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- PDB-5kc9: Crystal structure of the amino-terminal domain (ATD) of iGluR Del... -

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Basic information

Entry
Database: PDB / ID: 5kc9
TitleCrystal structure of the amino-terminal domain (ATD) of iGluR Delta-1 (GluD1)
ComponentsGlutamate receptor ionotropic, delta-1
KeywordsSIGNALING PROTEIN / ionotropic glutamate receptor (iGluR) / neurotransmission
Function / homology
Function and homology information


trans-synaptic protein complex / synaptic signaling via neuropeptide / regulation of postsynapse organization / social behavior / regulation of postsynaptic membrane neurotransmitter receptor levels / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / postsynaptic density membrane / GABA-ergic synapse / postsynaptic membrane / glutamatergic synapse ...trans-synaptic protein complex / synaptic signaling via neuropeptide / regulation of postsynapse organization / social behavior / regulation of postsynaptic membrane neurotransmitter receptor levels / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / postsynaptic density membrane / GABA-ergic synapse / postsynaptic membrane / glutamatergic synapse / metal ion binding / identical protein binding
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
1,4-BUTANEDIOL / Glutamate receptor ionotropic, delta-1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsElegheert, J. / Clay, J.E. / Siebold, C. / Aricescu, A.R.
CitationJournal: Science / Year: 2016
Title: Structural basis for integration of GluD receptors within synaptic organizer complexes.
Authors: Elegheert, J. / Kakegawa, W. / Clay, J.E. / Shanks, N.F. / Behiels, E. / Matsuda, K. / Kohda, K. / Miura, E. / Rossmann, M. / Mitakidis, N. / Motohashi, J. / Chang, V.T. / Siebold, C. / ...Authors: Elegheert, J. / Kakegawa, W. / Clay, J.E. / Shanks, N.F. / Behiels, E. / Matsuda, K. / Kohda, K. / Miura, E. / Rossmann, M. / Mitakidis, N. / Motohashi, J. / Chang, V.T. / Siebold, C. / Greger, I.H. / Nakagawa, T. / Yuzaki, M. / Aricescu, A.R.
History
DepositionJun 5, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jul 27, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 3, 2016Group: Structure summary
Revision 1.2Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / 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_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Jan 10, 2024Group: 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
Revision 1.4Oct 23, 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 ionotropic, delta-1
B: Glutamate receptor ionotropic, delta-1
C: Glutamate receptor ionotropic, delta-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)148,52252
Polymers145,1873
Non-polymers3,33449
Water3,225179
1
A: Glutamate receptor ionotropic, delta-1
B: Glutamate receptor ionotropic, delta-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,48639
Polymers96,7922
Non-polymers2,69537
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10860 Å2
ΔGint-21 kcal/mol
Surface area34400 Å2
MethodPISA
2
C: Glutamate receptor ionotropic, delta-1
hetero molecules

C: Glutamate receptor ionotropic, delta-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,07126
Polymers96,7922
Non-polymers1,28024
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-x+y,-z+2/31
Buried area7280 Å2
ΔGint-83 kcal/mol
Surface area32300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)128.420, 128.420, 153.230
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
SymmetryPoint symmetry: (Schoenflies symbol: C2 (2 fold cyclic))

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Components

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Protein / Sugars , 2 types, 6 molecules ABC

#1: Protein Glutamate receptor ionotropic, delta-1 / GluR delta-1 subunit


Mass: 48395.785 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Grid1 / Plasmid: pHLsec / Cell line (production host): HEK293S / Production host: Homo sapiens (human) / References: UniProt: Q61627
#5: 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.: 3
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

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Non-polymers , 5 types, 225 molecules

#2: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 29 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-BU1 / 1,4-BUTANEDIOL


Mass: 90.121 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O2
#6: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 179 / 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: 51.04 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1 M MES (2-ethanesulfonic acid)/imidazole pH 6.5, 10% (w/v) polyethylene glycol 8000, 20% (w/v) ethylene glycol, 0.02 M 1,6-hexanediol, 0.02 M (RS)-1,2-propanediol, 0.02 M 1-butanol, 0.02 ...Details: 0.1 M MES (2-ethanesulfonic acid)/imidazole pH 6.5, 10% (w/v) polyethylene glycol 8000, 20% (w/v) ethylene glycol, 0.02 M 1,6-hexanediol, 0.02 M (RS)-1,2-propanediol, 0.02 M 1-butanol, 0.02 M 2-propanol, 0.02 M 1,4-butanediol and 0.02 M 1,3-propanediol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9173 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Apr 28, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9173 Å / Relative weight: 1
ReflectionResolution: 2.3→59.22 Å / Num. obs: 65080 / % possible obs: 99.7 % / Redundancy: 8.5 % / Biso Wilson estimate: 57.3 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.051 / Net I/σ(I): 22.6
Reflection shellResolution: 2.3→2.36 Å / Redundancy: 8.7 % / Rmerge(I) obs: 1.222 / Mean I/σ(I) obs: 1.9 / % possible all: 98.5

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Processing

Software
NameVersionClassification
PHENIXdev_1772refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5KC8

5kc8


Resolution: 2.3→59.22 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.45 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2273 3276 5.03 %
Rwork0.1992 --
obs0.2006 65074 99.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 77.6 Å2
Refinement stepCycle: LAST / Resolution: 2.3→59.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9096 0 197 179 9472
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0049437
X-RAY DIFFRACTIONf_angle_d0.85512689
X-RAY DIFFRACTIONf_dihedral_angle_d12.1863501
X-RAY DIFFRACTIONf_chiral_restr0.0361441
X-RAY DIFFRACTIONf_plane_restr0.0031626
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3001-2.33440.33971330.29762597X-RAY DIFFRACTION98
2.3344-2.37090.33521550.29472659X-RAY DIFFRACTION100
2.3709-2.40980.27481410.26862636X-RAY DIFFRACTION99
2.4098-2.45130.30831560.27892617X-RAY DIFFRACTION100
2.4513-2.49590.29261340.26922678X-RAY DIFFRACTION100
2.4959-2.54390.2661570.25292621X-RAY DIFFRACTION100
2.5439-2.59580.28631300.25122718X-RAY DIFFRACTION100
2.5958-2.65230.30351360.24052625X-RAY DIFFRACTION100
2.6523-2.7140.25451230.23862699X-RAY DIFFRACTION100
2.714-2.78180.27491650.23212658X-RAY DIFFRACTION100
2.7818-2.8570.22261430.21622681X-RAY DIFFRACTION100
2.857-2.94110.21541480.22242665X-RAY DIFFRACTION100
2.9411-3.0360.25541280.21712684X-RAY DIFFRACTION100
3.036-3.14450.25661330.22482684X-RAY DIFFRACTION100
3.1445-3.27040.24791430.2352693X-RAY DIFFRACTION99
3.2704-3.41930.26641440.21822671X-RAY DIFFRACTION100
3.4193-3.59950.25861480.20322694X-RAY DIFFRACTION100
3.5995-3.8250.20761500.19042696X-RAY DIFFRACTION100
3.825-4.12030.20111350.17972724X-RAY DIFFRACTION100
4.1203-4.53480.18421500.16772726X-RAY DIFFRACTION100
4.5348-5.19060.18841520.16032724X-RAY DIFFRACTION100
5.1906-6.53830.25381350.19792761X-RAY DIFFRACTION99
6.5383-59.24030.19721370.17982887X-RAY DIFFRACTION100

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