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- PDB-4o3a: Crystal structure of the glua2 ligand-binding domain in complex w... -

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Basic information

Entry
Database: PDB / ID: 4o3a
TitleCrystal structure of the glua2 ligand-binding domain in complex with L-aspartate at 1.80 a resolution
ComponentsGlutamate receptor 2
KeywordsMEMBRANE PROTEIN/AGONIST / AMPA RECEPTOR LIGAND-BINDING DOMAIN / MEMBRANE PROTEIN-AGONIST complex
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 / extracellularly glutamate-gated ion channel activity / cellular response to glycine / asymmetric synapse / regulation of receptor recycling / Unblocking of NMDA receptors, glutamate binding and activation / positive regulation of synaptic transmission / glutamate receptor binding / 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 / somatodendritic compartment / dendrite membrane / cellular response to brain-derived neurotrophic factor stimulus / cytoskeletal protein binding / ligand-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / ionotropic glutamate receptor 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
ACETATE ION / ASPARTIC ACID / DI(HYDROXYETHYL)ETHER / Glutamate receptor 2
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.8 Å
AuthorsKrintel, C. / Frydenvang, F. / Gajhede, M. / Kastrup, J.S.
Citation
Journal: Febs J. / Year: 2014
Title: L-Asp is a useful tool in the purification of the ionotropic glutamate receptor A2 ligand-binding domain.
Authors: Krintel, C. / Frydenvang, K. / Ceravalls de Rabassa, A. / Kaern, A.M. / Gajhede, M. / Pickering, D.S. / Kastrup, J.S.
#1: Journal: Neuron / Year: 2000
Title: Mechanisms for activation and antagonism of an AMPA-sensitive glutamate receptor: crystal structures of the GluR2 ligand binding core.
Authors: Armstrong, N. / Gouaux, E.
History
DepositionDec 18, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 16, 2014Provider: repository / Type: Initial release
Revision 1.1Jun 18, 2014Group: Database references
Revision 1.2Dec 14, 2016Group: Structure summary
Revision 1.3May 31, 2017Group: Structure summary
Revision 1.4Mar 7, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.5Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _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.value / _struct_conn.pdbx_dist_value / _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 / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.6Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)90,80942
Polymers87,6653
Non-polymers3,14339
Water11,133618
1
A: Glutamate receptor 2
hetero molecules

A: Glutamate receptor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,56128
Polymers58,4432
Non-polymers2,11826
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-x-1,-y,z1
Buried area5680 Å2
ΔGint-147 kcal/mol
Surface area24000 Å2
MethodPISA
2
B: Glutamate receptor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,26713
Polymers29,2221
Non-polymers1,04512
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Glutamate receptor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,26115
Polymers29,2221
Non-polymers1,03914
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)114.661, 162.211, 47.346
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

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Protein , 1 types, 3 molecules ABC

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


Mass: 29221.682 Da / Num. of mol.: 3
Fragment: Ligand binding domain (unp residues 413-527 and unp residues 653-736)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Gria2, Glur2 / Plasmid: pET-22b(+) / Production host: Escherichia coli (E. coli) / Strain (production host): Origami B (DE3) / References: UniProt: P19491

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Non-polymers , 7 types, 657 molecules

#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-ASP / ASPARTIC ACID


Type: L-peptide linking / Mass: 133.103 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H7NO4
#4: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Zn
#5: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C2H3O2
#6: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H10O3
#7: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 618 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.51 Å3/Da / Density % sol: 51.02 %
Crystal growTemperature: 279 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 24.4 % PEG 4000, 0.1 M zinc acetate and 0.1 M sodium acetate., pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 279K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I911-3 / Wavelength: 1 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: May 14, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→29.252 Å / Num. all: 81356 / Num. obs: 81356 / % possible obs: 98.3 % / Redundancy: 5.9 % / Biso Wilson estimate: 18.6 Å2 / Rsym value: 0.079 / Net I/σ(I): 12.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.8-1.95.70.4241.868282118890.42499.5
1.9-2.015.80.2612.965376112390.26199.6
2.01-2.155.80.1624.661630105440.16299
2.15-2.325.90.1235.75785298450.12399.3
2.32-2.555.90.1016.85338190360.10198.5
2.55-2.855.90.0827.84832881520.08298.1
2.85-3.295.90.0698.44272271860.06997.6
3.29-4.0260.069.53630460850.0696.5
4.02-5.695.90.0559.72815247360.05595.8
5.69-29.2525.70.05210.31499526440.05292.6

