[English] 日本語
Yorodumi
- PDB-5fwy: Crystal structure of the AMPA receptor GluA2/A3 N-terminal domain... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5fwy
TitleCrystal structure of the AMPA receptor GluA2/A3 N-terminal domain heterodimer
Components(GLUTAMATE RECEPTOR ...) x 2
KeywordsTRANSPORT PROTEIN
Function / homology
Function and homology information


Trafficking of AMPA receptors / ligand-gated calcium channel activity / Synaptic adhesion-like molecules / regulation of synaptic plasticity by chemical substance / spine synapse / dendritic spine neck / dendritic spine cytoplasm / cellular response to amine stimulus / response to phorbol 13-acetate 12-myristate / dendritic spine head ...Trafficking of AMPA receptors / ligand-gated calcium channel activity / Synaptic adhesion-like molecules / regulation of synaptic plasticity by chemical substance / spine synapse / dendritic spine neck / dendritic spine cytoplasm / cellular response to amine stimulus / response to phorbol 13-acetate 12-myristate / dendritic spine head / Activation of AMPA receptors / protein heterotetramerization / ligand-gated monoatomic cation channel activity / perisynaptic space / response to lithium ion / Trafficking of GluR2-containing AMPA receptors / AMPA glutamate receptor activity / AMPA glutamate receptor clustering / regulation of receptor recycling / parallel fiber to Purkinje cell synapse / kainate selective glutamate receptor activity / AMPA glutamate receptor complex / extracellularly glutamate-gated ion channel activity / ionotropic glutamate receptor complex / cellular response to glycine / immunoglobulin binding / asymmetric synapse / Unblocking of NMDA receptors, glutamate binding and activation / response to fungicide / glutamate receptor binding / positive regulation of synaptic transmission / conditioned place preference / regulation of synaptic transmission, glutamatergic / cytoskeletal protein binding / extracellular ligand-gated monoatomic ion channel activity / glutamate-gated receptor activity / cellular response to brain-derived neurotrophic factor stimulus / regulation of long-term synaptic depression / glutamate-gated calcium ion channel activity / somatodendritic compartment / presynaptic active zone membrane / synaptic cleft / ionotropic glutamate receptor binding / excitatory synapse / ionotropic glutamate receptor signaling pathway / ligand-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / dendrite cytoplasm / dendrite membrane / positive regulation of excitatory postsynaptic potential / SNARE binding / establishment of protein localization / synaptic membrane / synaptic transmission, glutamatergic / PDZ domain binding / cerebral cortex development / dendritic shaft / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / protein tetramerization / long-term synaptic potentiation / receptor internalization / postsynaptic density membrane / Schaffer collateral - CA1 synapse / modulation of chemical synaptic transmission / terminal bouton / synaptic vesicle membrane / synaptic vesicle / signaling receptor activity / amyloid-beta binding / presynapse / growth cone / chemical synaptic transmission / scaffold protein binding / presynaptic membrane / dendritic spine / protein homotetramerization / perikaryon / neuron projection / postsynaptic membrane / postsynaptic density / external side of plasma membrane / axon / neuronal cell body / dendrite / protein kinase binding / synapse / glutamatergic synapse / protein-containing complex binding / perinuclear region of cytoplasm / cell surface / endoplasmic reticulum / protein-containing complex / membrane / identical protein binding / plasma membrane
Similarity search - Function
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 ...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
Glutamate receptor 2 / Glutamate receptor 3
Similarity search - Component
Biological speciesRATTUS NORVEGICUS (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.12 Å
AuthorsHerguedas, B. / Garcia-Nafria, J. / Greger, I.H.
CitationJournal: Science / Year: 2016
Title: Structure and organization of heteromeric AMPA-type glutamate receptors.
Authors: Beatriz Herguedas / Javier García-Nafría / Ondrej Cais / Rafael Fernández-Leiro / James Krieger / Hinze Ho / Ingo H Greger /
Abstract: AMPA-type glutamate receptors (AMPARs), which are central mediators of rapid neurotransmission and synaptic plasticity, predominantly exist as heteromers of the subunits GluA1 to GluA4. Here we ...AMPA-type glutamate receptors (AMPARs), which are central mediators of rapid neurotransmission and synaptic plasticity, predominantly exist as heteromers of the subunits GluA1 to GluA4. Here we report the first AMPAR heteromer structures, which deviate substantially from existing GluA2 homomer structures. Crystal structures of the GluA2/3 and GluA2/4 N-terminal domains reveal a novel compact conformation with an alternating arrangement of the four subunits around a central axis. This organization is confirmed by cysteine cross-linking in full-length receptors, and it permitted us to determine the structure of an intact GluA2/3 receptor by cryogenic electron microscopy. Two models in the ligand-free state, at resolutions of 8.25 and 10.3 angstroms, exhibit substantial vertical compression and close associations between domain layers, reminiscent of N-methyl-D-aspartate receptors. Model 1 resembles a resting state and model 2 a desensitized state, thus providing snapshots of gating transitions in the nominal absence of ligand. Our data reveal organizational features of heteromeric AMPARs and provide a framework to decipher AMPAR architecture and signaling.
History
DepositionFeb 21, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 16, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 23, 2016Group: Database references
Revision 1.2May 11, 2016Group: Database references
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations ...Data collection / Derived calculations / Other / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_database_status.status_code_sf / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.5Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: GLUTAMATE RECEPTOR 2
B: GLUTAMATE RECEPTOR 3
C: GLUTAMATE RECEPTOR 2
D: GLUTAMATE RECEPTOR 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)180,72323
Polymers177,6514
Non-polymers3,07319
Water6,341352
1
A: GLUTAMATE RECEPTOR 2
B: GLUTAMATE RECEPTOR 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,50413
Polymers88,8252
Non-polymers1,67811
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3690 Å2
ΔGint-52.7 kcal/mol
Surface area30700 Å2
MethodPISA
2
C: GLUTAMATE RECEPTOR 2
D: GLUTAMATE RECEPTOR 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,22010
Polymers88,8252
Non-polymers1,3948
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3040 Å2
ΔGint-24.9 kcal/mol
Surface area31370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.270, 78.519, 107.850
Angle α, β, γ (deg.)83.36, 87.40, 64.94
Int Tables number1
Space group name H-MP1

