[English] 日本語
Yorodumi
- PDB-9gig: NMDA bound to compound 387 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9gig
TitleNMDA bound to compound 387
Components
  • Glutamate receptor
  • Isoform 1 of Glutamate receptor ionotropic, NMDA 1
KeywordsTRANSPORT PROTEIN / ion transport ligand gated ion channel
Function / homology
Function and homology information


glycine-gated cation channel activity / excitatory chemical synaptic transmission / directional locomotion / serotonin metabolic process / Synaptic adhesion-like molecules / protein localization to postsynaptic membrane / response to glycine / propylene metabolic process / sleep / regulation of monoatomic cation transmembrane transport ...glycine-gated cation channel activity / excitatory chemical synaptic transmission / directional locomotion / serotonin metabolic process / Synaptic adhesion-like molecules / protein localization to postsynaptic membrane / response to glycine / propylene metabolic process / sleep / regulation of monoatomic cation transmembrane transport / Assembly and cell surface presentation of NMDA receptors / NMDA glutamate receptor activity / Neurexins and neuroligins / neurotransmitter receptor complex / NMDA selective glutamate receptor complex / ligand-gated sodium channel activity / calcium ion transmembrane import into cytosol / glutamate binding / protein heterotetramerization / glycine binding / positive regulation of reactive oxygen species biosynthetic process / positive regulation of calcium ion transport into cytosol / Negative regulation of NMDA receptor-mediated neuronal transmission / startle response / dopamine metabolic process / Unblocking of NMDA receptors, glutamate binding and activation / monoatomic cation transmembrane transport / regulation of neuronal synaptic plasticity / Long-term potentiation / monoatomic cation transport / excitatory synapse / positive regulation of excitatory postsynaptic potential / monoatomic ion channel complex / synaptic cleft / calcium ion homeostasis / glutamate-gated calcium ion channel activity / neurogenesis / sensory perception of pain / EPHB-mediated forward signaling / sodium ion transmembrane transport / response to amphetamine / Ras activation upon Ca2+ influx through NMDA receptor / ionotropic glutamate receptor signaling pathway / positive regulation of synaptic transmission, glutamatergic / regulation of membrane potential / excitatory postsynaptic potential / synaptic membrane / protein catabolic process / postsynaptic density membrane / terminal bouton / brain development / visual learning / negative regulation of protein catabolic process / calcium ion transmembrane transport / regulation of synaptic plasticity / memory / response to wounding / long-term synaptic potentiation / synaptic vesicle / signaling receptor activity / amyloid-beta binding / presynaptic membrane / RAF/MAP kinase cascade / chemical synaptic transmission / dendritic spine / response to ethanol / postsynaptic membrane / calmodulin binding / neuron projection / postsynaptic density / positive regulation of apoptotic process / response to xenobiotic stimulus / synapse / dendrite / calcium ion binding / endoplasmic reticulum membrane / protein-containing complex binding / glutamatergic synapse / cell surface / endoplasmic reticulum / positive regulation of transcription by RNA polymerase II / plasma membrane / cytoplasm
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 / : ...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 I
Similarity search - Domain/homology
: / GLUTAMIC ACID / Glutamate receptor / Glutamate receptor ionotropic, NMDA 1
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.09 Å
AuthorsCarr, K.H. / Ascic, E. / Leonard, P.M.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: J.Med.Chem. / Year: 2024
Title: Advancements in NMDA Receptor-Targeted Antidepressants: From d-Cycloserine Discovery to Preclinical Efficacy of Lu AF90103.
Authors: Ascic, E. / Marigo, M. / David, L. / Frisch Herrik, K. / Grupe, M. / Hougaard, C. / Mork, A. / Jones, C.R. / Badolo, L. / Frederiksen, K. / Boonen, H.C.M. / Jensen, H.S. / Kilburn, J.P.
History
DepositionAug 19, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 27, 2024Provider: repository / Type: Initial release
Revision 1.1Dec 11, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

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


Theoretical massNumber of molelcules
Total (without water)65,6874
Polymers65,2042
Non-polymers4822
Water1,874104
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2740 Å2
ΔGint-13 kcal/mol
Surface area24690 Å2
Unit cell
Length a, b, c (Å)54.09, 90.77, 122.88
Angle α, β, γ (deg.)90, 90, 90
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Glutamate receptor


Mass: 31939.469 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Grin2a / Plasmid: pET-22b / Production host: Escherichia coli (E. coli) / Strain (production host): Origami B (DE3) / Variant (production host): Origami B (DE3) / References: UniProt: G3V9C5
#2: Protein Isoform 1 of Glutamate receptor ionotropic, NMDA 1 / GluN1 / Glutamate [NMDA] receptor subunit zeta-1 / N-methyl-D-aspartate receptor subunit NR1 / NMD-R1


Mass: 33264.945 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GRIN1, NMDAR1 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta-gami (DE3) / Variant (production host): Rosetta-gami (DE3) / References: UniProt: Q05586
#3: Chemical ChemComp-GLU / GLUTAMIC ACID


