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- PDB-5fth: Crystal structure of the GluA2 K738M-T744K LBD in complex with gl... -

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Basic information

Entry
Database: PDB / ID: 5fth
TitleCrystal structure of the GluA2 K738M-T744K LBD in complex with glutamate (zinc form)
ComponentsGLUTAMATE RECEPTOR 2
KeywordsSIGNALING PROTEIN
Function / homology
Function and homology information


spine synapse / dendritic spine neck / dendritic spine head / Activation of AMPA receptors / perisynaptic space / AMPA glutamate receptor activity / ligand-gated monoatomic cation channel activity / Trafficking of GluR2-containing AMPA receptors / response to lithium ion / immunoglobulin binding ...spine synapse / dendritic spine neck / dendritic spine head / Activation of AMPA receptors / perisynaptic space / AMPA glutamate receptor activity / ligand-gated monoatomic cation channel activity / Trafficking of GluR2-containing AMPA receptors / response to lithium ion / immunoglobulin binding / AMPA glutamate receptor complex / kainate selective glutamate receptor activity / ionotropic glutamate receptor complex / cellular response to glycine / extracellularly glutamate-gated ion channel activity / asymmetric synapse / regulation of receptor recycling / Unblocking of NMDA receptors, glutamate binding and activation / positive regulation of synaptic transmission / glutamate receptor binding / glutamate-gated receptor activity / regulation of synaptic transmission, glutamatergic / response to fungicide / cytoskeletal protein binding / ionotropic glutamate receptor binding / presynaptic active zone membrane / extracellular ligand-gated monoatomic ion channel activity / somatodendritic compartment / glutamate-gated calcium ion channel activity / cellular response to brain-derived neurotrophic factor stimulus / ligand-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / dendrite membrane / dendrite cytoplasm / ionotropic glutamate receptor signaling pathway / 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 / synaptic membrane / modulation of chemical synaptic transmission / postsynaptic density membrane / terminal bouton / Schaffer collateral - CA1 synapse / cerebral cortex development / receptor internalization / synaptic vesicle membrane / synaptic vesicle / presynapse / signaling receptor activity / amyloid-beta binding / presynaptic membrane / growth cone / scaffold protein binding / chemical synaptic transmission / dendritic spine / perikaryon / postsynaptic membrane / neuron projection / postsynaptic density / axon / neuronal cell body / synapse / dendrite / protein-containing complex binding / protein kinase binding / glutamatergic synapse / cell surface / endoplasmic reticulum / protein-containing complex / identical protein binding / membrane / plasma membrane
Similarity search - Function
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 ...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 II / Periplasmic binding protein-like I / D-Maltodextrin-Binding Protein; domain 2 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
GLUTAMIC ACID / Glutamate receptor 2
Similarity search - Component
Biological speciesRATTUS NORVEGICUS (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsNayeem, N. / Green, T.
CitationJournal: Neuron / Year: 2016
Title: Distinct Structural Pathways Coordinate the Activation of Ampa Receptor-Auxiliary Subunit Complexes.
Authors: Dawe, G.B. / Musgaard, M. / Aurousseau, M.R.P. / Nayeem, N. / Green, T. / Biggin, P.C. / Bowie, D.
History
DepositionJan 13, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 3, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 16, 2016Group: Database references
Revision 1.2Mar 30, 2016Group: Database references
Revision 1.3Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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 / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,56111
Polymers96,7923
Non-polymers7688
Water00
1
A: GLUTAMATE RECEPTOR 2
B: GLUTAMATE RECEPTOR 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,0848
Polymers64,5282
Non-polymers5566
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1850 Å2
ΔGint-100.8 kcal/mol
Surface area22530 Å2
MethodPISA
2
C: GLUTAMATE RECEPTOR 2
hetero molecules

C: GLUTAMATE RECEPTOR 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,9536
Polymers64,5282
Non-polymers4254
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_558x,-y,-z+31
Buried area1760 Å2
ΔGint-65.6 kcal/mol
Surface area23190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.375, 110.523, 167.245
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121

