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- PDB-4tll: Crystal structure of GluN1/GluN2B NMDA receptor, structure 1 -

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Basic information

Entry
Database: PDB / ID: 4tll
TitleCrystal structure of GluN1/GluN2B NMDA receptor, structure 1
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 / excitatory postsynaptic potential / regulation of membrane potential / long-term synaptic potentiation / late endosome / chemical synaptic transmission / postsynaptic membrane ...NMDA glutamate receptor activity / NMDA selective glutamate receptor complex / response to zinc ion / response to magnesium ion / excitatory postsynaptic potential / regulation of membrane potential / long-term synaptic potentiation / late endosome / chemical synaptic transmission / postsynaptic membrane / lysosome / neuron projection / 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 / Response regulator / Ionotropic glutamate receptor, metazoa / Ligated ion channel L-glutamate- and glycine-binding site / : ...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 / Response regulator / 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 / 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: 3.59 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)373,44612
Polymers371,6224
Non-polymers1,8248
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16030 Å2
ΔGint-112 kcal/mol
Surface area137970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)201.460, 117.260, 218.760
Angle α, β, γ (deg.)90.00, 106.70, 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, 4 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


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 4 / 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


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: 3.34 Å3/Da / Density % sol: 63.21 %
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: 3.47→48.1 Å / Num. obs: 54471 / % possible obs: 85.7 % / Redundancy: 6.51 % / Net I/σ(I): 6.44

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.9_1692) / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.59→48.08 Å / SU ML: 0.58 / Cross valid method: FREE R-VALUE / σ(F): 1.41 / Phase error: 32.03 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.305 2655 4.97 %
Rwork0.2664 --
obs0.2684 53377 93.17 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.59→48.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18635 0 124 0 18759
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00319112
X-RAY DIFFRACTIONf_angle_d0.87826320
X-RAY DIFFRACTIONf_dihedral_angle_d9.3625486
X-RAY DIFFRACTIONf_chiral_restr0.0833204
X-RAY DIFFRACTIONf_plane_restr0.0043548
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.59-3.65530.3811880.3351521X-RAY DIFFRACTION54
3.6553-3.72550.2792850.31041900X-RAY DIFFRACTION67
3.7255-3.80160.31671160.29892210X-RAY DIFFRACTION77
3.8016-3.88420.38361380.33562598X-RAY DIFFRACTION90
3.8842-3.97450.34831450.31992700X-RAY DIFFRACTION96
3.9745-4.07380.34871510.28772793X-RAY DIFFRACTION98
4.0738-4.18390.29441570.26812814X-RAY DIFFRACTION98
4.1839-4.3070.32981420.26482830X-RAY DIFFRACTION99
4.307-4.44590.30091260.23912803X-RAY DIFFRACTION99
4.4459-4.60470.25481640.23242807X-RAY DIFFRACTION99
4.6047-4.78890.26121300.23542830X-RAY DIFFRACTION99
4.7889-5.00660.29771560.23032811X-RAY DIFFRACTION99
5.0066-5.27030.2591500.24482839X-RAY DIFFRACTION99
5.2703-5.60.31861460.25552846X-RAY DIFFRACTION99
5.6-6.03160.28821460.2672845X-RAY DIFFRACTION99
6.0316-6.63720.31971420.27622857X-RAY DIFFRACTION99
6.6372-7.59440.30691580.27842865X-RAY DIFFRACTION99
7.5944-9.55580.27541600.2352900X-RAY DIFFRACTION100
9.5558-48.08420.31141550.27142953X-RAY DIFFRACTION100
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)
17.6091-0.8438-1.38373.410.3221.84240.0554-0.26491.3834-0.33260.23090.1494-0.322-0.1082-0.21440.47750.119-0.01090.35530.01590.7616109.974688.4154413.3668
26.08030.0491-0.00114.2186-2.35913.6642-0.1656-1.1198-0.26540.54810.13110.43970.47460.21780.07051.17130.68980.38672.1544-0.02731.340181.535676.768454.0727
30.92541.0747-0.81212.6217-1.95341.2686-2.4825-0.17121.29070.1186-0.94811.02773.3041-0.72382.06372.6046-0.39772.04953.839-0.46674.366267.354150.1516506.0754
42.92390.5156-0.25675.40040.6647.1369-0.9757-0.7829-1.0744-0.2477-0.25190.43351.1951-0.71030.73260.67620.04880.4029-0.1995-0.27161.4334114.10656.4981422.7222
56.0872-0.4529-1.14223.88061.12443.2559-0.06780.1592-3.32680.9598-0.9717-0.2462.6281.27680.54013.33041.51670.10753.01620.67452.5396109.910543.779473.1219
60.64290.4512-0.69720.1758-0.60035.0486-1.198-0.17440.9709-2.50391.79870.57041.48941.5809-0.22944.371-0.5993-0.51885.4186-0.18411.839978.233161.2874518.7895
76.24390.6508-1.42566.7937-3.64424.7212-0.1035-1.2923-1.3373-0.0761-0.12850.05991.20761.47170.23821.61190.86-0.22642.2357-0.18151.3448162.45464.0978454.1609
83.4918-1.48271.87447.9337-1.80294.1585-1.1835-1.718-0.17631.1104-0.4903-2.42081.64162.13051.46282.18050.93540.30732.97390.56752.0021125.374162.6439490.6193
91.87650.75-0.16841.7464-0.77460.03110.0033-0.87083.681-0.88413.14450.0593-0.7167-1.1564-1.5681.7523-0.13282.83024.866-0.51232.582773.723378.0591504.6186
108.14011.00161.95744.25030.81455.6016-0.0329-1.44951.07960.86630.5263-0.7758-0.0931.3842-0.4491.46490.3182-0.47441.8762-0.48481.1124150.136794.1145458.5828
113.58820.78-0.10764.55861.45777.2908-0.3482-0.26391.06851.35920.5531-1.2023-0.2522-0.1289-0.14351.21080.6556-0.22642.1385-0.37681.765299.896494.7651470.3801
120.9243-0.2479-1.12422.72110.32421.836-0.25082.14570.2736-0.0391-1.1175-0.2533-0.015-0.98211.45091.6161-0.6588-0.20424.58980.82342.844861.090269.3952498.0589
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 23 through 396 )
2X-RAY DIFFRACTION2chain 'A' and ((resid 397 through 540) or (resid 652 through 789))
3X-RAY DIFFRACTION3chain 'A' and ((resid 541 through 651) or (resid 811 through 831))
4X-RAY DIFFRACTION4chain 'B' and (resid 26 through 385 )
5X-RAY DIFFRACTION5chain 'B' and ((resid 398 through 535) or (resid 647 through 789))
6X-RAY DIFFRACTION6chain 'B' and ((resid 539 through 646) or (resid 805 through 826))
7X-RAY DIFFRACTION7chain 'C' and (resid 23 through 396 )
8X-RAY DIFFRACTION8chain 'C' and ((resid 397 through 540) or (resid 652 through 790))
9X-RAY DIFFRACTION9chain 'C' and (resid 541 through 651)
10X-RAY DIFFRACTION10chain 'D' and (resid 27 through 390)
11X-RAY DIFFRACTION11chain 'D' and ((resid 397 through 535) or (resid 647 through 789))
12X-RAY DIFFRACTION12chain 'D' and ((resid 541 through 646) or (resid 790 through 827))

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