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- PDB-4tlm: Crystal structure of GluN1/GluN2B NMDA receptor, structure 2 -

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Basic information

Entry
Database: PDB / ID: 4tlm
TitleCrystal structure of GluN1/GluN2B NMDA receptor, structure 2
Components(receptor subunit ...) x 2
KeywordsSIGNALING PROTEIN / neurotransmitter receptor / NMDA receptor / GluN1/GluN2B / membrane protein / ion channel
Function / homology
Function and homology information


NMDA glutamate receptor activity / NMDA selective glutamate receptor complex / response to zinc ion / response to magnesium ion / late endosome / postsynaptic membrane / lysosome / metal ion binding / plasma membrane
Similarity search - Function
Glutamate [NMDA] receptor, epsilon subunit, C-terminal / N-methyl D-aspartate receptor 2B3 C-terminus / 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 / : / Response regulator / Ligand-gated ion channel / Ionotropic glutamate receptor, L-glutamate and glycine-binding domain ...Glutamate [NMDA] receptor, epsilon subunit, C-terminal / N-methyl D-aspartate receptor 2B3 C-terminus / 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 / : / Response regulator / 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 / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
1-AMINOCYCLOPROPANECARBOXYLIC ACID / trans-1-aminocyclobutane-1,3-dicarboxylic acid / Chem-QEM / Glutamate receptor ionotropic, NMDA 1 / Glutamate receptor ionotropic, NMDA 2B / Glutamate receptor ionotropic, NMDA 1
Similarity search - Component
Biological speciesXenopus laevis (African clawed frog)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.77 Å
AuthorsGouaux, E. / Lee, C.-H. / Lu, W.
CitationJournal: Nature / Year: 2014
Title: NMDA receptor structures reveal subunit arrangement and pore architecture.
Authors: Lee, C.H. / Lu, W. / Michel, J.C. / Goehring, A. / Du, J. / Song, X. / Gouaux, E.
History
DepositionMay 30, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 2, 2014Provider: repository / Type: Initial release
Revision 1.1Jul 9, 2014Group: Database references / Structure summary
Revision 1.2Jul 16, 2014Group: Database references
Revision 1.3Sep 24, 2014Group: Database references
Revision 1.4Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description / Source and taxonomy / Structure summary
Category: chem_comp / citation ...chem_comp / citation / entity / entity_src_gen / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_nonpoly / pdbx_struct_oper_list / refine_hist / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _citation.journal_id_CSD / _entity.pdbx_description / _entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _pdbx_entity_nonpoly.name / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.5Dec 27, 2023Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: receptor subunit GluN1
B: receptor subunit GluN2B
C: receptor subunit GluN1
D: receptor subunit GluN2B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)374,10915
Polymers371,6224
Non-polymers2,48811
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19170 Å2
ΔGint-160 kcal/mol
Surface area141120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)203.490, 118.430, 226.590
Angle α, β, γ (deg.)90.00, 103.82, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Receptor subunit ... , 2 types, 4 molecules ACBD

#1: Protein receptor subunit GluN1 / / N-methyl-D-aspartate receptor subunit NR1-8a


Mass: 92722.305 Da / Num. of mol.: 2 / Fragment: UNP residues 22-836
Mutation: C22A, K51F, K52F, N300Q, N350Q, N368D, N440D, N469D, K493A, K494A, E495A, G610R, I617L, D656R, N769E, Del(K588-E595), Replacement of 845-853 with SRAEAKRMK
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Production host: Homo sapiens (human) / References: UniProt: C0KD18, UniProt: A0A1L8F5J9*PLUS
#2: Protein receptor subunit GluN2B / / Ionotropic glutamate receptor subunit NR2B


