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- PDB-2v3u: Structure of the ligand-binding core of the ionotropic glutamate ... -

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Basic information

Entry
Database: PDB / ID: 2v3u
TitleStructure of the ligand-binding core of the ionotropic glutamate receptor-like GluRdelta2 in complex with D-serine
ComponentsGLUTAMATE RECEPTOR DELTA-2 SUBUNIT
KeywordsRECEPTOR / POSTSYNAPTIC MEMBRANE / IONOTROPIC GLUTAMATE RECEPTORS / TRANSMEMBRANE / MEMBRANE PROTEIN / LIGAND-BINDING CORE / GLYCOPROTEIN / IONIC CHANNEL / ION TRANSPORT / MEMBRANE / D-SERINE / TRANSPORT
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
D-SERINE / THIOCYANATE ION / Glutamate receptor ionotropic, delta-2
Similarity search - Component
Biological speciesRATTUS NORVEGICUS (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.74 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 / 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
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval
Revision 1.4Dec 13, 2023Group: 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
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_atom_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_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_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: GLUTAMATE RECEPTOR DELTA-2 SUBUNIT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,2176
Polymers29,9381
Non-polymers2805
Water2,432135
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)36.801, 40.307, 44.393
Angle α, β, γ (deg.)66.88, 79.31, 86.46
Int Tables number1
Space group name H-MP1

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Components

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Protein , 1 types, 1 molecules A

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


Mass: 29937.670 Da / Num. of mol.: 1 / Fragment: LIGAND-BINDING CORE, RESIDUES 440-551,664-813
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

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Non-polymers , 5 types, 140 molecules

#2: Chemical ChemComp-DSN / D-SERINE


Type: D-peptide linking / Mass: 105.093 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H7NO3
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-SCN / THIOCYANATE ION


Mass: 58.082 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CNS
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 135 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsTHE NATIVE GLURDELTA2 IS A MEMBRANE PROTEIN. THE CRYSTALLIZED PROTEIN IS THE EXTRACELLULAR LIGAND- ...THE NATIVE GLURDELTA2 IS A MEMBRANE PROTEIN. THE CRYSTALLIZED PROTEIN IS 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 OF THE SEQUENCE IS A REMNANT OF A TRYPSIN CLEVAGE 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 Å3/Da / Density % sol: 40 %
Description: THE TWO SEPARATE DOMAINS OF THE APO STRUCTURE WERE USED AS SEARCH MODELS AS BINDING OF D-SERINE WAS EXPECTED TO INDUCE CONFORMATIONAL CHANGES.
Crystal growMethod: vapor diffusion, hanging drop / pH: 6.5
Details: HANGING DROP VAPOR DIFFUSION. 20% PEG4000, 0.1 M CACODYLATE PH 6.5, 0.2 M SODIUM THIOCYANATE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.95373
DetectorType: MARRESEARCH / Detector: CCD / Date: Jan 14, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95373 Å / Relative weight: 1
ReflectionResolution: 1.73→40 Å / Num. obs: 23508 / % possible obs: 92.3 % / Observed criterion σ(I): 6 / Redundancy: 3.8 % / Biso Wilson estimate: 23.59 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 12
Reflection shellResolution: 1.73→1.82 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.26 / Mean I/σ(I) obs: 2.1 / % possible all: 70.1

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Processing

Software
NameVersionClassification
REFMAC5.2.0016refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2V3T

2v3t


Resolution: 1.74→40.19 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.923 / SU B: 2.762 / SU ML: 0.091 / Cross valid method: THROUGHOUT / ESU R: 0.148 / ESU R Free: 0.144 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUES 167-171, 215-217 AND 262-265 ARE DISORDERED AND COULD NOT BE MODELED.
RfactorNum. reflection% reflectionSelection details
Rfree0.25 1154 5.2 %RANDOM
Rwork0.197 ---
obs0.2 21250 95.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.16 Å2
Baniso -1Baniso -2Baniso -3
1--0.73 Å20.26 Å20.54 Å2
2--0.64 Å2-0.07 Å2
3----0.09 Å2
Refinement stepCycle: LAST / Resolution: 1.74→40.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2022 0 15 135 2172
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0222088
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5261.9512827
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg11.4785250
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.77624.175103
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.31515347
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.3711513
X-RAY DIFFRACTIONr_chiral_restr0.1110.2306
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021598
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2140.2999
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3120.21431
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1360.2151
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2210.246
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1270.212
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0191.51262
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.7522035
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.4153867
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.7854.5792
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.74→1.79 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.347 80
Rwork0.27 1378

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