Type: L-peptide linking / Mass: 147.129 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H9NO4
#4: Chemical ChemComp-A1ILO / (2~{R})-2-azanyl-3-[[3-(5-ethyl-3-methyl-1,2-oxazol-4-yl)-5-fluoranyl-phenyl]carbonylamino]propanoic acid


Mass: 335.330 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C16H18FN3O4 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 104 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.36 Å3/Da / Density % sol: 47.9 %
Crystal growTemperature: 282.15 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 10-15% PEG 3350, 0.1 M HEPES pH 7.0, 1 mM sodium azide, 1% tryptone

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9686 Å
DetectorType: DECTRIS PILATUS3 X 6M / Detector: PIXEL / Date: May 15, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9686 Å / Relative weight: 1
ReflectionResolution: 2.09→46.47 Å / Num. obs: 36660 / % possible obs: 100 % / Redundancy: 6.4 % / Biso Wilson estimate: 33.917 Å2 / CC1/2: 0.964 / Rmerge(I) obs: 0.242 / Rpim(I) all: 0.152 / Rrim(I) all: 0.292 / Net I/σ(I): 4.3
Reflection shellResolution: 2.09→2.13 Å / Rmerge(I) obs: 1.027 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 1801 / CC1/2: 0.578 / Rpim(I) all: 0.657 / % possible all: 100

-
Processing

Software
NameVersionClassification
REFMAC5.8.0430 (refmacat 0.4.82)refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.09→46.47 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.925 / SU B: 6.633 / SU ML: 0.171 / Cross valid method: THROUGHOUT / ESU R: 0.223 / ESU R Free: 0.195
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflectionSelection details
Rfree0.2566 1861 5.085 %RANDOM
Rwork0.2058 34737 --
all0.208 ---
obs-36598 99.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 44.433 Å2
Baniso -1Baniso -2Baniso -3
1--2.307 Å2-0 Å2-0 Å2
2--0.569 Å2-0 Å2
3---1.738 Å2
Refinement stepCycle: LAST / Resolution: 2.09→46.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4276 0 34 104 4414
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0124403
X-RAY DIFFRACTIONr_bond_other_d0.0010.0164109
X-RAY DIFFRACTIONr_angle_refined_deg1.5831.8285965
X-RAY DIFFRACTIONr_angle_other_deg0.5541.7669475
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.95545
X-RAY DIFFRACTIONr_dihedral_angle_2_deg6.769522
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.50510745
X-RAY DIFFRACTIONr_dihedral_angle_6_deg14.26910189
X-RAY DIFFRACTIONr_chiral_restr0.080.2673
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.025129
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021006
X-RAY DIFFRACTIONr_nbd_refined0.2170.2775
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1840.23586
X-RAY DIFFRACTIONr_nbtor_refined0.1820.22166
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0820.22403
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1880.2127
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.1560.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1770.210
X-RAY DIFFRACTIONr_nbd_other0.1920.229
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1250.26
X-RAY DIFFRACTIONr_mcbond_it4.014.262198
X-RAY DIFFRACTIONr_mcbond_other4.014.2612198
X-RAY DIFFRACTIONr_mcangle_it5.6017.6482737
X-RAY DIFFRACTIONr_mcangle_other5.67.6472738
X-RAY DIFFRACTIONr_scbond_it5.1184.6622205
X-RAY DIFFRACTIONr_scbond_other5.1184.6632204
X-RAY DIFFRACTIONr_scangle_it7.5518.383228
X-RAY DIFFRACTIONr_scangle_other7.558.3793229
X-RAY DIFFRACTIONr_lrange_it9.65351.43817491
X-RAY DIFFRACTIONr_lrange_other9.65351.45317456
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.09-2.1440.3291220.2882533X-RAY DIFFRACTION99.9247
2.144-2.2030.2771310.2542476X-RAY DIFFRACTION99.9617
2.203-2.2670.2731110.2412411X-RAY DIFFRACTION100
2.267-2.3360.2661210.2512322X-RAY DIFFRACTION99.9591
2.336-2.4130.31290.2382250X-RAY DIFFRACTION99.916
2.413-2.4970.3071210.2382184X-RAY DIFFRACTION99.9566
2.497-2.5910.3091200.2242131X-RAY DIFFRACTION99.9556
2.591-2.6960.3141190.222022X-RAY DIFFRACTION99.9533
2.696-2.8160.283990.21948X-RAY DIFFRACTION99.9512
2.816-2.9530.247900.1971885X-RAY DIFFRACTION99.9494
2.953-3.1120.2281000.1861802X-RAY DIFFRACTION100
3.112-3.30.269950.181686X-RAY DIFFRACTION99.9439
3.3-3.5260.231970.1891611X-RAY DIFFRACTION99.9415
3.526-3.8070.216880.1961479X-RAY DIFFRACTION100
3.807-4.1670.226640.1821402X-RAY DIFFRACTION99.9318
4.167-4.6550.233770.1731247X-RAY DIFFRACTION99.9245
4.655-5.3660.201550.1841139X-RAY DIFFRACTION100
5.366-6.550.285530.234962X-RAY DIFFRACTION100
6.55-9.1720.306450.215771X-RAY DIFFRACTION99.8776
9.172-46.470.272240.236476X-RAY DIFFRACTION99.6016

+
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