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- PDB-3o2j: Structure of the GluA2 NTD-dimer interface mutant, N54A -

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Basic information

Entry
Database: PDB / ID: 3o2j
TitleStructure of the GluA2 NTD-dimer interface mutant, N54A
ComponentsGlutamate receptor 2GRIA2
KeywordsTRANSPORT PROTEIN / AMPA / periplasmatic binding protein / NTD / ATD / Oligomerization
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 / : / Response regulator / 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 ...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 / : / Response regulator / 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
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsRossmann, M. / Sukumaran, M. / Penn, A.C. / Veprintsev, D.B. / Greger, I.H.
CitationJournal: Embo J. / Year: 2011
Title: Subunit-selective N-terminal domain associations organize the formation of AMPA receptor heteromers
Authors: Rossmann, M. / Sukumaran, M. / Penn, A.C. / Veprintsev, D.B. / Babu, M.M. / Greger, I.H.
History
DepositionJul 22, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 9, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Nov 1, 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)88,3664
Polymers87,9232
Non-polymers4422
Water7,296405
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2710 Å2
ΔGint-15 kcal/mol
Surface area30220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.330, 92.580, 102.480
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Glutamate receptor 2 / GRIA2 / GluR-2 / GluR-B / GluR-K2 / Glutamate receptor ionotropic / AMPA 2 / GluA2 / AMPA-selective ...GluR-2 / GluR-B / GluR-K2 / Glutamate receptor ionotropic / AMPA 2 / GluA2 / AMPA-selective glutamate receptor 2


Mass: 43961.613 Da / Num. of mol.: 2 / Fragment: N-terminal domain / Mutation: N54A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Gria2, Glur2 / Production host: Homo sapiens (human) / References: UniProt: P19491
#2: 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.: 2
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
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 405 / Source method: isolated from a natural source / Formula: H2O

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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: 2.22 Å3/Da / Density % sol: 44.62 % / Mosaicity: 0.99 °
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 18% PEG 3350, 100mM sodium citrate, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.95→68.698 Å / Num. all: 57819 / Num. obs: 57819 / % possible obs: 100 % / Redundancy: 6.9 % / Rsym value: 0.128 / Net I/σ(I): 10.6
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) allRmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRrim(I) allRsym valueNet I/σ(I) obs% possible all
1.95-2.0670.7880.72915812983510.2970.7880.7292.7100
2.06-2.1870.5320.4921.55528978940.20.5320.4924.1100
2.18-2.3370.3620.3352.35213774250.1360.3620.3355.8100
2.33-2.5270.2640.2443.14846169290.0990.2640.2447.6100
2.52-2.766.90.1860.1724.44434763960.070.1860.1729.9100
2.76-3.086.90.130.126.24020358160.0490.130.1213.1100
3.08-3.566.90.10.0937.23563851650.0380.10.09317.5100
3.56-4.366.80.0930.0867.12952643730.0360.0930.08622.299.9
4.36-6.176.50.0730.0678.22249334590.0290.0730.06724100
6.17-51.246.70.0330.03117.91350220110.0130.0330.03125.899.8

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Processing

Software
NameVersionClassificationNB
SCALA3.3.16data processing
PHENIX1.6.1_357refinement
PDB_EXTRACT3.1data extraction
ADSCQuantumdata collection
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3HSY

3hsy


Resolution: 1.95→51.24 Å / Occupancy max: 1 / Occupancy min: 0.47 / FOM work R set: 0.8591 / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 0.28 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2466 2342 4.06 %
Rwork0.1911 --
obs0.1933 57693 99.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 60.73 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso max: 92.38 Å2 / Biso mean: 29.6242 Å2 / Biso min: 9.69 Å2
Baniso -1Baniso -2Baniso -3
1-0.4791 Å20 Å2-0 Å2
2--0.1655 Å2-0 Å2
3----0.6446 Å2
Refinement stepCycle: LAST / Resolution: 1.95→51.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5649 0 28 405 6082
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0075836
X-RAY DIFFRACTIONf_angle_d0.9997904
X-RAY DIFFRACTIONf_chiral_restr0.068880
X-RAY DIFFRACTIONf_plane_restr0.0041017
X-RAY DIFFRACTIONf_dihedral_angle_d13.3042108
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
1.95-1.98980.28911430.224332043347
1.9898-2.03310.28761390.219532233362
2.0331-2.08040.28551240.219132133337
2.0804-2.13240.28791240.208332273351
2.1324-2.19010.2631290.194732273356
2.1901-2.25450.26931360.184232353371
2.2545-2.32730.2561610.175631993360
2.3273-2.41040.22591490.181432063355
2.4104-2.5070.26321410.177332423383
2.507-2.6210.24691140.18432573371
2.621-2.75920.22661430.178132413384
2.7592-2.93210.24671390.190332653404
2.9321-3.15840.24411290.188532563385
3.1584-3.47620.24841290.184632683397
3.4762-3.97910.23471470.170933013448
3.9791-5.01250.19651340.171533223456
5.0125-51.25770.25661610.225134653626

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