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Components

#1: Protein GLUTAMATE RECEPTOR 2 / 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: 32264.088 Da / Num. of mol.: 3
Fragment: LIGAND BINDING DOMAIN, UNP RESIDUES 404-527,653-796
Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) RATTUS NORVEGICUS (Norway rat) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / Variant (production host): ROSETTA-GAMI B / References: UniProt: P19491
#2: Chemical ChemComp-GLU / GLUTAMIC ACID


Type: L-peptide linking / Mass: 147.129 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C5H9NO4
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Zn
Has protein modificationY
Nonpolymer detailsZINC ION (ZN): LOCATIONS IDENTIFIED USING MR-SAD
Sequence detailsEXPRESSED FRAGMENT INCLUDES TWO NON-CONTIGUOUS REGIONS FROM GENE, JOINED BY GLYTHR LINKER MAPPED TO ...EXPRESSED FRAGMENT INCLUDES TWO NON-CONTIGUOUS REGIONS FROM GENE, JOINED BY GLYTHR LINKER MAPPED TO FLIP ISOFORM, P19491-2

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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: 1.9 Å3/Da / Density % sol: 35 %
Description: R-MEAS FOR HIGHEST RESOLUTION SHELL WAS 1.68. HAVE ENTERED AS 1.5 TO AVOID ERROR.
Crystal growpH: 6 / Details: 15% PEG 8,000, 200 MM ZN ACETATE, 100MM MES PH 6.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97625
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 2.9→92.2 Å / Num. obs: 36525 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 5 % / Biso Wilson estimate: 70.41 Å2 / Rmerge(I) obs: 0.22 / Net I/σ(I): 4.5
Reflection shellResolution: 2.9→3.08 Å / Redundancy: 5.1 % / Rmerge(I) obs: 1.5 / Mean I/σ(I) obs: 1.1 / % possible all: 100

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Processing

Software
NameClassification
XDSdata reduction
Aimlessdata scaling
REFMACphasing
PHENIXphasing
PHENIXrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2UXA

