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- PDB-2rc9: Crystal structure of the NR3A ligand binding core complex with AC... -

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Basic information

Entry
Database: PDB / ID: 2rc9
TitleCrystal structure of the NR3A ligand binding core complex with ACPC at 1.96 Angstrom resolution
ComponentsGlutamate [NMDA] receptor subunit 3A
KeywordsMEMBRANE PROTEIN / Cell junction / Glycoprotein / Ion transport / Ionic channel / Magnesium / Postsynaptic cell membrane / Receptor / Synapse / Transmembrane / Transport
Function / homology
Function and homology information


serine binding / negative regulation of dendritic spine development / Assembly and cell surface presentation of NMDA receptors / transmitter-gated monoatomic ion channel activity / glutamate receptor activity / NMDA glutamate receptor activity / NMDA selective glutamate receptor complex / neurotransmitter receptor complex / glycine binding / monoatomic cation transmembrane transport ...serine binding / negative regulation of dendritic spine development / Assembly and cell surface presentation of NMDA receptors / transmitter-gated monoatomic ion channel activity / glutamate receptor activity / NMDA glutamate receptor activity / NMDA selective glutamate receptor complex / neurotransmitter receptor complex / glycine binding / monoatomic cation transmembrane transport / dendrite development / monoatomic ion channel complex / neuron development / prepulse inhibition / glutamate-gated receptor activity / presynaptic modulation of chemical synaptic transmission / ionotropic glutamate receptor signaling pathway / protein phosphatase 2A binding / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / synaptic transmission, glutamatergic / postsynaptic density membrane / modulation of chemical synaptic transmission / regulation of synaptic plasticity / calcium channel activity / calcium ion transport / rhythmic process / presynapse / response to ethanol / postsynaptic membrane / neuron projection / neuronal cell body / synapse / endoplasmic reticulum membrane / glutamatergic synapse / identical protein binding / membrane / plasma membrane / cytoplasm
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
1-AMINOCYCLOPROPANECARBOXYLIC ACID / Glutamate receptor ionotropic, NMDA 3A
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.96 Å
AuthorsYao, Y. / Mayer, M.L.
Citation
Journal: Embo J. / Year: 2008
Title: Molecular mechanism of ligand recognition by NR3 subtype glutamate receptors.
Authors: Yao, Y. / Harrison, C.B. / Freddolino, P.L. / Schulten, K. / Mayer, M.L.
#1: Journal: J.NEUROSCI. / Year: 2006
Title: Characterization of a soluble ligand binding domain of the NMDA receptor regulatory subunit NR3A
Authors: Yao, Y. / Mayer, M.L.
History
DepositionSep 19, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 5, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Aug 23, 2017Group: Source and taxonomy / Category: entity_src_gen
Revision 1.3Aug 30, 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 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 999RESIDUES 153 AND 154, GLY AND THR, ARE INSERTED AS A LINK REPLACING RESIDUES 661-775 OF THE PROTEIN ...RESIDUES 153 AND 154, GLY AND THR, ARE INSERTED AS A LINK REPLACING RESIDUES 661-775 OF THE PROTEIN FROM THE UNP entry Q9R1M7

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glutamate [NMDA] receptor subunit 3A
B: Glutamate [NMDA] receptor subunit 3A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,0754
Polymers65,8732
Non-polymers2022
Water9,242513
1
A: Glutamate [NMDA] receptor subunit 3A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,0372
Polymers32,9361
Non-polymers1011
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Glutamate [NMDA] receptor subunit 3A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,0372
Polymers32,9361
Non-polymers1011
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)49.675, 103.552, 59.798
Angle α, β, γ (deg.)90.00, 95.04, 90.00
Int Tables number4
Space group name H-MP1211
DetailsThe biological unit is believed to be a dimer of dimers. Molecular packing in the present structure is not biologically relevant.

