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- PDB-4u4f: Structure of GluA2* in complex with partial agonist (S)-5-Nitrowi... -

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Basic information

Entry
Database: PDB / ID: 4u4f
TitleStructure of GluA2* in complex with partial agonist (S)-5-Nitrowillardiine
ComponentsGlutamate receptor 2GRIA2
KeywordsTRANSPORT PROTEIN / Ionotropic glutamate receptor / AMPA receptor / partial agonist / tetramer / complex
Function / homology
Function and homology information


spine synapse / dendritic spine neck / dendritic spine head / Activation of AMPA receptors / response to lithium ion / perisynaptic space / cellular response to glycine / AMPA glutamate receptor activity / Trafficking of GluR2-containing AMPA receptors / immunoglobulin binding ...spine synapse / dendritic spine neck / dendritic spine head / Activation of AMPA receptors / response to lithium ion / perisynaptic space / cellular response to glycine / AMPA glutamate receptor activity / Trafficking of GluR2-containing AMPA receptors / immunoglobulin binding / AMPA glutamate receptor complex / kainate selective glutamate receptor activity / ionotropic glutamate receptor complex / extracellularly glutamate-gated ion channel activity / 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 / cellular response to brain-derived neurotrophic factor stimulus / somatodendritic compartment / dendrite membrane / ligand-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / ionotropic glutamate receptor binding / ionotropic glutamate receptor signaling pathway / dendrite cytoplasm / cytoskeletal protein binding / SNARE binding / dendritic shaft / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / synaptic membrane / synaptic transmission, glutamatergic / PDZ domain binding / postsynaptic density membrane / protein tetramerization / modulation of chemical synaptic transmission / Schaffer collateral - CA1 synapse / establishment of protein localization / terminal bouton / receptor internalization / synaptic vesicle membrane / cerebral cortex development / synaptic vesicle / presynapse / signaling receptor activity / presynaptic membrane / amyloid-beta binding / growth cone / perikaryon / chemical synaptic transmission / postsynaptic membrane / scaffold protein binding / dendritic spine / postsynaptic density / neuron projection / axon / dendrite / neuronal cell body / glutamatergic synapse / synapse / protein-containing complex binding / endoplasmic reticulum membrane / protein kinase binding / cell surface / endoplasmic reticulum / protein-containing complex / membrane / identical protein binding / 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 I
Similarity search - Domain/homology
Chem-NWD / Glutamate receptor 2
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.79 Å
AuthorsYelshanskaya, M.V. / Li, M. / Sobolevsky, A.I.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)NS083660 United States
CitationJournal: Science / Year: 2014
Title: Structure of an agonist-bound ionotropic glutamate receptor.
Authors: Yelshanskaya, M.V. / Li, M. / Sobolevsky, A.I.
History
DepositionJul 23, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 27, 2014Provider: repository / Type: Initial release
Revision 1.1Oct 1, 2014Group: Database references
Revision 2.0Sep 13, 2017Group: Atomic model / Author supporting evidence ...Atomic model / Author supporting evidence / Database references / Derived calculations / Other / Source and taxonomy / Structure summary
Category: atom_site / citation ...atom_site / citation / entity / entity_src_gen / pdbx_audit_support / pdbx_database_status / pdbx_struct_assembly_gen / pdbx_struct_oper_list / struct_conn
Item: _atom_site.label_asym_id / _atom_site.label_entity_id ..._atom_site.label_asym_id / _atom_site.label_entity_id / _citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_label_asym_id
Revision 2.1Nov 22, 2017Group: Refinement description / Category: software / Item: _software.classification
Revision 2.2Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 3.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Refinement description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / 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_validate_close_contact / refine_hist / struct_asym / struct_conn / 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.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_entity_nonpoly.comp_id / _pdbx_entity_nonpoly.entity_id / _pdbx_entity_nonpoly.name / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 3.1Sep 27, 2023Group: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)371,42412
Polymers368,9534
Non-polymers2,4718
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area25540 Å2
ΔGint-185 kcal/mol
Surface area139470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)141.374, 166.575, 566.604
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein
Glutamate receptor 2 / GRIA2 / 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: 92238.320 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Gria2, Glur2 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P19491
#2: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 3 / Source method: obtained synthetically
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#3: Chemical
ChemComp-NWD / 3-(5-nitro-2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-L-alanine / nitrowillardiine


Type: L-peptide linking / Mass: 244.162 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C7H8N4O6
#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 / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1 / Source method: obtained synthetically / 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

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 4.49 Å3/Da / Density % sol: 72.62 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: 11-14% (w/v) PEG 3,000, 50 mM lithium sulfate, 0.1 M tricine
PH range: 7.0-7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 12, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
ReflectionResolution: 4.79→50 Å / Num. obs: 30052 / % possible obs: 89.9 % / Redundancy: 4.7 % / Biso Wilson estimate: 268.82 Å2 / Rmerge(I) obs: 0.063 / Net I/σ(I): 18.7
Reflection shellResolution: 4.79→4.97 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.992 / Mean I/σ(I) obs: 1.6 / % possible all: 85.2

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE: 1.8_1069)refinement
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3H5V, 3KG2, 3RTW

3h5v

3kg2

3rtw


Resolution: 4.79→39.95 Å / SU ML: 0.64 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 28.9 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.262 1510 5.04 %Random selection
Rwork0.228 ---
obs0.229 29984 89.8 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 4.79→39.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms23901 0 166 0 24067
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00324567
X-RAY DIFFRACTIONf_angle_d0.70833209
X-RAY DIFFRACTIONf_dihedral_angle_d13.2758909
X-RAY DIFFRACTIONf_chiral_restr0.0483736
X-RAY DIFFRACTIONf_plane_restr0.0034192
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
4.7909-4.94530.31061390.31022398X-RAY DIFFRACTION84
4.9453-5.12170.34971120.28342419X-RAY DIFFRACTION85
5.1217-5.32630.32651320.27072438X-RAY DIFFRACTION86
5.3263-5.56810.30611390.25142448X-RAY DIFFRACTION85
5.5681-5.86080.24881340.23482488X-RAY DIFFRACTION88
5.8608-6.22680.28161290.23092529X-RAY DIFFRACTION89
6.2268-6.70550.28251400.21412620X-RAY DIFFRACTION91
6.7055-7.37640.26181340.20842680X-RAY DIFFRACTION93
7.3764-8.43510.23371390.18522814X-RAY DIFFRACTION96
8.4351-10.59440.20861650.19052808X-RAY DIFFRACTION98
10.5944-39.94720.28821470.25032832X-RAY DIFFRACTION93

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