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- PDB-2rca: Crystal structure of the NR3B ligand binding core complex with gl... -

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Basic information

Entry
Database: PDB / ID: 2rca
TitleCrystal structure of the NR3B ligand binding core complex with glycine at 1.58 Angstrom resolution
ComponentsGlutamate [NMDA] receptor subunit 3B
KeywordsMEMBRANE PROTEIN / Cell junction / Glycoprotein / Ion transport / Ionic channel / Magnesium / Postsynaptic cell membrane / Receptor / Synapse / Transmembrane / Transport
Function / homology
Function and homology information


neurotransmitter receptor activity / glutamate receptor activity / NMDA selective glutamate receptor complex / glycine binding / cellular response to glycine / protein insertion into membrane / regulation of calcium ion transport / presynaptic active zone membrane / monoatomic cation channel activity / ligand-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential ...neurotransmitter receptor activity / glutamate receptor activity / NMDA selective glutamate receptor complex / glycine binding / cellular response to glycine / protein insertion into membrane / regulation of calcium ion transport / presynaptic active zone membrane / monoatomic cation channel activity / ligand-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / hippocampal mossy fiber to CA3 synapse / ionotropic glutamate receptor signaling pathway / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / synaptic transmission, glutamatergic / calcium ion transmembrane transport / postsynaptic density membrane / modulation of chemical synaptic transmission / neuronal cell body / endoplasmic reticulum membrane / plasma membrane
Similarity search - Function
Bacterial extracellular solute-binding proteins, family 3 / Solute-binding protein family 3/N-terminal domain of MltF / 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. ...Bacterial extracellular solute-binding proteins, family 3 / Solute-binding protein family 3/N-terminal domain of MltF / 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. / 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
GLYCINE / Glutamate receptor ionotropic, NMDA 3B
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.58 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 151 AND 152 GLY AND THR, ARE INSERTED AS A LINK REPLACING RESIDUES 561-675 OF THE PROTEIN ...RESIDUES 151 AND 152 GLY AND THR, ARE INSERTED AS A LINK REPLACING RESIDUES 561-675 OF THE PROTEIN FROM THE UNP entry Q8VHN2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)64,6045
Polymers64,3612
Non-polymers2423
Water9,494527
1
A: Glutamate [NMDA] receptor subunit 3B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,4234
Polymers32,1811
Non-polymers2423
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Glutamate [NMDA] receptor subunit 3B


Theoretical massNumber of molelcules
Total (without water)32,1811
Polymers32,1811
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)45.915, 83.597, 145.153
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
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 3B / N-methyl-D-aspartate receptor subtype 3B / NR3B / NMDAR3B


Mass: 32180.646 Da / Num. of mol.: 2 / Fragment: unp residues 413-560, 676-815
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat)
Description: Peptides corresponding to A413-R560 and E676-K815 were coupled by a GT dipeptid e synthetic linker
Gene: Grin3b / Plasmid: pET22b(+) modified / Production host: Escherichia coli (E. coli) / Strain (production host): ORIGAMIB (DE3) / References: UniProt: Q8VHN2
#2: Chemical ChemComp-GLY / GLYCINE / Glycine


Type: peptide linking / Mass: 75.067 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H5NO2
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 527 / 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: 2.16 Å3/Da / Density % sol: 43.16 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.2
Details: 0.1 M NaCitrate, 17% PEG 4000, pH 6.2, 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: Oct 23, 2006
RadiationMonochromator: Si 220 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.58→40 Å / Num. all: 76724 / Num. obs: 76724 / % possible obs: 92.3 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 4.5 % / Rmerge(I) obs: 0.048 / Net I/σ(I): 16.6
Reflection shellResolution: 1.58→1.64 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.326 / Mean I/σ(I) obs: 3.25 / % possible all: 91.4

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Processing

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

2rcb


Resolution: 1.58→36.3 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.938 / SU B: 3.262 / SU ML: 0.061 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0.97931 / ESU R: 0.107 / ESU R Free: 0.107 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23133 5502 7.8 %RANDOM
Rwork0.1917 ---
all0.19478 65212 --
obs0.19478 65212 92.02 %-
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: 19.573 Å2
Baniso -1Baniso -2Baniso -3
1-1.38 Å20 Å20 Å2
2---0.65 Å20 Å2
3----0.73 Å2
Refinement stepCycle: LAST / Resolution: 1.58→36.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4390 0 16 527 4933
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0214588
X-RAY DIFFRACTIONr_angle_refined_deg1.5791.9646233
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0575580
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.26722.6200
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.38115737
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.781536
X-RAY DIFFRACTIONr_chiral_restr0.1140.2677
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.023540
X-RAY DIFFRACTIONr_nbd_refined0.2310.32113
X-RAY DIFFRACTIONr_nbtor_refined0.3160.53263
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1850.5773
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2790.347
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2290.521
X-RAY DIFFRACTIONr_mcbond_it1.49422933
X-RAY DIFFRACTIONr_mcangle_it2.08134618
X-RAY DIFFRACTIONr_scbond_it1.82821859
X-RAY DIFFRACTIONr_scangle_it2.65331615
LS refinement shellResolution: 1.58→1.625 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.243 347 -
Rwork0.195 4606 -
obs--88.67 %
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)
11.33620.2146-0.06910.6652-0.25161.18470.08110.15260.1214-0.0114-0.00360.1127-0.149-0.1281-0.07760.02080.01230.02860.050.00420.056244.74927.15413.664
20.8842-0.1163-0.05841.0005-0.37751.23150.0673-0.0943-0.0530.0619-0.0754-0.11750.00130.21010.00820.0202-0.05110.00210.0911-0.00290.055763.7619.28326.161
30.6623-0.1409-0.01021.9319-0.36210.89890.0736-0.0677-0.05820.0175-0.0375-0.02850.03690.1012-0.03610.0184-0.0351-0.00150.07570.00390.047757.67914.59626.652
41.322-0.567-1.08910.88540.44872.36670.0768-0.18640.19650.05940.0442-0.142-0.3041-0.0777-0.1210.06360.00250.05450.0255-0.0510.04945.95134.79631.68
50.993-0.22110.0931.4970.2380.927-0.056-0.0828-0.00850.28860.0149-0.28620.05390.25310.04110.08490.0485-0.04230.02470.02890.011162.772-14.75521.996
60.8641-0.66110.05911.6087-0.50360.703-0.0126-0.0422-0.0259-0.12960.02530.0540.1072-0.0194-0.01280.0696-0.0055-0.01760.0439-0.00060.035249.157-8.3515.899
70.687-0.673-0.01532.37250.00610.1360.08750.06670.0462-0.2518-0.0645-0.03210.0798-0.0196-0.02310.07230.0138-0.01250.03430.00290.022447.9590.5736.97
80.8848-0.5470.20041.939-0.40860.3469-0.0951-0.1936-0.16820.09160.07780.33330.1127-0.06920.01730.0430.00420.03370.03810.01860.049546.807-18.59814.602
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA4 - 1134 - 113
2X-RAY DIFFRACTION2AA114 - 192114 - 192
3X-RAY DIFFRACTION3AA193 - 259193 - 259
4X-RAY DIFFRACTION4AA260 - 285260 - 285
5X-RAY DIFFRACTION5BB4 - 1024 - 102
6X-RAY DIFFRACTION6BB103 - 170103 - 170
7X-RAY DIFFRACTION7BB171 - 228171 - 228
8X-RAY DIFFRACTION8BB229 - 285229 - 285

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