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Components

#1: Protein Glutamate [NMDA] receptor subunit 3A / N-methyl-D-aspartate receptor subtype 3A / NR3A / NMDAR-L / NMDAR-L1 / N-methyl-D-aspartate receptor / Chi-1


Mass: 32936.301 Da / Num. of mol.: 2 / Fragment: unp residues 511-660, 776-915
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat)
Description: Peptides corresponding to N511-R660 and E776-K915 were coupled by a GT dipeptid e synthetic linker
Gene: Grin3a / Plasmid: pET22b(+) modified / Production host: Escherichia coli (E. coli) / Strain (production host): ORIGAMIB (DE3) / References: UniProt: Q9R1M7
#2: Chemical ChemComp-1AC / 1-AMINOCYCLOPROPANECARBOXYLIC ACID


Type: peptide linking / Mass: 101.104 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H7NO2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 513 / Source method: isolated from a natural source / Formula: H2O

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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: 2.33 Å3/Da / Density % sol: 47.11 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.7
Details: 0.2 M Mg Acetate, 0.1 M NaCitrate, 14% PEG 3350, pH 5.7, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 15, 2007
RadiationMonochromator: Si 220 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.96→40 Å / Num. all: 43239 / Num. obs: 43239 / % possible obs: 97.9 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 2.9 % / Rmerge(I) obs: 0.088 / Net I/σ(I): 8.5
Reflection shellResolution: 1.96→2.03 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.362 / Rsym value: 0.0259 / % possible all: 96.4

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Processing

Software
NameVersionClassification
REFMAC5.3.0038refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Pdb entry 2RC7

2rc7


Resolution: 1.96→19.91 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.933 / SU B: 6.756 / SU ML: 0.101 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.163 / ESU R Free: 0.153 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21114 2106 5 %RANDOM
Rwork0.15646 ---
all0.15921 40128 --
obs0.15921 40128 97.85 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 14.799 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å20.04 Å2
2--0.01 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.96→19.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4524 0 14 513 5051
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0224816
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.451.966559
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0895605
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.75724.118221
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.96615802
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.0321523
X-RAY DIFFRACTIONr_chiral_restr0.1020.2706
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023727
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2090.22244
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3070.23376
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1540.2470
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2110.266
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.280.232
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8611.53030
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.38324801
X-RAY DIFFRACTIONr_scbond_it2.24132021
X-RAY DIFFRACTIONr_scangle_it3.5134.51752
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.96→2.011 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.283 133 -
Rwork0.205 2893 -
obs--95.82 %
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)
12.4265-0.4127-0.26071.92570.02560.537-0.0030.39130.1167-0.27360.01150.3369-0.0124-0.1384-0.0085-0.0002-0.0043-0.05110.04850.0242-0.0075-1.563-3.249-6.637
21.92520.2440.16660.7906-0.15260.62670.0067-0.00850.21460.0719-0.00780.0142-0.0934-0.01170.00110.05160.00920.0052-0.0048-0.01350.03312.3892.9948.92
31.40510.0534-0.27262.117-1.28743.71470.02230.00410.26020.158-0.05220.0416-0.2199-0.18730.030.02180.0051-0.0142-0.0443-0.00550.082619.11512.8877.882
41.19520.14670.38360.87120.26520.75550.00130.1504-0.0055-0.07280.0043-0.0862-0.01080.0937-0.00560.04410.00990.00450.0566-0.00020.029716.756-8.2432.03
52.08560.4340.04670.91510.81111.9910.0175-0.2582-0.45020.20740.0801-0.20310.3630.3418-0.09770.00930.0539-0.0421-0.02120.05180.045838.373-28.04124.027
61.6037-0.1386-0.24350.43880.21940.961-0.0139-0.1249-0.03750.0330.0013-0.034-0.04440.02660.01270.0483-0.011-0.01310.03160.00680.010827.208-12.84724.025
71.4425-0.1994-0.62530.7779-0.11572.50550.0418-0.14020.09430.1209-0.01710.0107-0.11590.0706-0.02460.0462-0.0163-0.00740.0861-0.0347-0.025317.051-9.11137.26
80.9978-0.2986-0.33940.92370.44340.9535-0.03180.0227-0.16990.0699-0.04310.07870.0807-0.10870.0750.0383-0.0136-0.01390.03740.00640.048920.558-19.7217.993
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA4 - 824 - 82
2X-RAY DIFFRACTION2AA83 - 18183 - 181
3X-RAY DIFFRACTION3AA182 - 223182 - 223
4X-RAY DIFFRACTION4AA224 - 290224 - 290
5X-RAY DIFFRACTION5BB4 - 824 - 82
6X-RAY DIFFRACTION6BB83 - 16283 - 162
7X-RAY DIFFRACTION7BB163 - 221163 - 221
8X-RAY DIFFRACTION8BB222 - 287222 - 287

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