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

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Basic information

Entry
Database: PDB / ID: 5fti
TitleCrystal structure of the GluA2 K738M-T744K LBD in complex with glutamate (lithium 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 / extracellularly glutamate-gated ion channel activity ...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 / extracellularly glutamate-gated ion channel activity / immunoglobulin binding / AMPA glutamate receptor complex / kainate selective glutamate receptor activity / ionotropic glutamate receptor complex / cellular response to glycine / asymmetric synapse / regulation of receptor recycling / Unblocking of NMDA receptors, glutamate binding and activation / glutamate receptor binding / positive regulation of synaptic transmission / extracellular ligand-gated monoatomic ion channel activity / glutamate-gated receptor activity / response to fungicide / glutamate-gated calcium ion channel activity / presynaptic active zone membrane / regulation of synaptic transmission, glutamatergic / ionotropic glutamate receptor binding / somatodendritic compartment / dendrite membrane / cellular response to brain-derived neurotrophic factor stimulus / ligand-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / cytoskeletal protein binding / dendrite cytoplasm / ionotropic glutamate receptor signaling pathway / SNARE binding / dendritic shaft / synaptic transmission, glutamatergic / synaptic membrane / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / PDZ domain binding / protein tetramerization / postsynaptic density membrane / establishment of protein localization / modulation of chemical synaptic transmission / Schaffer collateral - CA1 synapse / terminal bouton / receptor internalization / cerebral cortex development / synaptic vesicle membrane / synaptic vesicle / presynapse / signaling receptor activity / presynaptic membrane / amyloid-beta binding / growth cone / scaffold protein binding / chemical synaptic transmission / perikaryon / postsynaptic membrane / dendritic spine / postsynaptic density / neuron projection / axon / neuronal cell body / glutamatergic synapse / dendrite / synapse / protein-containing complex binding / protein kinase binding / 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: 1.35 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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_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_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _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_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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,40512
Polymers64,5282
Non-polymers87710
Water12,394688
1
A: GLUTAMATE RECEPTOR 2
hetero molecules

A: GLUTAMATE RECEPTOR 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,40512
Polymers64,5282
Non-polymers87710
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_457-x-1,y,-z+21
Buried area3120 Å2
ΔGint-76.1 kcal/mol
Surface area24290 Å2
MethodPISA
2
B: GLUTAMATE RECEPTOR 2
hetero molecules

B: GLUTAMATE RECEPTOR 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,40512
Polymers64,5282
Non-polymers87710
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_358-x-2,y,-z+31
Buried area3020 Å2
ΔGint-65.5 kcal/mol
Surface area24050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.316, 47.562, 96.754
Angle α, β, γ (deg.)90.00, 95.65, 90.00
Int Tables number3
Space group name H-MP121
Components on special symmetry positions
IDModelComponents
11A-2134-

HOH

21B-2113-

HOH

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Components

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Protein , 1 types, 2 molecules AB

#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.: 2
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

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Non-polymers , 5 types, 698 molecules

#2: Chemical ChemComp-GLU / GLUTAMIC ACID


Type: L-peptide linking / Mass: 147.129 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H9NO4
#3: Chemical ChemComp-LI / LITHIUM ION


Mass: 6.941 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Li
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 688 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.7 Å3/Da / Density % sol: 54 % / Description: NONE
Crystal growpH: 5
Details: 22% PEG 4,000, 200 MM LI SULPHATE, 100MM ACETATE PH 5.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.976
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 1.35→67 Å / Num. obs: 126864 / % possible obs: 94.7 % / Observed criterion σ(I): 2 / Redundancy: 3.5 % / Biso Wilson estimate: 15.72 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 10.9
Reflection shellResolution: 1.35→1.39 Å / Redundancy: 3.6 % / Rmerge(I) obs: 1.11 / Mean I/σ(I) obs: 1.88 / % possible all: 92.5

