[English] 日本語
Yorodumi
- PDB-4kfq: Crystal structure of the NMDA receptor GluN1 ligand binding domai... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4kfq
TitleCrystal structure of the NMDA receptor GluN1 ligand binding domain in complex with 1-thioxo-1,2-dihydro-[1,2,4]triazolo[4,3-a]quinoxalin-4(5H)-one
ComponentsGlutamate receptor ionotropic, NMDA 1
KeywordsMEMBRANE PROTEIN / ligand binding domain / Ionotropic Glutamate Receptor
Function / homology
Function and homology information


EPHB-mediated forward signaling / pons maturation / Assembly and cell surface presentation of NMDA receptors / regulation of cell communication / positive regulation of Schwann cell migration / olfactory learning / conditioned taste aversion / dendritic branch / regulation of respiratory gaseous exchange / protein localization to postsynaptic membrane ...EPHB-mediated forward signaling / pons maturation / Assembly and cell surface presentation of NMDA receptors / regulation of cell communication / positive regulation of Schwann cell migration / olfactory learning / conditioned taste aversion / dendritic branch / regulation of respiratory gaseous exchange / protein localization to postsynaptic membrane / transmitter-gated monoatomic ion channel activity / suckling behavior / propylene metabolic process / response to glycine / RAF/MAP kinase cascade / response to amine / Synaptic adhesion-like molecules / regulation of monoatomic cation transmembrane transport / NMDA glutamate receptor activity / response to glycoside / NMDA selective glutamate receptor complex / voltage-gated monoatomic cation channel activity / glutamate binding / neurotransmitter receptor complex / ligand-gated sodium channel activity / regulation of axonogenesis / calcium ion transmembrane import into cytosol / neuromuscular process / response to morphine / regulation of dendrite morphogenesis / protein heterotetramerization / male mating behavior / regulation of synapse assembly / glycine binding / startle response / positive regulation of reactive oxygen species biosynthetic process / parallel fiber to Purkinje cell synapse / monoatomic cation transmembrane transport / monoatomic ion channel complex / cellular response to glycine / positive regulation of calcium ion transport into cytosol / associative learning / positive regulation of dendritic spine maintenance / regulation of neuronal synaptic plasticity / social behavior / Unblocking of NMDA receptors, glutamate binding and activation / monoatomic cation transport / glutamate receptor binding / prepulse inhibition / long-term memory / phosphatase binding / positive regulation of synaptic transmission, glutamatergic / response to fungicide / monoatomic cation channel activity / synaptic cleft / calcium ion homeostasis / glutamate-gated receptor activity / cellular response to manganese ion / glutamate-gated calcium ion channel activity / presynaptic active zone membrane / dendrite membrane / excitatory synapse / sensory perception of pain / ionotropic glutamate receptor signaling pathway / ligand-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / regulation of neuron apoptotic process / synaptic membrane / sodium ion transmembrane transport / positive regulation of excitatory postsynaptic potential / response to amphetamine / hippocampal mossy fiber to CA3 synapse / adult locomotory behavior / learning / synaptic transmission, glutamatergic / excitatory postsynaptic potential / regulation of membrane potential / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / neuron cellular homeostasis / response to calcium ion / regulation of long-term neuronal synaptic plasticity / regulation of synaptic plasticity / cerebral cortex development / visual learning / postsynaptic density membrane / calcium ion transmembrane transport / memory / calcium channel activity / intracellular calcium ion homeostasis / terminal bouton / synaptic vesicle / calcium ion transport / rhythmic process / synaptic vesicle membrane / signaling receptor activity / amyloid-beta binding / presynaptic membrane / protein-containing complex assembly / dendritic spine / response to ethanol / chemical synaptic transmission
Similarity search - Function
: / : / 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. ...: / : / 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. / 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-KFQ / Glutamate receptor ionotropic, NMDA 1
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsSteffensen, T.B. / Tabrizi, F.M. / Gajhede, M. / Kastrup, J.S.
Citation
Journal: J.Biol.Chem. / Year: 2013
Title: Crystal structure and pharmacological characterization of a novel N-methyl-D-aspartate (NMDA) receptor antagonist at the GluN1 glycine binding site.
Authors: Kvist, T. / Steffensen, T.B. / Greenwood, J.R. / Mehrzad Tabrizi, F. / Hansen, K.B. / Gajhede, M. / Pickering, D.S. / Traynelis, S.F. / Kastrup, J.S. / Brauner-Osborne, H.
#1: Journal: Embo J. / Year: 2003
Title: Mechanisms of activation, inhibition and specificity: crystal structures of the NMDA RECEPTOR NR1 ligand-binding core
Authors: Furukawa, H. / Gouaux, E.
History
DepositionApr 27, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 9, 2013Provider: repository / Type: Initial release
Revision 1.1Jul 1, 2015Group: Database references / Structure summary
Revision 1.2Aug 23, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 1.3Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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
Revision 1.4Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

