[English] 日本語
Yorodumi
- PDB-5ewj: CRYSTAL STRUCTURE OF AMINO TERMINAL DOMAINS OF THE NMDA RECEPTOR ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5ewj
TitleCRYSTAL STRUCTURE OF AMINO TERMINAL DOMAINS OF THE NMDA RECEPTOR SUBUNIT GLUN1 AND GLUN2B IN COMPLEX WITH IFENPRODIL
Components
  • Glutamate receptor ionotropic, NMDA 2B
  • NMDA glutamate receptor subunit
KeywordsTRANSPORT PROTEIN / Glutamate receptor / allosteric modulator / GluN2B antagonists
Function / homology
Function and homology information


excitatory chemical synaptic transmission / Activated NTRK2 signals through FYN / Synaptic adhesion-like molecules / positive regulation of cysteine-type endopeptidase activity / negative regulation of dendritic spine maintenance / regulation of monoatomic cation transmembrane transport / glutamate receptor signaling pathway / NMDA glutamate receptor activity / Assembly and cell surface presentation of NMDA receptors / Neurexins and neuroligins ...excitatory chemical synaptic transmission / Activated NTRK2 signals through FYN / Synaptic adhesion-like molecules / positive regulation of cysteine-type endopeptidase activity / negative regulation of dendritic spine maintenance / regulation of monoatomic cation transmembrane transport / glutamate receptor signaling pathway / NMDA glutamate receptor activity / Assembly and cell surface presentation of NMDA receptors / Neurexins and neuroligins / NMDA selective glutamate receptor complex / glutamate-gated calcium ion channel activity / calcium ion transmembrane import into cytosol / protein heterotetramerization / glutamate binding / glycine binding / response to zinc ion / Negative regulation of NMDA receptor-mediated neuronal transmission / Unblocking of NMDA receptors, glutamate binding and activation / monoatomic cation transmembrane transport / regulation of neuronal synaptic plasticity / positive regulation of excitatory postsynaptic potential / Long-term potentiation / MECP2 regulates neuronal receptors and channels / ligand-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / EPHB-mediated forward signaling / ionotropic glutamate receptor signaling pathway / Ras activation upon Ca2+ influx through NMDA receptor / excitatory postsynaptic potential / positive regulation of synaptic transmission, glutamatergic / synaptic membrane / synaptic transmission, glutamatergic / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / regulation of membrane potential / long-term synaptic potentiation / postsynaptic density membrane / regulation of synaptic plasticity / brain development / late endosome / amyloid-beta binding / RAF/MAP kinase cascade / chemical synaptic transmission / postsynaptic membrane / response to ethanol / postsynaptic density / learning or memory / lysosome / cytoskeleton / neuron projection / endoplasmic reticulum membrane / cell surface / zinc ion binding / metal ion binding / plasma membrane / cytoplasm
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 / Response regulator / Ionotropic glutamate receptor, metazoa / Ligated ion channel L-glutamate- and glycine-binding site / : ...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 / Response regulator / 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 I / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-QEL / Glutamate receptor ionotropic, NMDA 1 / Glutamate receptor ionotropic, NMDA 2B / Glutamate receptor ionotropic, NMDA 1
Similarity search - Component
Biological speciesXenopus laevis (African clawed frog)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.77 Å
AuthorsPandit, J.
CitationJournal: Mol.Pharmacol. / Year: 2016
Title: A Novel Binding Mode Reveals Two Distinct Classes of NMDA Receptor GluN2B-selective Antagonists.
Authors: Stroebel, D. / Buhl, D.L. / Knafels, J.D. / Chanda, P.K. / Green, M. / Sciabola, S. / Mony, L. / Paoletti, P. / Pandit, J.
History
DepositionNov 20, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 2, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 9, 2016Group: Database references
Revision 1.2Apr 13, 2016Group: Database references
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / citation / diffrn_radiation_wavelength / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / pdbx_struct_oper_list / struct_asym / struct_conn / struct_conn_type / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.pdbx_formal_charge / _atom_site.type_symbol / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.type_symbol / _chem_comp.name / _chem_comp.type / _citation.journal_id_CSD / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.value / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn_type.id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: NMDA glutamate receptor subunit
B: Glutamate receptor ionotropic, NMDA 2B
C: NMDA glutamate receptor subunit
D: Glutamate receptor ionotropic, NMDA 2B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)173,15515
Polymers170,2204
Non-polymers2,93511
Water6,323351
1
A: NMDA glutamate receptor subunit
B: Glutamate receptor ionotropic, NMDA 2B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,0338
Polymers85,1102
Non-polymers1,9236
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2720 Å2
ΔGint-20 kcal/mol
Surface area28880 Å2
MethodPISA
2
C: NMDA glutamate receptor subunit
D: Glutamate receptor ionotropic, NMDA 2B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,1227
Polymers85,1102
Non-polymers1,0125
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2740 Å2
ΔGint-20 kcal/mol
Surface area29260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)268.460, 60.100, 145.000
Angle α, β, γ (deg.)90.000, 116.220, 90.000
Int Tables number5
Space group name H-MC121

