.19181660.17862910X-RAY DIFFRACTION99.71
Refinement TLS params.Method: refined / Origin x: 40.641021733 Å / Origin y: 75.7939187105 Å / Origin z: 25.8618815501 Å
111213212223313233
T0.120877267696 Å20.011177973847 Å2-0.00993028708522 Å2-0.120861570207 Å2-0.0121694689064 Å2--0.1350322277 Å2
L0.488895915089 °20.0276130656443 °20.345632831137 °2-0.334070916736 °20.115681141885 °2--0.766871497565 °2
S-0.0476689282065 Å °-0.0529783100083 Å °0.0543292491198 Å °0.0262555929198 Å °0.0362754184958 Å °-0.0700900186789 Å °-0.0684946246588 Å °-0.0494018452899 Å °-0.00479742315588 Å °
Refinement TLS groupSelection details: all

+
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