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- PDB-2v3t: Structure of the ligand-binding core of the ionotropic glutamate ... -

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Basic information

Entry
Database: PDB / ID: 2v3t
TitleStructure of the ligand-binding core of the ionotropic glutamate receptor-like GluRdelta2 in the apo form
ComponentsGLUTAMATE RECEPTOR DELTA-2 SUBUNIT SYNONYM GLURDELTA2, GLUR DELTA-2
KeywordsRECEPTOR / MEMBRANE / TRANSPORT / GLYCOPROTEIN / POSTSYNAPTIC MEMBRANE / IONOTROPIC GLUTAMATE RECEPTORS / MEMBRANE PROTEIN / LIGAND-BINDING CORE / IONIC CHANNEL / ION TRANSPORT / TRANSMEMBRANE
Function / homology
Function and homology information


excitatory synapse assembly / cerebellar granule cell differentiation / positive regulation of long-term synaptic depression / regulation of postsynaptic density assembly / glutamate receptor activity / positive regulation of synapse assembly / parallel fiber to Purkinje cell synapse / heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules / regulation of neuron projection development / ionotropic glutamate receptor complex ...excitatory synapse assembly / cerebellar granule cell differentiation / positive regulation of long-term synaptic depression / regulation of postsynaptic density assembly / glutamate receptor activity / positive regulation of synapse assembly / parallel fiber to Purkinje cell synapse / heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules / regulation of neuron projection development / ionotropic glutamate receptor complex / regulation of presynapse assembly / prepulse inhibition / regulation of neuron apoptotic process / somatodendritic compartment / excitatory postsynaptic potential / synaptic transmission, glutamatergic / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / PDZ domain binding / postsynaptic density membrane / modulation of chemical synaptic transmission / protein localization / scaffold protein binding / postsynaptic membrane / dendritic spine / glutamatergic synapse / synapse / identical protein binding / membrane / plasma membrane
Similarity search - Function
Ionotropic glutamate receptor, metazoa / Ligated ion channel L-glutamate- and glycine-binding site / : / Ligand-gated ion channel / Ionotropic glutamate receptor, L-glutamate and glycine-binding domain / Ligated ion channel L-glutamate- and glycine-binding site / 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 / : / Ligand-gated ion channel / Ionotropic glutamate receptor, L-glutamate and glycine-binding domain / Ligated ion channel L-glutamate- and glycine-binding site / 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
Glutamate receptor ionotropic, delta-2
Similarity search - Component
Biological speciesRATTUS NORVEGICUS (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.75 Å
AuthorsNaur, P. / Vestergaard, B. / Gajhede, M. / Kastrup, J.S.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2007
Title: Ionotropic Glutamate-Like Receptor {Delta}2 Binds D-Serine and Glycine.
Authors: Naur, P. / Hansen, K.B. / Kristensen, A.S. / Dravid, S.M. / Pickering, D.S. / Olsen, L. / Vestergaard, B. / Egebjerg, J. / Gajhede, M. / Traynelis, S.F. / Kastrup, J.S.
History
DepositionJun 22, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 7, 2007Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 2019Group: Data collection / Derived calculations ...Data collection / Derived calculations / Experimental preparation / Other
Category: database_PDB_rev / database_PDB_rev_record ...database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / pdbx_seq_map_depositor_info / struct_conn
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval ..._exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval / _pdbx_seq_map_depositor_info.one_letter_code_mod / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Jul 24, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: GLUTAMATE RECEPTOR DELTA-2 SUBUNIT SYNONYM GLURDELTA2, GLUR DELTA-2
B: GLUTAMATE RECEPTOR DELTA-2 SUBUNIT SYNONYM GLURDELTA2, GLUR DELTA-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,6124
Polymers60,5322
Non-polymers802
Water54030
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2020 Å2
ΔGint-5.2 kcal/mol
Surface area29380 Å2
MethodPQS
Unit cell
Length a, b, c (Å)70.971, 91.031, 177.393
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number24
Space group name H-MI212121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.2938, -0.9496, 0.1097), (-0.9445, -0.306, -0.1195), (0.1471, -0.06847, -0.9868)
Vector: 14.67, 14.05, -47.2)