-
Components

-
GLUTAMATE RECEPTOR ... , 2 types, 4 molecules ACBD

#1: Protein GLUTAMATE RECEPTOR 2 / GLUR-2 / AMPA-SELECTIVE GLUTAMATE RECEPTOR 2 / GLUR-B / GLUR-K 2 / GLUTAMATE RECEPTOR IONOTROPIC / ...GLUR-2 / AMPA-SELECTIVE GLUTAMATE RECEPTOR 2 / GLUR-B / GLUR-K 2 / GLUTAMATE RECEPTOR IONOTROPIC / AMPA 2 / GLUA2 / GLUA2 AMPA RECEPT OR N-TERMINAL DOMAIN


Mass: 43731.359 Da / Num. of mol.: 2 / Fragment: RESIDUES 25-400
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) RATTUS NORVEGICUS (Norway rat) / Cell line (production host): HEK293 GNT1 / Production host: HOMO SAPIENS (human) / References: UniProt: P19491
#2: Protein GLUTAMATE RECEPTOR 3 / GLUR-3 / AMPA-SELECTIVE GLUTAMATE RECEPTOR 3 / GLUR-C / GLUR-K 3 / GLUTAMATE RECEPTOR IONOTROPIC / ...GLUR-3 / AMPA-SELECTIVE GLUTAMATE RECEPTOR 3 / GLUR-C / GLUR-K 3 / GLUTAMATE RECEPTOR IONOTROPIC / AMPA 3 / GLUA3 / GLUA3 AMPA RECEPT OR N-TERMINAL DOMAIN


Mass: 45093.953 Da / Num. of mol.: 2 / Fragment: RESIDUES 23-403
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) RATTUS NORVEGICUS (Norway rat) / Cell line (production host): HEK293 GNT1 / Production host: HOMO SAPIENS (human) / References: UniProt: P19492

-
Sugars , 1 types, 10 molecules

#3: 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.: 10
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, 361 molecules

#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 352 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.81 Å3/Da / Density % sol: 56.18 % / Description: NONE
Crystal growDetails: 14-16 % PEG 3350, 0.27 M AMMONIUM SULPHATE AND 0.1 M BICINE PH 9

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92
DetectorType: DECTRIS PIXEL / Detector: PIXEL / Date: Dec 9, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 2.12→41.75 Å / Num. obs: 100269 / % possible obs: 90.4 % / Observed criterion σ(I): 2 / Redundancy: 1.9 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 6
Reflection shellResolution: 2.12→2.18 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 1.9 / % possible all: 87.8

-
Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
xia2data reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 3HSY AND 3O21

3hsy

3o21


Resolution: 2.12→41.76 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.929 / SU B: 12.006 / SU ML: 0.15 / Cross valid method: THROUGHOUT / ESU R: 0.226 / ESU R Free: 0.187 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.23113 4984 5 %RANDOM
Rwork0.19223 ---
obs0.19418 95272 90.32 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 39.088 Å2
Baniso -1Baniso -2Baniso -3
1--1.04 Å2-1.06 Å2-0.06 Å2
2--0.94 Å20.57 Å2
3----1.13 Å2
Refinement stepCycle: LAST / Resolution: 2.12→41.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11992 0 186 352 12530
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.01912470
X-RAY DIFFRACTIONr_bond_other_d0.0020.0211617
X-RAY DIFFRACTIONr_angle_refined_deg1.7341.94816888
X-RAY DIFFRACTIONr_angle_other_deg1.048326600
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.27951491
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.32823.856625
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.604152069
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.7691586
X-RAY DIFFRACTIONr_chiral_restr0.1020.21860
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0214162
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023092
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.2781.9015973
X-RAY DIFFRACTIONr_mcbond_other1.2751.9015972
X-RAY DIFFRACTIONr_mcangle_it2.22.8417452
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.7832.2226497
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.12→2.175 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.293 370 -
Rwork0.271 6792 -
obs--87.67 %
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)
10.41640.0409-0.18790.32490.02480.2272-0.01040.02850.00380.0090.00890.050.03210.01180.00150.32820.0468-0.01730.0401-0.00050.2568-2.03-17.041-8.337
20.2802-0.1087-0.09830.28610.07770.11970.027-0.0176-0.0184-0.0327-0.0032-0.0071-0.08050.0271-0.02370.32530.0246-0.01870.04530.00260.26343.10715.954.551
30.3263-0.09460.21260.3594-0.14830.24850.0029-0.0509-0.00810.00890.01010.0145-0.0105-0.0136-0.01310.31860.03740.00080.06130.00750.25083.2833.88846.811
40.5090.40060.13860.78660.02680.0525-0.0085-0.0234-0.1012-0.20140.0267-0.10160.0362-0.0132-0.01820.34270.04040.03380.01860.00290.3168.437-29.01434.009
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 377
2X-RAY DIFFRACTION2B1 - 382
3X-RAY DIFFRACTION3C1 - 377
4X-RAY DIFFRACTION4D1 - 382

+
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