[English] 日本語
Yorodumi
- PDB-4yma: Structure of the ligand-binding domain of GluA2 in complex with t... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4yma
TitleStructure of the ligand-binding domain of GluA2 in complex with the antagonist CNG10109
ComponentsGlutamate receptor 2
KeywordsSIGNALING PROTEIN / Ionotropic glutamate receptor / AMPA receptor GluA2 / ligand-binding domain / antagonist
Function / homology
Function and homology information


spine synapse / dendritic spine neck / dendritic spine head / Activation of AMPA receptors / perisynaptic space / AMPA glutamate receptor activity / Trafficking of GluR2-containing AMPA receptors / response to lithium ion / immunoglobulin binding / AMPA glutamate receptor complex ...spine synapse / dendritic spine neck / dendritic spine head / Activation of AMPA receptors / perisynaptic space / AMPA glutamate receptor activity / Trafficking of GluR2-containing AMPA receptors / response to lithium ion / immunoglobulin binding / AMPA glutamate receptor complex / kainate selective glutamate receptor activity / ionotropic glutamate receptor complex / extracellularly glutamate-gated ion channel activity / cellular response to glycine / asymmetric synapse / regulation of receptor recycling / Unblocking of NMDA receptors, glutamate binding and activation / glutamate receptor binding / positive regulation of synaptic transmission / glutamate-gated receptor activity / presynaptic active zone membrane / response to fungicide / regulation of synaptic transmission, glutamatergic / somatodendritic compartment / cellular response to brain-derived neurotrophic factor stimulus / dendrite membrane / ligand-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / cytoskeletal protein binding / ionotropic glutamate receptor signaling pathway / dendrite cytoplasm / SNARE binding / dendritic shaft / synaptic membrane / synaptic transmission, glutamatergic / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / PDZ domain binding / protein tetramerization / postsynaptic density membrane / ionotropic glutamate receptor binding / Schaffer collateral - CA1 synapse / modulation of chemical synaptic transmission / establishment of protein localization / terminal bouton / receptor internalization / cerebral cortex development / synaptic vesicle membrane / synaptic vesicle / presynapse / presynaptic membrane / signaling receptor activity / amyloid-beta binding / growth cone / scaffold protein binding / chemical synaptic transmission / postsynaptic membrane / perikaryon / dendritic spine / postsynaptic density / neuron projection / axon / neuronal cell body / glutamatergic synapse / synapse / dendrite / protein-containing complex binding / endoplasmic reticulum membrane / protein kinase binding / cell surface / endoplasmic reticulum / protein-containing complex / identical protein binding / membrane / plasma membrane
Similarity search - Function
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. ...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
(3R)-3-(3-carboxy-5-hydroxyphenyl)-L-proline / ACETATE ION / Glutamate receptor 2
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.895 Å
AuthorsMoller, C. / Tapken, D. / Kastrup, J.S. / Frydenvang, K.
Funding support Denmark, 1items
OrganizationGrant numberCountry
Denmark
Citation
Journal: J.Med.Chem. / Year: 2015
Title: Structure-Activity Relationship Study of Ionotropic Glutamate Receptor Antagonist (2S,3R)-3-(3-Carboxyphenyl)pyrrolidine-2-carboxylic Acid.
Authors: Krogsgaard-Larsen, N. / Storgaard, M. / Moller, C. / Demmer, C.S. / Hansen, J. / Han, L. / Monrad, R.N. / Nielsen, B. / Tapken, D. / Pickering, D.S. / Kastrup, J.S. / Frydenvang, K. / Bunch, L.
#1: Journal: FEBS J. / Year: 2014
Title: L-Asp is a useful tool in the purification of the ionotropic glutamate receptor A2 ligand-binding domain.
Authors: Krintel, C. / Frydenvang, K. / Ceravalls de Rabassa, A. / Kaern, A.M. / Gajhede, M. / Pickering, D.S. / Kastrup, J.S.
History
DepositionMar 6, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Aug 5, 2015Provider: repository / Type: Initial release
Revision 1.1Aug 26, 2015Group: Database references
Revision 1.2Aug 9, 2017Group: Data collection / Database references / Category: citation_author / diffrn_source
Item: _citation_author.name / _diffrn_source.pdbx_synchrotron_site
Revision 1.3Mar 7, 2018Group: Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_variant
Revision 1.4Jan 10, 2024Group: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
B: Glutamate receptor 2
A: Glutamate receptor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,00415
Polymers58,5572
Non-polymers1,44613
Water12,574698
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)48.880, 65.250, 91.550
Angle α, β, γ (deg.)90.000, 92.360, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

-
Protein , 1 types, 2 molecules BA

#1: Protein Glutamate receptor 2 / GluR-2 / AMPA-selective glutamate receptor 2 / GluR-B / GluR-K2 / Glutamate receptor ionotropic / ...GluR-2 / AMPA-selective glutamate receptor 2 / GluR-B / GluR-K2 / Glutamate receptor ionotropic / AMPA 2 / GluA2


Mass: 29278.732 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: The protein comprises segment S1 residues 413-527, a GT linker and S2 residues 653-797.
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Gria2, Glur2 / Plasmid: pET22B(+) / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Origami B / References: UniProt: P19491

-
Non-polymers , 6 types, 711 molecules

#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-4E5 / (3R)-3-(3-carboxy-5-hydroxyphenyl)-L-proline


Mass: 251.235 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H13NO5
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 698 / 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: 2.55 Å3/Da / Density % sol: 51.73 %
Crystal growTemperature: 280 K / Method: vapor diffusion, hanging drop / pH: 4.5 / Details: PEG4000, lithium sulfate, phosphate citrate