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2UXA

2uxa


Resolution: 1.35→66.989 Å / SU ML: 0.13 / σ(F): 1.36 / Phase error: 19.21 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1775 2538 2 %
Rwork0.1612 --
obs0.1615 126864 94.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.35→66.989 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4039 0 54 688 4781
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0114284
X-RAY DIFFRACTIONf_angle_d1.3915787
X-RAY DIFFRACTIONf_dihedral_angle_d12.1871653
X-RAY DIFFRACTIONf_chiral_restr0.094641
X-RAY DIFFRACTIONf_plane_restr0.007719
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.35-1.3760.29051370.27996702X-RAY DIFFRACTION93
1.376-1.40410.27321380.27096767X-RAY DIFFRACTION93
1.4041-1.43460.28011370.25366731X-RAY DIFFRACTION93
1.4346-1.4680.26291380.24826767X-RAY DIFFRACTION93
1.468-1.50470.26371380.2296766X-RAY DIFFRACTION94
1.5047-1.54540.21961400.20286811X-RAY DIFFRACTION94
1.5454-1.59080.19791400.18366876X-RAY DIFFRACTION94
1.5908-1.64220.1981410.16846914X-RAY DIFFRACTION95
1.6422-1.70090.18651400.16196886X-RAY DIFFRACTION95
1.7009-1.7690.19891430.15946966X-RAY DIFFRACTION96
1.769-1.84950.18171420.15736951X-RAY DIFFRACTION96
1.8495-1.9470.17311420.15226983X-RAY DIFFRACTION96
1.947-2.0690.16751440.157078X-RAY DIFFRACTION96
2.069-2.22880.17231440.14467025X-RAY DIFFRACTION96
2.2288-2.45310.16541430.15177000X-RAY DIFFRACTION96
2.4531-2.80810.19031420.16156982X-RAY DIFFRACTION95
2.8081-3.53790.16931420.14896972X-RAY DIFFRACTION94
3.5379-67.07140.14571470.14667149X-RAY DIFFRACTION95
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)
12.4282-0.5601-0.30072.57110.34362.26120.175-0.39970.05110.3364-0.09540.0495-0.00910.0354-0.05540.1621-0.04540.01070.1687-0.0050.092-54.413546.8361116.5313
20.45470.4212-0.18182.0060.50310.69730.06310.00550.0786-0.0003-0.04770.1598-0.0542-0.0515-0.03010.1010.0115-0.00270.14570.00690.1258-57.510647.414100.6585
31.08220.3341-0.44041.3333-0.53092.6167-0.05990.1103-0.0039-0.05220.03620.03350.12-0.17360.02230.0689-0.0047-0.00680.1288-0.00440.1026-62.801632.232694.736
42.06250.34740.07642.7469-0.80191.67230.086-0.1304-0.0820.1332-0.0702-0.06740.01530.1272-0.00530.0904-0.00030.00090.1408-0.0120.0746-45.287944.0807107.6681
52.01061.99632.00092.00331.99861.99810.09330.35840.04610.6953-0.0760.76580.3408-0.1221-0.04450.15360.00450.00470.1553-0.00780.158-58.394942.452798.5826
62.22970.3933-1.13441.552-0.19132.68260.00620.01750.0012-0.1523-0.0136-0.12150.10830.1630.01610.19810.00020.04080.1308-0.01610.1057-72.789327.77124.1822
70.9246-0.53230.14313.8232-0.42871.0784-0.052-0.0284-0.0332-0.16080.08580.15780.0139-0.0883-0.0010.1716-0.02770.00850.1528-0.0040.1045-86.95129.9244131.4672
83.80210.22240.07362.4035-0.39482.3679-0.05830.0150.1621-0.0380.09670.14-0.1333-0.19-0.04170.24940.00690.0030.1499-0.00770.1505-92.998143.6031128.2369
92.66930.6505-0.43132.6407-1.15642.73010.0359-0.18350.11160.019-0.0214-0.1807-0.21720.39230.01770.1841-0.02840.03810.1957-0.03070.0881-73.068431.2065137.2582
106.6467-5.98134.29188.73690.38818.16570.2122-0.13370.4097-0.4663-0.23020.02250.0504-0.15560.01430.2983-0.01950.03330.1575-0.01450.1753-87.373333.4051130.106
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN 'A' AND (RESID 392:436 )
2X-RAY DIFFRACTION2CHAIN 'A' AND (RESID 437:635 )
3X-RAY DIFFRACTION3CHAIN 'A' AND (RESID 636:729 )
4X-RAY DIFFRACTION4CHAIN 'A' AND (RESID 730:774 )
5X-RAY DIFFRACTION5CHAIN 'A' AND (RESID 900:900 )
6X-RAY DIFFRACTION6CHAIN 'B' AND (RESID 393:454 )
7X-RAY DIFFRACTION7CHAIN 'B' AND (RESID 455:635 )
8X-RAY DIFFRACTION8CHAIN 'B' AND (RESID 636:729 )
9X-RAY DIFFRACTION9CHAIN 'B' AND (RESID 730:774 )
10X-RAY DIFFRACTION10CHAIN 'B' AND (RESID 900:900 )

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