Mass: 93088.461 Da / Num. of mol.: 2 / Fragment: UNP residues 20-839
Mutation: M20S, G21R, C22A, A64E, N69Q, K216C, N343D, T490V, C585A, E654R, E655R, V615L, Del(K382-V385), Del(R584-G593), Replacement of 854-864 with YKSRAEAKRMK
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Gene: NR2B / Production host: Homo sapiens (human) / References: UniProt: A7XY94

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Sugars , 1 types, 7 molecules

#3: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 3 types, 4 molecules

#4: Chemical ChemComp-1AC / 1-AMINOCYCLOPROPANECARBOXYLIC ACID / 1-Aminocyclopropane-1-carboxylic acid


Type: peptide linking / Mass: 101.104 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H7NO2
#5: Chemical ChemComp-QEM / 4-[(1R,2S)-3-(4-benzylpiperidin-1-yl)-1-hydroxy-2-methylpropyl]phenol


Mass: 339.471 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C22H29NO2
#6: Chemical ChemComp-JEG / trans-1-aminocyclobutane-1,3-dicarboxylic acid


Mass: 159.140 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H9NO4

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.58 Å3/Da / Density % sol: 65.66 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: vapor diffusion, hanging drop, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 20, 2014
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.77→48.2 Å / Num. obs: 44066 / % possible obs: 97.4 % / Redundancy: 3.44 % / Net I/σ(I): 7.46

