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- PDB-3hsy: High resolution structure of a dimeric GluR2 N-terminal domain (NTD) -

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Basic information

Entry
Database: PDB / ID: 3hsy
TitleHigh resolution structure of a dimeric GluR2 N-terminal domain (NTD)
ComponentsGlutamate receptor 2
KeywordsTRANSPORT PROTEIN / GLUTAMATE RECEPTOR / LIGAND-GATED ION CHANNEL / SYNAPSE / CELL JUNCTION / CELL MEMBRANE / ENDOPLASMIC RETICULUM / GLYCOPROTEIN / ION TRANSPORT / IONIC CHANNEL / LIPOPROTEIN / MEMBRANE / PALMITATE / PHOSPHOPROTEIN / POSTSYNAPTIC CELL MEMBRANE / RECEPTOR / RNA EDITING / TRANSMEMBRANE / TRANSPORT
Function / homology
Function and homology information


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 ...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 / kainate selective glutamate receptor activity / AMPA glutamate receptor complex / cellular response to glycine / extracellularly glutamate-gated ion channel activity / ionotropic glutamate receptor complex / immunoglobulin binding / asymmetric synapse / conditioned place preference / regulation of receptor recycling / glutamate receptor binding / Unblocking of NMDA receptors, glutamate binding and activation / positive regulation of synaptic transmission / regulation of synaptic transmission, glutamatergic / response to fungicide / glutamate-gated receptor activity / cytoskeletal protein binding / regulation of long-term synaptic depression / 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 / SNARE binding / dendritic shaft / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / synaptic transmission, glutamatergic / PDZ domain binding / protein tetramerization / establishment of protein localization / postsynaptic density membrane / modulation of chemical synaptic transmission / cerebral cortex development / receptor internalization / Schaffer collateral - CA1 synapse / terminal bouton / synaptic vesicle / synaptic vesicle membrane / presynapse / signaling receptor activity / amyloid-beta binding / growth cone / presynaptic membrane / scaffold protein binding / perikaryon / chemical synaptic transmission / dendritic spine / 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
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.75 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
DepositionJun 11, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 16, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / 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 / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.auth_asym_id / _atom_site.auth_seq_id ..._atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_entity_id / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 3.0Dec 25, 2024Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_distant_solvent_atoms / pdbx_entry_details / pdbx_modification_feature / pdbx_nonpoly_scheme / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_close_contact / struct_conn
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_seq_id / _atom_site.label_asym_id / _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nonpoly_scheme.asym_id / _pdbx_nonpoly_scheme.auth_seq_num / _pdbx_nonpoly_scheme.ndb_seq_num / _pdbx_nonpoly_scheme.pdb_seq_num / _pdbx_nonpoly_scheme.pdb_strand_id / _pdbx_unobs_or_zero_occ_atoms.auth_seq_id

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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)86,4439
Polymers85,0302
Non-polymers1,4137
Water11,458636
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2730 Å2
ΔGint-15 kcal/mol
Surface area31440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.452, 93.695, 101.466
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 / GluR-2 / GluR-B / GluR-K2 / Glutamate receptor ionotropic / AMPA 2 / AMPA-selective glutamate receptor 2


Mass: 42515.012 Da / Num. of mol.: 2 / Fragment: N-terminal Domain, UNP residues 25-400
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Gria2, Glur2 / Plasmid: pFastBac1 / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): High5 / References: UniProt: P19491
#2: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}}LINUCSPDB-CARE
#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.: 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
#4: Chemical
ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 636 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.3 Å3/Da / Density % sol: 46.63 % / Mosaicity: 0 °
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.8
Details: 200mM ammonium phosphatre, 20% PEG3350, pH4.8, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.95294 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: May 15, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95294 Å / Relative weight: 1
ReflectionRedundancy: 5 % / Number: 35008 / Rmerge(I) obs: 0.123 / Rsym value: 0.064 / D res high: 2.1 Å / Num. obs: 30290 / % possible obs: 34.5
Diffraction reflection shell

ID: 1

Highest resolution (Å)Lowest resolution (Å)Num. obs% possible obs (%)Rmerge(I) obsRsym valueRedundancy
6.2444.61106131.90.0240.0254.8
4.436.24209635.20.0360.034.9
3.624.43285337.10.040.0375
3.143.62348338.10.0670.0495.1
2.813.14386737.60.1590.0665.1
2.572.81416436.40.2770.0915.1
2.382.57443235.80.4740.1365.1
2.222.38463334.80.590.2075.1
2.12.223701261.0240.3565.1
ReflectionResolution: 1.75→68.84 Å / Num. obs: 79848 / % possible obs: 100 % / Redundancy: 5 % / Biso Wilson estimate: 21.01 Å2 / Rsym value: 0.064
Reflection shellResolution: 1.75→1.84 Å / Redundancy: 5 % / Mean I/σ(I) obs: 2.8 / Num. unique all: 11530 / Rsym value: 0.581 / % possible all: 100