-
Components

-
Protein , 2 types, 4 molecules ACBD

#1: Protein NMDA glutamate receptor subunit


Mass: 43757.977 Da / Num. of mol.: 2 / Fragment: Amino Terminal Domain (UNP residues 23-408) / Mutation: N61Q,N371Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Gene: grin1, NR1 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q91977, UniProt: A0A1L8F5J9*PLUS
#2: Protein Glutamate receptor ionotropic, NMDA 2B / GluN2B / Glutamate [NMDA] receptor subunit epsilon-2 / N-methyl D-aspartate receptor subtype 2B / ...GluN2B / Glutamate [NMDA] receptor subunit epsilon-2 / N-methyl D-aspartate receptor subtype 2B / NR2B / N-methyl-D-aspartate receptor subunit 3 / hNR3


Mass: 41351.902 Da / Num. of mol.: 2 / Fragment: Amino Terminal Domain (UNP residues 31-394) / Mutation: N348D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GRIN2B, NMDAR2B / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q13224

-
Sugars , 2 types, 7 molecules

#3: Polysaccharide alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 910.823 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3[DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,5,4/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3/a4-b1_b4-c1_c3-d1_c6-e1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#5: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

-
Non-polymers , 3 types, 355 molecules

#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#6: Chemical ChemComp-QEL / 4-[(1R,2S)-2-(4-benzylpiperidin-1-yl)-1-hydroxypropyl]phenol / Ifenprodil


Mass: 325.445 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H27NO2 / Comment: inhibitor*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 351 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.08 Å3/Da / Density % sol: 60.09 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: 3.6M Na Formate, 0.1 M Hepes pH 7.0 / PH range: 6.8-7.2

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 20, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.77→120.42 Å / Num. obs: 53122 / % possible obs: 99 % / Redundancy: 3.3 % / Biso Wilson estimate: 78.81 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.056 / Rpim(I) all: 0.036 / Net I/σ(I): 17 / Num. measured all: 177049
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) all% possible all
2.77-3.913.40.1468.3116766343560.9810.09399.7
3.91-120.423.20.02833.160283187660.9990.01997.6

-
Processing

Software
NameVersionClassification
BUSTER-TNTBUSTER 2.11.6refinement
Aimless0.3.5data scaling
PDB_EXTRACT3.15data extraction
XDSdata reduction
BUSTERphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 3QEL

3qel


Resolution: 2.77→27.92 Å / Cor.coef. Fo:Fc: 0.9407 / Cor.coef. Fo:Fc free: 0.9261 / SU R Cruickshank DPI: 0.638 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.627 / SU Rfree Blow DPI: 0.269 / SU Rfree Cruickshank DPI: 0.274
RfactorNum. reflection% reflectionSelection details
Rfree0.2112 2685 5.08 %RANDOM
Rwork0.1742 ---
obs0.1761 52883 98.94 %-
Displacement parametersBiso max: 177.76 Å2 / Biso mean: 75.14 Å2 / Biso min: 22.4 Å2
Baniso -1Baniso -2Baniso -3
1-5.6808 Å20 Å211.8071 Å2
2---8.8446 Å20 Å2
3---3.1638 Å2
Refine analyzeLuzzati coordinate error obs: 0.311 Å
Refinement stepCycle: final / Resolution: 2.77→27.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11017 0 194 351 11562
Biso mean--93.25 68.26 -
Num. residues----1421
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d3912SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes266HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1673HARMONIC5
X-RAY DIFFRACTIONt_it11466HARMONIC20
X-RAY DIFFRACTIONt_nbd3SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion1605SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact12891SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d11466HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg15613HARMONIC21.19
X-RAY DIFFRACTIONt_omega_torsion3.02
X-RAY DIFFRACTIONt_other_torsion20.53
LS refinement shellResolution: 2.77→2.84 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2695 206 5.23 %
Rwork0.2234 3735 -
all0.2257 3941 -
obs--99.72 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.241-0.35240.19530.9856-0.27022.2563-0.07260.04580.09880.0246-0.0150.0334-0.1318-0.01120.0876-0.111-0.05380.0241-0.1414-0.0343-0.073185.78517.0621-54.0168
21.73760.48670.47651.81010.22822.5867-0.1418-0.33280.1720.2525-0.02780.1446-0.4067-0.26120.1696-0.0580.06560.0107-0.1177-0.0565-0.201580.873314.9138-20.9994
32.18770.47151.11372.17060.35932.17660.1029-0.0289-0.1760.4976-0.07590.18150.1488-0.1035-0.027-0.11250.05510.0212-0.15590.2086-0.14422.6556-2.2073-11.0039
42.7359-0.12480.95871.0969-0.38661.6067-0.05270.5062-0.1979-0.11780.172-0.0065-0.06480.2447-0.1194-0.2390.0370.00610.1762-0.0268-0.141825.47643.3498-44.3376
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A23 - 407
2X-RAY DIFFRACTION2{ B|* }B32 - 393
3X-RAY DIFFRACTION3{ C|* }C23 - 407
4X-RAY DIFFRACTION4{ D|* }D32 - 394

+
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