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Components

#1: Protein GLUTAMATE RECEPTOR DELTA-2 SUBUNIT SYNONYM GLURDELTA2, GLUR DELTA-2


Mass: 30265.932 Da / Num. of mol.: 2 / Fragment: LIGAND-BINDING CORE, RESIDUES 440-551 AND 664-813
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) RATTUS NORVEGICUS (Norway rat) / Plasmid: PET28 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): ORIGAMI 2 / References: UniProt: Q63226
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 30 / Source method: isolated from a natural source / Formula: H2O
Compound detailsRECEPTOR FOR GLUTAMATE. L-GLUTAMATE ACTS AS AN EXCITATORY NEUROTRANSMITTER AT MANY SYNAPSES IN THE ...RECEPTOR FOR GLUTAMATE. L-GLUTAMATE ACTS AS AN EXCITATORY NEUROTRANSMITTER AT MANY SYNAPSES IN THE CENTRAL NERVOUS SYSTEM. THE POSTSYNAPTIC ACTIONS OF GLU ARE MEDIATED BY A VARIETY OF RECEPTORS THAT ARE NAMED ACCORDING TO THEIR SELECTIVE AGONISTS.
Sequence detailsTHE NATIVE GLURDELTA2 IS A MEMBRANE PROTEIN. THE CRYSTALLIZED PROTEIN IS A SE-MET DERIVATIVE OF THE ...THE NATIVE GLURDELTA2 IS A MEMBRANE PROTEIN. THE CRYSTALLIZED PROTEIN IS A SE-MET DERIVATIVE OF THE EXTRACELLULAR LIGAND-BINDING CORE OF GLURDELTA2. TRANSMEMBRANE REGIONS WERE GENETICALLY REMOVED AND REPLACED WITH A GLY-THR LINKER. CONSEQUENTLY, THE PROTEIN SEQUENCE MATCHES DISCONTINOUSLY WITH THE REFERENCE DATABASE. THE FIRST GLYCINE IS A REMNANT OF A TRYPSIN CLEAVAGE SITE.

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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: 2.47 Å3/Da / Density % sol: 50.2 % / Description: NONE
Crystal growMethod: vapor diffusion, hanging drop / pH: 8.5
Details: 11% PEG4000, 0.1 M TRIS-HCL PH 8.5, 50 MM CACL2. HANGING DROP VAPOR DIFFUSION.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X12 / Wavelength: 0.9537
DetectorType: MARRESEARCH / Detector: CCD / Date: Oct 26, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.75→12 Å / Num. obs: 27717 / % possible obs: 97.6 % / Observed criterion σ(I): 3 / Redundancy: 9.2 % / Biso Wilson estimate: 72 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 20
Reflection shellResolution: 2.75→2.85 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 2.2 / % possible all: 83.2

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
SHELXphasing
autoSHARPphasing
CNS1.1refinement
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 2.75→30 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 10000 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.2867 1293 4.5 %RANDOM
Rwork0.2314 ---
obs0.2314 26508 91.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 37.5106 Å2 / ksol: 0.372268 e/Å3
Displacement parametersBiso mean: 43.6 Å2
Baniso -1Baniso -2Baniso -3
1--8.058 Å20 Å20 Å2
2--2.18 Å20 Å2
3---5.878 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.53 Å0.39 Å
Luzzati d res low-5 Å
Luzzati sigma a0.65 Å0.55 Å
Refinement stepCycle: LAST / Resolution: 2.75→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3990 0 2 30 4022
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.00761
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.4371
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.3
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.07
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.51.5
X-RAY DIFFRACTIONc_mcangle_it2.562
X-RAY DIFFRACTIONc_scbond_it1.952
X-RAY DIFFRACTIONc_scangle_it3.152.5
LS refinement shellResolution: 2.75→2.79 Å / Rfactor Rfree error: 0.143 / Total num. of bins used: 25
RfactorNum. reflection% reflection
Rfree0.6256 19 3 %
Rwork0.489 624 -
obs--56.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2DNA-RNA_REP.PARAMDNA-RNA.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION4ION.PARAMION.TOP

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