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation1.8 Å29.25 Å
Translation4.82 Å29.25 Å

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Processing

Software
NameVersionClassificationNB
SCALA3.3.21data scaling
PHASER2.5.2phasing
PHENIX1.8.2_1309refinement
PDB_EXTRACT3.11data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1M5B

1m5b


Resolution: 1.8→29.252 Å / Occupancy max: 1 / Occupancy min: 0.25 / SU ML: 0.17 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0.28 / Phase error: 18.13 / Stereochemistry target values: ML
Details: refinement done with TLS, isotropic B-factors and riding hydrogens
RfactorNum. reflection% reflectionSelection details
Rfree0.1881 4056 4.99 %RANDOM
Rwork0.1532 ---
obs0.1549 77227 98.34 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 110.02 Å2 / Biso mean: 25.5309 Å2 / Biso min: 8.83 Å2
Refinement stepCycle: LAST / Resolution: 1.8→29.252 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6120 0 177 618 6915
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0116475
X-RAY DIFFRACTIONf_angle_d1.2988684
X-RAY DIFFRACTIONf_chiral_restr0.076951
X-RAY DIFFRACTIONf_plane_restr0.0061091
X-RAY DIFFRACTIONf_dihedral_angle_d13.9342468
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection allNum. reflection obs% reflection obs (%)
1.8-1.82050.27952810.236949885269498899
1.8205-1.84190.28842420.2223497252144972100
1.8419-1.86430.20852430.1979501452575014100
1.8643-1.88790.24462710.1974501152825011100
1.8879-1.91280.22872340.199849645198496499
1.9128-1.9390.25922600.195502352835023100
1.939-1.96670.24622510.186850235274502399
1.9667-1.9960.23072680.183648555123485599
1.996-2.02720.22072600.1663505553155055100
2.0272-2.06040.20362490.160749715220497198
2.0604-2.09590.18622630.1585495252154952100
2.0959-2.1340.21272780.156349705248497099
2.134-2.17510.20382410.153449785219497898
2.1751-2.21940.20542590.1543496552244965100
2.2194-2.26770.19592590.146249205179492098
2.2677-2.32040.21332520.1533496852204968100
2.3204-2.37840.18982830.150348905173489098
2.3784-2.44270.17412430.1484499052334990100
2.4427-2.51450.19252550.143849425197494298
2.5145-2.59560.16882580.141549255183492599
2.5956-2.68840.17182900.137348725162487298
2.6884-2.79590.19592800.151148855165488597
2.7959-2.92310.18372360.148949085144490899
2.9231-3.0770.18032900.145148515141485198
3.077-3.26960.17742810.14648465127484697
3.2696-3.52160.15562950.14348045099480497
3.5216-3.87530.15252330.134448705103487096
3.8753-4.43440.16072580.127747995057479996
4.4344-5.58050.17842240.136247875011478796
5.5805-29.25580.20642290.186747144943471493
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)
11.9504-0.28060.62752.113-0.19151.8089-0.03240.11710.1445-0.0522-0.0115-0.1272-0.12530.20140.01330.0942-0.02490.00990.13730.00550.0951-39.490110.4733-12.8686
