[English] 日本語
Yorodumi
- PDB-5fwx: Crystal structure of the AMPA receptor GluA2/A4 N-terminal domain... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5fwx
TitleCrystal structure of the AMPA receptor GluA2/A4 N-terminal domain heterodimer
Components
  • GLUTAMATE RECEPTOR 2
  • GLUTAMATE RECEPTOR 4
KeywordsTRANSPORT PROTEIN
Function / homology
Function and homology information


Trafficking of AMPA receptors / kainate selective glutamate receptor complex / regulation of synapse structure or activity / Synaptic adhesion-like molecules / spine synapse / dendritic spine neck / dendritic spine head / cellular response to amine stimulus / Activation of AMPA receptors / perisynaptic space ...Trafficking of AMPA receptors / kainate selective glutamate receptor complex / regulation of synapse structure or activity / Synaptic adhesion-like molecules / spine synapse / dendritic spine neck / dendritic spine head / cellular response to amine stimulus / Activation of AMPA receptors / perisynaptic space / ligand-gated monoatomic cation channel activity / AMPA glutamate receptor activity / Trafficking of GluR2-containing AMPA receptors / response to lithium ion / negative regulation of smooth muscle cell apoptotic process / kainate selective glutamate receptor activity / cellular response to glycine / AMPA glutamate receptor complex / extracellularly glutamate-gated ion channel activity / immunoglobulin binding / asymmetric synapse / ionotropic glutamate receptor complex / conditioned place preference / regulation of receptor recycling / glutamate receptor binding / Unblocking of NMDA receptors, glutamate binding and activation / positive regulation of synaptic transmission / positive regulation of synaptic transmission, glutamatergic / regulation of synaptic transmission, glutamatergic / response to fungicide / glutamate-gated receptor activity / regulation of long-term synaptic depression / cytoskeletal protein binding / extracellular ligand-gated monoatomic ion channel activity / cellular response to brain-derived neurotrophic factor stimulus / glutamate-gated calcium ion channel activity / presynaptic active zone membrane / somatodendritic compartment / ionotropic glutamate receptor binding / dendrite membrane / ligand-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / dendrite cytoplasm / ionotropic glutamate receptor signaling pathway / synaptic membrane / dendritic shaft / SNARE binding / PDZ domain binding / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / synaptic transmission, glutamatergic / protein tetramerization / establishment of protein localization / postsynaptic density membrane / cerebral cortex development / modulation of chemical synaptic transmission / receptor internalization / Schaffer collateral - CA1 synapse / terminal bouton / synaptic vesicle / synaptic vesicle membrane / signaling receptor activity / presynapse / amyloid-beta binding / growth cone / presynaptic membrane / scaffold protein binding / perikaryon / dendritic spine / chemical synaptic transmission / postsynaptic membrane / neuron projection / postsynaptic density / axon / external side of plasma membrane / neuronal cell body / synapse / dendrite / protein kinase binding / protein-containing complex binding / glutamatergic synapse / cell surface / endoplasmic reticulum / protein-containing complex / identical protein binding / membrane / plasma membrane
Similarity search - Function
Response regulator / 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 ...Response regulator / 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 / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Glutamate receptor 2 / Glutamate receptor 4
Similarity search - Component
Biological speciesRATTUS NORVEGICUS (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsGarcia-Nafria, J. / Herguedas, B. / 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 1.5Nov 13, 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 4
C: GLUTAMATE RECEPTOR 2
D: GLUTAMATE RECEPTOR 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)177,60511
Polymers176,5584
Non-polymers1,0487
Water2,252125
1
A: GLUTAMATE RECEPTOR 2
B: GLUTAMATE RECEPTOR 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,9136
Polymers88,2792
Non-polymers6354
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 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,6925
Polymers88,2792
Non-polymers4133
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)61.070, 156.630, 77.120
Angle α, β, γ (deg.)90.00, 90.02, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#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 RECEPTOR 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 4 / GLUR-4 / GLUR4 / AMPA-SELECTIVE GLUTAMATE RECEPTOR 4 / GLUR-D / GLUTAMATE RECEPTOR IONOTROPIC / ...GLUR-4 / GLUR4 / AMPA-SELECTIVE GLUTAMATE RECEPTOR 4 / GLUR-D / GLUTAMATE RECEPTOR IONOTROPIC / AMPA 4 / GLUA4 / GLUA4 AMPA RECEPTOR N-TERMINAL DOMAIN


Mass: 44547.430 Da / Num. of mol.: 2 / Fragment: RESIDUES 22-401
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: P19493
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: 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.: 3
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
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 125 / 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: 2.5 Å3/Da / Density % sol: 40.01 % / Description: NONE
Crystal growDetails: 17% PEG 3350 WITH 0.1-0.35 M AMMONIUM SULPHATE

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92
DetectorType: DECTRIS PILATUS / 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
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.497
11-h,-k,l20.503
ReflectionResolution: 2.5→39.68 Å / Num. obs: 45771 / % possible obs: 96.3 % / Observed criterion σ(I): 2 / Redundancy: 3.2 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 12.2
Reflection shellResolution: 2.5→2.64 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.35 / Mean I/σ(I) obs: 3 / % possible all: 96

-
Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 4GPA AND 3HSY

4gpa

3hsy


Resolution: 2.5→39.16 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.936 / SU B: 15.791 / SU ML: 0.187 / Cross valid method: THROUGHOUT / ESU R: 0.499 / ESU R Free: 0.065 / 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
Rfree0.23816 2398 5 %RANDOM
Rwork0.17159 ---
obs0.17507 45771 96.15 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 58.23 Å2
Baniso -1Baniso -2Baniso -3
1-33.78 Å20 Å29.74 Å2
2---46.52 Å20 Å2
3---12.74 Å2
Refinement stepCycle: LAST / Resolution: 2.5→39.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11148 0 62 125 11335
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.01911466
X-RAY DIFFRACTIONr_bond_other_d0.0020.0210467
X-RAY DIFFRACTIONr_angle_refined_deg1.6241.94415592
X-RAY DIFFRACTIONr_angle_other_deg1.022323896
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.04851447
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.89224.078515
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.243151736
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.9931558
X-RAY DIFFRACTIONr_chiral_restr0.0920.21767
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0213201
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022761
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_it2.7215.095818
X-RAY DIFFRACTIONr_mcbond_other2.7215.095817
X-RAY DIFFRACTIONr_mcangle_it4.4437.6237252
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.2755.015648
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: 2.499→2.564 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.325 186 -
Rwork0.204 3387 -
obs--96.05 %
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)
10.30660.05350.19420.76250.11410.18950.01670.0078-0.01790.07670.0801-0.0686-0.0328-0.0035-0.09680.05510.01660.06510.0916-0.01970.126812.41620.73836.587
20.5766-0.0363-0.07550.82850.06050.0536-0.0474-0.02310.03680.12860.0768-0.08790.04250.0004-0.02940.1050.03610.03340.05030.02060.0812.551-15.17438.562
30.6590.0067-0.1280.60970.1760.47970.0376-0.0214-0.0091-0.10460.1122-0.04990.05830.0047-0.14990.1016-0.03650.04090.0306-0.00960.125411.823-16.6581.939
40.5397-0.08910.1450.99130.15750.0808-0.1108-0.0326-0.0413-0.22190.1444-0.0237-0.09090.0315-0.03360.1304-0.03610.0760.08120.01660.091513.39119.1320.134
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A5 - 377
2X-RAY DIFFRACTION2B2 - 378
3X-RAY DIFFRACTION3C5 - 377
4X-RAY DIFFRACTION4D2 - 379

+
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