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassificationNB
SCALA3.3.15data processing
SHARPphasing
PHENIX1.6.1_357refinement
PDB_EXTRACT3.1data extraction
ADSCQuantumdata collection
XDSdata reduction
SCALAdata scaling
autoSHARPphasing
RefinementResolution: 1.75→42.533 Å / Occupancy max: 1 / Occupancy min: 0.21 / FOM work R set: 0.887 / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 18.46 / Stereochemistry target values: ML / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.205 1588 1.99 %RANDOM
Rwork0.178 78175 --
obs0.178 79763 99.95 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 38.88 Å2 / ksol: 0.356 e/Å3
Displacement parametersBiso max: 154.51 Å2 / Biso mean: 28.616 Å2 / Biso min: 6.88 Å2
Baniso -1Baniso -2Baniso -3
1-0.185 Å2-0 Å20 Å2
2---0.252 Å20 Å2
3---0.067 Å2
Refinement stepCycle: LAST / Resolution: 1.75→42.533 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5785 0 87 636 6508
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0066101
X-RAY DIFFRACTIONf_angle_d1.0648282
X-RAY DIFFRACTIONf_chiral_restr0.131919
X-RAY DIFFRACTIONf_plane_restr0.0051067
X-RAY DIFFRACTIONf_dihedral_angle_d13.1862252
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.75-1.8130.2611560.22177157871
1.813-1.8850.2141620.19977117873
1.885-1.9710.2251570.17777317888
1.971-2.0750.1921360.16777877923
2.075-2.2050.2331400.16477847924
2.205-2.3750.171590.16177707929
2.375-2.6140.1991570.16878157972
2.614-2.9920.2141690.17978388007
2.992-3.770.1891810.16978948075
3.77-42.5460.1891710.16881308301
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)
10.47610.45050.21260.91510.67520.48710.0416-0.03580.0419-0.0269-0.07810.043-0.0385-0.07720.03760.03420.00010.00290.046-0.00150.0192-3.184-2.685-4.2335
21.06571.1144-0.2311.4551-0.30160.7634-0.0471-0.0093-0.0567-0.06510.012-0.03250.01540.14650.02930.04080.01060.0020.0674-0.02180.048711.0252-18.8997-25.3197
30.0482-0.0067-0.18510.6326-0.03431.14890.02820.0167-0.05650.0064-0.17460.1615-0.0533-0.38680.10170.0374-0.019-0.01740.1338-0.03840.085-11.8439-13.6961-5.5984
40.42680.1263-0.18930.3046-0.57860.97590.0384-0.2901-0.20160.3296-0.1781-0.00020.428-0.09880.07780.007-0.0015-0.0353-0.07970.0203-0.01992.2423-18.3533-4.4323
51.53620.2282-0.1081-0.0433-0.07870.4657-0.0313-0.04210.08590.03850.030.0035-0.0634-0.01110.00270.0840.00850.00170.047-0.00080.072920.562816.1179-7.9777
60.71550.3257-0.04720.5019-0.39970.515-0.0646-0.064-0.17670.01130.0131-0.10180.05960.04730.05180.05920.03210.00760.04820.01940.088235.5607-9.944-15.3479
70.15660.25630.03150.39740.02960.0827-0.00010.02040.0321-0.00440.0027-0.0297-0.00320.0272-0.01060.0202-0.0227-0.00080.0496-0.00040.029735.017620.9165-9.1129
80.6632-0.2641-0.21870.45070.20550.2516-0.00610.11820.0144-0.017-0.0245-0.0443-0.03410.00560.02040.0297-0.0008-0.00540.05210.01740.015927.735714.0958-20.196
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 4:109)A4 - 109
2X-RAY DIFFRACTION2(chain A and resid 110:240)A110 - 240
3X-RAY DIFFRACTION3(chain A and resid 241:306)A241 - 306
4X-RAY DIFFRACTION4(chain A and resid 307:377)A307 - 377
5X-RAY DIFFRACTION5(chain B and resid 4:110)B4 - 110
6X-RAY DIFFRACTION6(chain B and resid 111:241)B111 - 241
7X-RAY DIFFRACTION7(chain B and resid 242:301)B242 - 301
8X-RAY DIFFRACTION8(chain B and resid 302:379)B302 - 379

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