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: dev_1723) / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.77→29.959 Å / SU ML: 0.66 / Cross valid method: FREE R-VALUE / σ(F): 1.44 / Phase error: 33.39 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2921 2200 5 %
Rwork0.2527 --
obs0.2547 44008 83.15 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.77→29.959 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19381 0 166 0 19547
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00619903
X-RAY DIFFRACTIONf_angle_d1.43827448
X-RAY DIFFRACTIONf_dihedral_angle_d12.9355786
X-RAY DIFFRACTIONf_chiral_restr0.1053446
X-RAY DIFFRACTIONf_plane_restr0.0063640
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.7701-3.85190.4962800.44561330X-RAY DIFFRACTION43
3.8519-3.94130.4141770.34381503X-RAY DIFFRACTION47
3.9413-4.03960.2693850.27111806X-RAY DIFFRACTION58
4.0396-4.14860.27451180.24992008X-RAY DIFFRACTION65
4.1486-4.27030.32451250.24912233X-RAY DIFFRACTION72
4.2703-4.40780.31571090.24332454X-RAY DIFFRACTION78
4.4078-4.56480.2711500.22992636X-RAY DIFFRACTION85
4.5648-4.74680.25391490.22962936X-RAY DIFFRACTION93
4.7468-4.9620.30231620.23773051X-RAY DIFFRACTION97
4.962-5.22230.27751590.24693041X-RAY DIFFRACTION98
5.2223-5.54750.2771590.27143109X-RAY DIFFRACTION98
5.5475-5.97270.34451640.28753076X-RAY DIFFRACTION98
5.9727-6.56810.33571590.30133133X-RAY DIFFRACTION99
6.5681-7.50540.37671680.28683107X-RAY DIFFRACTION99
7.5054-9.40720.25641690.2273157X-RAY DIFFRACTION99
9.4072-29.95960.2491670.22363228X-RAY DIFFRACTION99
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)
12.4836-0.94280.59663.04280.73361.6178-0.30960.03540.9568-0.99710.6176-0.9674-0.77740.09080.33070.00280.053-0.18150.10840.14540.3419-19.908221.0723214.7501
20.4451-0.0588-0.56130.46120.97192.7708-0.16350.306-0.60060.1476-0.31250.13811.56590.22951.52441.62291.43070.64061.91010.0441.4409-52.78266.9343260.1204
36.64860.5835-4.38887.8261-4.66978.8209-0.684-1.5788-2.12281.0573-0.27111.35790.85771.01770.7744.3340.23081.23281.86630.18322.0787-66.0761-14.6409321.8718
40.582-0.30150.75820.45470.28631.8848-0.0040.4968-0.37611.00670.1540.55051.1782-0.37830.42592.28120.82830.92981.56250.02211.9078-48.86810.9653272.5793
51.77152.61070.82274.67870.08862.97490.0252-0.151-0.8928-0.60510.4029-0.84540.9432-0.23370.12650.7282-0.33270.34030.375-0.19781.7692-14.196-19.281204.743
61.95840.4806-1.94870.2610.37091.1118-0.6906-1.5874-1.15440.70780.5815-0.12691.22430.45261.13261.51780.53720.1821.26370.17592.0296-20.2897-12.9914251.4708
75.6909-4.89491.86044.2099-1.60010.60810.28190.2389-0.2134-0.33170.05460.29250.69080.9533-0.25555.23880.17061.92053.0964-1.05674.7275-28.1603-38.6351284.785
80.9317-0.0119-0.55590.02030.12960.7528-0.1083-0.1915-1.1241.2461-0.64362.00551.30430.71731.20453.75031.59871.37153.12780.07022.8975-22.1166-17.7522278.8144
94.84033.8764-4.76825.5207-2.32775.61650.17590.0927-0.10380.77620.4369-0.69690.30462.8306-0.6394.76350.32530.23114.8679-1.67752.2631-48.0657-20.2203318.4114
103.8096-0.17295.51440.0494-0.30048.0416-0.0409-2.01082.27851.8741-0.8903-0.231-2.5023-2.75920.86654.63151.473-0.41352.8146-0.74392.9419-51.2147-22.0535336.4033
111.04070.0050.41530.58260.05730.2295-0.4573-1.7828-0.26860.27630.7023-0.30790.71912.02710.12221.97641.21470.09893.28380.03131.761920.9133-3.3624267.9039
124.6029-1.88754.46978.0088-0.66514.5251.82820.24830.92860.994-1.41983.09710.18820.9785-0.53422.4914-0.031.1982.27910.08732.0995-70.30529.6324318.358
134.0778-0.8987-1.49570.23050.20793.3498-1.8603-0.2947-0.06690.69110.7919-0.17391.74921.11240.58073.09490.73660.07242.75870.56361.9443-21.5921-0.0282294.8459
141.25461.29520.06313.354-0.54860.1801-0.047-1.09540.73111.65710.6552-0.8671-0.31871.1167-0.23151.16030.3117-0.5032.7082-0.93811.99821.811126.473260.2026
150.67650.0626-0.63912.38310.99881.80210.5335-0.39110.52990.25680.0660.11290.10860.6471-0.26411.1640.64490.02422.4730.01591.051-36.243919.7033278.0006
162.09781.3099-1.11050.7335-0.40111.6536-0.1261-1.10590.37730.9760.04440.90730.76991.2261-0.22671.99940.69410.40341.89340.34581.4087-45.02820.8639282.4929
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 23:399)
2X-RAY DIFFRACTION2(chain A and resid 400:592)
3X-RAY DIFFRACTION3(chain A and resid 593:619)
4X-RAY DIFFRACTION4(chain A and resid 620:827)
5X-RAY DIFFRACTION5(chain B and resid 27:88)
6X-RAY DIFFRACTION6(chain B and resid 89:687)
7X-RAY DIFFRACTION7(chain B and resid 688:694)
8X-RAY DIFFRACTION8(chain B and resid 695:803)
9X-RAY DIFFRACTION9(chain B and resid 804:813)
10X-RAY DIFFRACTION10(chain B and resid 814:828)
11X-RAY DIFFRACTION11(chain C and resid 23:592)
12X-RAY DIFFRACTION12(chain C and resid 593:619)
13X-RAY DIFFRACTION13(chain C and resid 620:821)
14X-RAY DIFFRACTION14(chain D and resid 30:371)
15X-RAY DIFFRACTION15(chain D and resid 372:618)
16X-RAY DIFFRACTION16(chain D and resid 619:827)

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