2uxa


Resolution: 2.9→92.208 Å / SU ML: 0.41 / σ(F): 0 / Phase error: 34.66 / Stereochemistry target values: ML
Details: INITIAL REFINEMENT CARRIED OUT WITH REFMAC5, USING SHARPENED MAPS. FINAL REFINEMENT CYCLES CARRIED OUT USING PHENIX.REFINE AND FEATURE ENHANCED MAPS.
RfactorNum. reflection% reflection
Rfree0.2829 1818 5 %
Rwork0.2429 --
obs0.2449 36525 99.34 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.9→92.208 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5873 0 35 0 5908
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0066013
X-RAY DIFFRACTIONf_angle_d1.0358057
X-RAY DIFFRACTIONf_dihedral_angle_d13.6152259
X-RAY DIFFRACTIONf_chiral_restr0.04899
X-RAY DIFFRACTIONf_plane_restr0.004996
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9001-2.97850.44981390.40552616X-RAY DIFFRACTION100
2.9785-3.06620.44781490.37582728X-RAY DIFFRACTION100
3.0662-3.16520.35891450.34852633X-RAY DIFFRACTION99
3.1652-3.27830.35581350.29542677X-RAY DIFFRACTION99
3.2783-3.40960.30991360.26752681X-RAY DIFFRACTION100
3.4096-3.56470.32531480.23862716X-RAY DIFFRACTION100
3.5647-3.75270.26671440.23312616X-RAY DIFFRACTION99
3.7527-3.98780.27081390.22632649X-RAY DIFFRACTION99
3.9878-4.29570.26321430.19212678X-RAY DIFFRACTION100
4.2957-4.7280.23451300.17772654X-RAY DIFFRACTION98
4.728-5.41210.19731370.19032668X-RAY DIFFRACTION99
5.4121-6.81830.28721390.25932700X-RAY DIFFRACTION100
6.8183-92.25430.2681340.25252691X-RAY DIFFRACTION100
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)
13.23820.21620.07453.36480.16551.27150.1303-0.62240.6923-0.1691-0.0832-0.4346-0.08740.1397-0.0580.57640.00670.03210.69220.04560.823626.180621.3118207.0847
22.344-0.0229-0.37661.61770.44421.03340.21191.29981.3038-0.527-0.2324-0.045-0.22010.02420.03080.83220.080.03971.08330.3830.930410.907724.7314190.9329
31.3370.13590.63031.6744-0.05261.14660.04110.35860.30490.08750.12480.5078-0.04640.0105-0.23810.6137-0.0520.02030.84140.21480.804116.416813.4532200.3588
44.3306-0.3963-0.11291.9062-0.32963.1875-0.2878-0.12830.4985-0.12230.03740.794-0.4183-1.56580.36430.65920.1348-0.01060.98180.05530.92598.860412.6415209.7766
52.5111-0.2257-0.14294.16590.79222.36670.32961.0468-0.2735-0.61130.0518-0.29330.22240.5468-0.5170.65140.13860.03551.0763-0.31240.92524.9509-9.5604180.7727
64.2647-0.39770.59150.16130.43592.0644-0.09590.55130.00860.2778-0.2896-0.36070.12190.30040.37810.84160.1123-0.01560.4302-0.00371.022727.3468-5.9256191.9601
74.2440.68270.01292.31750.50842.02780.2516-1.0472-1.91110.2369-0.13550.79090.5232-0.1589-0.10990.8105-0.0040.08490.7980.22011.73847.6325-15.1081199.4797
81.5805-0.2824-0.26493.0975-0.03331.4408-0.0370.5209-0.1485-0.34750.00061.0357-0.3022-0.9872-0.00290.68690.2238-0.07291.2496-0.01740.935613.2933-1.668184.8822
90.0198-0.0761-0.12541.21320.03851.25670.0052-0.1635-0.09620.05610.0198-0.1031-0.5678-0.5729-0.08290.714-0.2777-0.11111.40680.32750.636731.712217.907240.8655
104.2524-1.53242.71272.8385-0.67712.15350.29660.03720.19810.098-0.0558-0.0729-0.14430.4148-0.1571.25110.1002-0.19220.91430.17310.744330.234529.1051240.3899
112.34450.6050.12862.2012-0.42321.52960.14090.69490.48480.0593-0.1464-0.3588-0.220.2395-0.04430.823-0.20590.00991.27070.34020.588534.782913.4823240.4271
120.96110.2032-0.65181.3294-0.65091.7778-0.02620.10790.43780.1439-0.22040.5168-0.19730.49120.13620.7472-0.1942-0.0081.83730.6979-0.014529.04345.9036239.1389
131.8126-0.07761.1672.05030.40362.62940.3651-0.20950.0335-0.0145-0.3121-0.0250.5896-0.3964-0.06280.7798-0.15840.03221.21460.38420.648615.47253.6361229.6991
141.0820.1794-0.05091.77020.31881.09030.0110.0122-0.08150.2362-0.353-0.0531-0.1730.0850.37610.739-0.00890.03471.46150.28380.570626.842711.2396250.7069
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESID 393:475)
2X-RAY DIFFRACTION2(CHAIN A AND (RESID 476:711 OR RESID 900))
3X-RAY DIFFRACTION3(CHAIN A AND RESID 712:756)
4X-RAY DIFFRACTION4(CHAIN A AND RESID 757:773)
5X-RAY DIFFRACTION5(CHAIN B AND RESID 393:460)
6X-RAY DIFFRACTION6(CHAIN B AND (RESID 461:495 OR RESID 900))
7X-RAY DIFFRACTION7(CHAIN B AND RESID 496:706)
8X-RAY DIFFRACTION8(CHAIN B AND RESID 707:773)
9X-RAY DIFFRACTION9(CHAIN C AND RESID 393:407)
10X-RAY DIFFRACTION10(CHAIN C AND RESID 408:421)
11X-RAY DIFFRACTION11(CHAIN C AND RESID 422:461)
12X-RAY DIFFRACTION12(CHAIN C AND (RESID 462:632 OR RESID 900))
13X-RAY DIFFRACTION13(CHAIN C AND RESID 633:728)
14X-RAY DIFFRACTION14(CHAIN C AND RESID 729:773)

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