20.3728-0.21340.08831.00251.02413.1328-0.03110.0343-0.01070.0396-0.05230.0722-0.01160.03690.09620.0721-0.01420.00120.0950.00560.1018-52.763710.7187-6.3534
32.7173-0.57220.17023.3940.21692.0535-0.03590.12770.24950.013-0.05380.155-0.1794-0.02770.07270.125-0.0124-0.00220.10070.01690.1118-54.640519.59174.7332
42.0819-0.07740.4473.12550.57842.68910.0058-0.1578-0.21350.04660.0310.01890.10160.0933-0.0360.0551-0.00220.01360.13020.00970.1117-45.9337-0.4355-7.2501
52.59980.19270.08482.7337-0.10812.32930.0221-0.0186-0.1028-0.04170.0072-0.21690.17680.2383-0.00940.13070.0350.00740.120.00360.1496-37.773339.8363-2.4657
61.24970.47830.42220.8040.55423.295-0.0460.0060.1206-0.08730.0154-0.0079-0.2080.24710.02740.1236-0.00240.01640.10140.00170.1918-39.351655.95620.1798
72.74831.00970.6013.7968-1.34172.3026-0.01-0.20610.25190.0436-0.2026-0.1349-0.12880.17110.18420.1291-0.01450.0250.1957-0.0440.1824-33.99660.825614.0259
83.37940.1709-0.91730.94620.36794.5366-0.10720.2098-0.0528-0.15470.09920.11360.07-0.11830.01980.1450.0154-0.0120.07910.02360.186-50.75848.1748-5.787
94.51410.89373.28323.32670.67882.51380.3643-0.8336-0.14780.4032-0.26810.14940.3758-0.6281-0.01070.2128-0.0330.03780.23810.04070.1938-47.350640.605113.2385
101.8908-0.30830.41912.37170.94522.06370.0582-0.1579-0.18590.0862-0.00590.04710.1369-0.1326-0.03620.1048-0.0372-0.00180.12820.04370.1414-12.384814.60183.4258
111.7851-0.1815-0.03970.5984-0.14532.6710.08960.14940.0914-0.10230.0319-0.0429-0.3628-0.1701-0.09310.2308-0.02850.03820.1045-0.00120.183-9.88926.4443-10.2888
120.7-0.50730.46271.38950.34630.71050.0615-0.07250.24970.1375-0.0684-0.0843-0.1516-0.0970.0840.16090.00320.08690.09530.01180.0124-34.645838.0256-0.6259
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 1:79 )A1 - 79
2X-RAY DIFFRACTION2( CHAIN A AND RESID 80:123 )A80 - 123
3X-RAY DIFFRACTION3( CHAIN A AND RESID 124:217 )A124 - 217
4X-RAY DIFFRACTION4( CHAIN A AND RESID 218:261 )A218 - 261
5X-RAY DIFFRACTION5( CHAIN B AND RESID 1:65 )B1 - 65
6X-RAY DIFFRACTION6( CHAIN B AND RESID 66:123 )B66 - 123
7X-RAY DIFFRACTION7( CHAIN B AND RESID 124:217 )B124 - 217
8X-RAY DIFFRACTION8( CHAIN B AND RESID 218:243 )B218 - 243
9X-RAY DIFFRACTION9( CHAIN B AND RESID 244:263 )B244 - 263
10X-RAY DIFFRACTION10( CHAIN C AND RESID 1:93 )C1 - 93
11X-RAY DIFFRACTION11( CHAIN C AND RESID 94:262 )C94 - 262
12X-RAY DIFFRACTION12( CHAIN A AND RESID 302:302 ) OR ( CHAIN C AND RESID 301:301 ) OR ( CHAIN B AND RESID 301:301 )A302
13X-RAY DIFFRACTION12( CHAIN A AND RESID 302:302 ) OR ( CHAIN C AND RESID 301:301 ) OR ( CHAIN B AND RESID 301:301 )C301
14X-RAY DIFFRACTION12( CHAIN A AND RESID 302:302 ) OR ( CHAIN C AND RESID 301:301 ) OR ( CHAIN B AND RESID 301:301 )B301

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