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I911-3 / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 13, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.895→91.472 Å / Num. all: 45862 / Num. obs: 45862 / % possible obs: 100 % / Redundancy: 4.2 % / Biso Wilson estimate: 19.71 Å2 / Rpim(I) all: 0.047 / Rrim(I) all: 0.095 / Rsym value: 0.083 / Net I/av σ(I): 6.314 / Net I/σ(I): 11.3 / Num. measured all: 190896
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRsym valueNet I/σ(I) obs% possible all
1.89-24.10.37222712566310.2110.3723.6100
2-2.124.20.2373.12627463220.1330.2375.4100
2.12-2.264.20.1754.22471959270.0980.1757.4100
2.26-2.454.20.1295.82307755320.0720.1298.9100
2.45-2.684.20.0977.52133950920.0540.09711.3100
2.68-34.20.06810.51929445930.0380.06814.6100
3-3.464.20.05112.91718940960.0280.05118.7100
3.46-4.244.20.06101447534500.0340.0621.2100
4.24-5.994.20.0698.11130427070.0380.06921.6100
5.99-36.38940.04111610015120.0240.04121.499.5

-
Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.31 Å44.9 Å
Translation2.31 Å44.9 Å

-
Processing

Software
NameVersionClassification
PHENIXrefinement
SCALA3.3.20data scaling
PHASER2.5.1phasing
PDB_EXTRACT3.15data extraction
MOSFLMdata reduction
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3TZA

3tza


Resolution: 1.895→36.389 Å / FOM work R set: 0.8505 / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 22.58 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2278 2314 5.05 %Random
Rwork0.1704 43527 --
obs0.1733 45841 99.99 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 116.95 Å2 / Biso mean: 28.33 Å2 / Biso min: 9.46 Å2
Refinement stepCycle: final / Resolution: 1.895→36.389 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4046 0 90 701 4837
Biso mean--50.87 32.97 -
Num. residues----518
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0064274
X-RAY DIFFRACTIONf_angle_d15757
X-RAY DIFFRACTIONf_chiral_restr0.071630
X-RAY DIFFRACTIONf_plane_restr0.005716
X-RAY DIFFRACTIONf_dihedral_angle_d12.4811604
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 17 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.895-1.93370.2951450.25125372682
1.9337-1.97570.27431310.226125402671
1.9757-2.02170.2321410.198225462687
2.0217-2.07220.27921370.187325042641
2.0722-2.12830.24121240.179926012725
2.1283-2.19090.23831420.1924972639
2.1909-2.26160.30281390.198525722711
2.2616-2.34240.26371390.179225642703
2.3424-2.43620.30611240.185325612685
2.4362-2.5470.22571120.176225822694
2.547-2.68130.22241310.172125482679
2.6813-2.84920.2361510.180525522703
2.8492-3.06910.23161350.176725472682
3.0691-3.37770.22861180.163825952713
3.3777-3.8660.20941290.156425842713
3.866-4.8690.17231500.131125912741
4.869-36.39540.19251660.151226062772
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)
13.85141.5252-0.06742.63910.02791.63060.144-0.0416-0.33790.2646-0.1901-0.02850.6704-0.24090.04780.3261-0.0729-0.02330.185-0.04870.2096-6.4664-41.0949-27.567
22.0332-0.2202-0.14341.09881.10022.28810.09160.3898-0.0372-0.0294-0.19120.16560.0522-0.33290.05090.14290.0063-0.02320.2525-0.04470.1615-6.2484-26.4885-35.0241
32.1707-0.8488-1.01072.27380.45634.05510.2379-0.10280.1677-0.26080.1901-0.0729-0.35760.4467-0.33160.1569-0.03120.0180.1831-0.05740.238312.5776-21.6059-40.3433
42.59990.65150.4611.4602-0.05621.86860.1486-0.01950.01370.1854-0.24830.28590.0988-0.7008-0.00530.1445-0.04440.03540.2459-0.10740.2071-11.885-25.4406-22.3322
53.5587-0.0075-0.36033.02150.5972.87030.1844-0.2846-0.48720.1105-0.1574-0.12480.69020.57820.11270.28740.054-0.07140.18930.02830.19335.1364-34.476-19.9257
63.2334-1.61230.3253.2865-0.5582.3160.13460.0930.1963-0.3248-0.1777-0.0948-0.5709-0.16620.06080.29450.10260.03590.16410.02740.1958-5.10964.9402-19.0483
71.5898-0.44560.13421.18960.39432.2390.08870.0155-0.05930.095-0.22070.1816-0.071-0.34730.09450.1552-0.04760.03120.1374-0.04780.1791-7.0257-9.7698-11.523
81.98750.98880.22742.8682-1.03053.43050.1398-0.09460.09450.2581-0.06950.0164-0.10930.1988-0.07710.1153-0.02040.00430.1164-0.01450.192310.4348-15.5858-3.707
92.61830.792-0.51492.17780.49652.7771-0.00950.07010.0175-0.2075-0.1372-0.0289-0.2343-0.20780.11930.15920.0474-0.00050.0981-0.01130.1628-2.7384-6.9199-24.7195
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 4 through 47 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 48 through 123 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 124 through 217 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 218 through 243 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 244 through 263 )A0
6X-RAY DIFFRACTION6chain 'B' and (resid 4 through 47 )B0
7X-RAY DIFFRACTION7chain 'B' and (resid 48 through 123 )B0
8X-RAY DIFFRACTION8chain 'B' and (resid 124 through 217 )B0
9X-RAY DIFFRACTION9chain 'B' and (resid 218 through 261 )B0

+
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