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


Theoretical massNumber of molelcules
Total (without water)69,54330
Polymers66,6802
Non-polymers2,86328
Water7,458414
1
A: Glutamate receptor ionotropic, NMDA 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,77115
Polymers33,3401
Non-polymers1,43114
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Glutamate receptor ionotropic, NMDA 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,77115
Polymers33,3401
Non-polymers1,43114
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)43.950, 78.590, 109.630
Angle α, β, γ (deg.)90.00, 94.21, 90.00
Int Tables number4
Space group name H-MP1211

-
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.: 2 / Fragment: UNP residues 394-554, 663-800
Source method: isolated from a genetically manipulated source
Details: THE PROTEIN CRYSTALLIZED IS THE EXTRACELLULAR LIGAND BINDING DOMAIN OF GLUN1. TRANSMEMBRANE REGIONS WERE GENETICALLY REMOVED AND REPLACED WITH A GLY-THR LINKER (RESIDUES 153 AND 154 OF THE ...Details: THE PROTEIN CRYSTALLIZED IS THE EXTRACELLULAR LIGAND BINDING DOMAIN OF GLUN1. TRANSMEMBRANE REGIONS WERE GENETICALLY REMOVED AND REPLACED WITH A GLY-THR LINKER (RESIDUES 153 AND 154 OF THE STRUCTURE). THEREFORE, THE SEQUENCE MATCHES DISCONTINUOUSLY WITH THE REFERENCE DATABASE (394-554, 663-800)
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Grin1, GRIN1 OR NMDAR1, Nmdar1 / Plasmid: pET22c / Production host: Escherichia coli (E. coli) / Strain (production host): Origami B (DE3) / References: UniProt: P35439
#2: Chemical ChemComp-KFQ / 1-sulfanyl[1,2,4]triazolo[4,3-a]quinoxalin-4(5H)-one


Mass: 218.235 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H6N4OS
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 414 / 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: 2.83 Å3/Da / Density % sol: 56.56 %
Crystal growTemperature: 279 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 1-thioxo-1,2-dihydro-[1,2,4]triazolo[4,3-a]quinoxalin-4(5H)-one was added as solid compound and the solution was gently shaken overnight. 0.3 M ammonium sulfate, 0.1 M HEPES, and 30 % PEG ...Details: 1-thioxo-1,2-dihydro-[1,2,4]triazolo[4,3-a]quinoxalin-4(5H)-one was added as solid compound and the solution was gently shaken overnight. 0.3 M ammonium sulfate, 0.1 M HEPES, and 30 % PEG 4000, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 279K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91841 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 18, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 2.2→39.69 Å / Num. all: 37896 / Num. obs: 37846 / % possible obs: 99.9 % / Redundancy: 3.2 % / Biso Wilson estimate: 26 Å2 / Rmerge(I) obs: 0.09 / Rsym value: 0.09 / Net I/σ(I): 7.1
Reflection shellResolution: 2.2→2.32 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.392 / Mean I/σ(I) obs: 1.9 / Num. unique all: 5498 / Rsym value: 0.392 / % possible all: 100

-
Processing

Software
NameVersionClassification
MxCuBEdata collection
PHASERphasing
PHENIX(phenix.refine: 1.7.2_869)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1PBQ

1pbq


Resolution: 2.2→39.69 Å / SU ML: 0.62 / Isotropic thermal model: Restrained / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 21.78 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2315 1890 4.99 %RANDOM
Rwork0.1739 ---
obs0.1768 37839 99.9 %-
all-37896 --
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 48.896 Å2 / ksol: 0.376 e/Å3
Displacement parametersBiso mean: 27 Å2
Baniso -1Baniso -2Baniso -3
1--3.3764 Å2-0 Å20.2882 Å2
2---1.2115 Å20 Å2
3---4.5879 Å2
Refinement stepCycle: LAST / Resolution: 2.2→39.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4579 0 178 414 5171
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074858
X-RAY DIFFRACTIONf_angle_d1.026531
X-RAY DIFFRACTIONf_dihedral_angle_d15.3891843
X-RAY DIFFRACTIONf_chiral_restr0.069689
X-RAY DIFFRACTIONf_plane_restr0.004820
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)
2.2-2.25950.29381250.215827382738100
2.2595-2.3260.26291460.201127782778100
2.326-2.40110.26181310.195327532753100
2.4011-2.48690.28781500.195227292729100
2.4869-2.58640.25351440.187827882788100
2.5864-2.70410.2371630.178827302730100
2.7041-2.84660.25391370.178727622762100
2.8466-3.02490.25741640.177527572757100
3.0249-3.25840.24221290.169927722772100
3.2584-3.58610.21531430.156928002800100
3.5861-4.10450.20531500.150527592759100
4.1045-5.16950.19111490.146227722772100
5.1695-39.690.21831590.22811281199

+
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