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- PDB-2rcb: Crystal structure of the NR3B ligand binding core complex with D-... -

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Basic information

Entry
Database: PDB / ID: 2rcb
TitleCrystal structure of the NR3B ligand binding core complex with D-serine at 1.62 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 / transmitter-gated monoatomic ion channel activity / glutamate receptor activity / NMDA selective glutamate receptor complex / glycine binding / monoatomic cation transmembrane transport / protein insertion into membrane / regulation of calcium ion transport / cellular response to glycine / monoatomic cation channel activity ...neurotransmitter receptor activity / transmitter-gated monoatomic ion channel activity / glutamate receptor activity / NMDA selective glutamate receptor complex / glycine binding / monoatomic cation transmembrane transport / protein insertion into membrane / regulation of calcium ion transport / cellular response to glycine / monoatomic cation channel activity / presynaptic active zone membrane / ligand-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / ionotropic glutamate receptor signaling pathway / hippocampal mossy fiber to CA3 synapse / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / synaptic transmission, glutamatergic / modulation of chemical synaptic transmission / postsynaptic density membrane / calcium ion transmembrane transport / regulation of synaptic plasticity / presynaptic membrane / postsynaptic membrane / neuronal cell body / endoplasmic reticulum membrane / plasma membrane
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. / Periplasmic binding protein-like II / Periplasmic binding protein-like I ...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. / 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 / Glutamate receptor ionotropic, NMDA 3B
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.62 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
Revision 1.4Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
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

Downloads & links

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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)64,6645
Polymers64,3612
Non-polymers3023
Water8,557475
1
A: Glutamate [NMDA] receptor subunit 3B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,3783
Polymers32,1811
Non-polymers1972
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Glutamate [NMDA] receptor subunit 3B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,2862
Polymers32,1811
Non-polymers1051
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)45.779, 83.521, 144.959
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. In the present structure packing 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-DSN / D-SERINE


Type: D-peptide linking / Mass: 105.093 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H7NO3
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 475 / Source method: isolated from a natural source / Formula: H2O
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: 2.15 Å3/Da / Density % sol: 42.87 %
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: Dec 10, 2006
RadiationMonochromator: Si 220 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.62→40 Å / Num. all: 71657 / Num. obs: 71657 / % possible obs: 99.9 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 4.5 % / Rmerge(I) obs: 0.052 / Net I/σ(I): 14.5
Reflection shellResolution: 1.62→1.68 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.344 / Mean I/σ(I) obs: 3.96 / % possible all: 98.5

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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 1PB7

1pb7


Resolution: 1.62→36.25 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.938 / SU B: 3.529 / SU ML: 0.065 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.106 / ESU R Free: 0.105 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22754 5525 7.8 %RANDOM
Rwork0.19178 ---
all0.19455 65305 --
obs0.19455 65305 98.93 %-
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: 18.293 Å2
Baniso -1Baniso -2Baniso -3
1--0.08 Å20 Å20 Å2
2--0.08 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.62→36.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4390 0 20 475 4885
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0214615
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5441.9656273
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9075584
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.14822.574202
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.71415744
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.6041537
X-RAY DIFFRACTIONr_chiral_restr0.1080.2683
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023561
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.220.32161
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3180.53282
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1920.5751
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3220.352
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1630.518
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.40422939
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.98834642
X-RAY DIFFRACTIONr_scbond_it1.74521876
X-RAY DIFFRACTIONr_scangle_it2.47331630
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.62→1.662 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.251 400 -
Rwork0.196 4683 -
obs--97.73 %
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)
11.94870.5998-0.04221.0432-0.27912.0860.06870.27690.1934-0.05350.05710.2271-0.2563-0.2692-0.12590.00790.03290.0220.08970.02560.076641.101626.039211.4856
21.13270.0106-0.06510.7172-0.34271.41350.1273-0.04890.0460.0808-0.1029-0.0575-0.14560.1796-0.02440.0369-0.05280.0280.074-0.01290.065256.979522.702421.8742
30.9461-0.1624-0.16472.0877-0.59371.33790.1219-0.1208-0.01910.0825-0.0821-0.0149-0.06460.1568-0.03980.0294-0.05680.00760.09460.0030.057956.83417.582726.1783
40.9392-1.0871-0.56085.81382.49272.3027-0.0289-0.24790.14210.09920.094-0.2415-0.1737-0.0639-0.0650.0647-0.0010.07440.0399-0.04830.042244.462732.133433.9531
51.1086-0.35850.16712.04810.29981.4761-0.072-0.1232-0.03090.33630.0318-0.35410.1160.27460.04020.090.0696-0.03510.04150.04760.036862.4872-14.726822.0383
61.0056-0.6134-0.01011.8786-0.53960.82890.0082-0.0146-0.0583-0.2783-0.00590.07170.1784-0.0122-0.00230.0960.0073-0.02030.03570.00320.037848.7869-8.2276.0049
70.9003-0.6231-0.06153.29410.95890.87160.13170.06220.0503-0.3957-0.1176-0.08140.1013-0.0474-0.01410.11430.0334-0.00430.01380.01370.030148.97532.05695.6374
81.3139-0.93390.10352.4226-0.41290.8097-0.1155-0.2075-0.2243-0.00960.10610.35810.1782-0.08480.00940.061-0.00210.01310.04050.02520.057345.9466-16.079314.1737
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA4 - 574 - 57
2X-RAY DIFFRACTION2AA58 - 19258 - 192
3X-RAY DIFFRACTION3AA193 - 266193 - 266
4X-RAY DIFFRACTION4AA267 - 285267 - 285
5X-RAY DIFFRACTION5BB4 - 1024 - 102
6X-RAY DIFFRACTION6BB103 - 170103 - 170
7X-RAY DIFFRACTION7BB171 - 216171 - 216
8X-RAY DIFFRACTION8BB217 - 285217 - 285

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