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- PDB-4kcc: Crystal Structure of the NMDA Receptor GluN1 Ligand Binding Domai... -

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Basic information

Entry
Database: PDB / ID: 4kcc
TitleCrystal Structure of the NMDA Receptor GluN1 Ligand Binding Domain Apo State
ComponentsGlutamate receptor ionotropic, NMDA 1
KeywordsMEMBRANE PROTEIN
Function / homology
Function and homology information


pons maturation / positive regulation of Schwann cell migration / regulation of cell communication / EPHB-mediated forward signaling / Assembly and cell surface presentation of NMDA receptors / olfactory learning / conditioned taste aversion / dendritic branch / regulation of respiratory gaseous exchange / protein localization to postsynaptic membrane ...pons maturation / positive regulation of Schwann cell migration / regulation of cell communication / EPHB-mediated forward signaling / Assembly and cell surface presentation of NMDA receptors / olfactory learning / conditioned taste aversion / dendritic branch / regulation of respiratory gaseous exchange / protein localization to postsynaptic membrane / transmitter-gated monoatomic ion channel activity / response to glycine / propylene metabolic process / Synaptic adhesion-like molecules / regulation of monoatomic cation transmembrane transport / NMDA glutamate receptor activity / RAF/MAP kinase cascade / voltage-gated monoatomic cation channel activity / neurotransmitter receptor complex / NMDA selective glutamate receptor complex / ligand-gated sodium channel activity / response to morphine / calcium ion transmembrane import into cytosol / glutamate binding / regulation of axonogenesis / neuromuscular process / regulation of dendrite morphogenesis / protein heterotetramerization / regulation of synapse assembly / male mating behavior / glycine binding / positive regulation of reactive oxygen species biosynthetic process / parallel fiber to Purkinje cell synapse / positive regulation of calcium ion transport into cytosol / suckling behavior / response to amine / startle response / social behavior / monoatomic cation transmembrane transport / associative learning / regulation of neuronal synaptic plasticity / cellular response to glycine / monoatomic cation transport / excitatory synapse / positive regulation of excitatory postsynaptic potential / positive regulation of dendritic spine maintenance / monoatomic ion channel complex / Unblocking of NMDA receptors, glutamate binding and activation / long-term memory / cellular response to manganese ion / glutamate receptor binding / synaptic cleft / prepulse inhibition / phosphatase binding / monoatomic cation channel activity / glutamate-gated receptor activity / calcium ion homeostasis / response to fungicide / regulation of neuron apoptotic process / presynaptic active zone membrane / glutamate-gated calcium ion channel activity / ligand-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / dendrite membrane / sensory perception of pain / sodium ion transmembrane transport / response to amphetamine / ionotropic glutamate receptor signaling pathway / positive regulation of synaptic transmission, glutamatergic / hippocampal mossy fiber to CA3 synapse / adult locomotory behavior / learning / regulation of membrane potential / excitatory postsynaptic potential / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / synaptic transmission, glutamatergic / regulation of long-term neuronal synaptic plasticity / synaptic membrane / postsynaptic density membrane / terminal bouton / : / visual learning / cerebral cortex development / calcium ion transmembrane transport / regulation of synaptic plasticity / calcium channel activity / memory / neuron cellular homeostasis / intracellular calcium ion homeostasis / synaptic vesicle membrane / response to calcium ion / calcium ion transport / rhythmic process / synaptic vesicle / signaling receptor activity / amyloid-beta binding / presynaptic membrane / protein-containing complex assembly / chemical synaptic transmission / dendritic spine / negative regulation of neuron apoptotic process
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. ...: / : / 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
PHOSPHATE ION / Glutamate receptor ionotropic, NMDA 1
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.894 Å
AuthorsBerger, A.J. / Lau, A.Y. / Mayer, M.L.
CitationJournal: Structure / Year: 2013
Title: Conformational Analysis of NMDA Receptor GluN1, GluN2, and GluN3 Ligand-Binding Domains Reveals Subtype-Specific Characteristics.
Authors: Yao, Y. / Belcher, J. / Berger, A.J. / Mayer, M.L. / Lau, A.Y.
History
DepositionApr 24, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 31, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 6, 2013Group: Database references
Revision 1.2Aug 2, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 1.3Sep 20, 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 1.4Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glutamate receptor ionotropic, NMDA 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,4352
Polymers33,3401
Non-polymers951
Water4,017223
1
A: Glutamate receptor ionotropic, NMDA 1
hetero molecules

A: Glutamate receptor ionotropic, NMDA 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,8704
Polymers66,6802
Non-polymers1902
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area2900 Å2
ΔGint-19 kcal/mol
Surface area27320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.269, 66.359, 63.468
Angle α, β, γ (deg.)90.00, 105.21, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-301-

PO4

DetailsThe biological assembly is a dimer but this can not be generated by crystal symmetry operations for this structure

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Components

#1: Protein Glutamate receptor ionotropic, NMDA 1 / GluN1 / Glutamate [NMDA] receptor subunit zeta-1 / N-methyl-D-aspartate receptor subunit NR1 / NMD-R1


Mass: 33340.031 Da / Num. of mol.: 1
Fragment: Ligand Binding Domain (UNP residues 394-544, 663-800)
Source method: isolated from a genetically manipulated source
Details: THE PROTEIN CRYSTALLIZED IS THE EXTRACELLULAR LIGAND BINDING DOMAIN OF GluN1. T RANSMEMBRANE REGIONS WERE GENETICALLY REMOVED AND REPLACED WITH A GLY-THR LINKER THEREFORE, THE SEQUENCE ...Details: THE PROTEIN CRYSTALLIZED IS THE EXTRACELLULAR LIGAND BINDING DOMAIN OF GluN1. T RANSMEMBRANE REGIONS WERE GENETICALLY REMOVED AND REPLACED WITH A GLY-THR LINKER THEREFORE, THE SEQUENCE MATCHES DISCONTINUOUSLY WITH THE REFERENCE DATABASE (39 4-544 AND 663-800)
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Grin1, Nmdar1 / Plasmid: pET22 modified / Production host: Escherichia coli (E. coli) / Strain (production host): Origami B(DE3) / References: UniProt: P35439
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 223 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHE PROTEIN CRYSTALLIZED IS THE EXTRACELLULAR LIGAND BINDING DOMAIN OF GlUN1. TRANSMEMBRANE REGIONS ...THE PROTEIN CRYSTALLIZED IS THE EXTRACELLULAR LIGAND BINDING DOMAIN OF GlUN1. TRANSMEMBRANE REGIONS WERE GENETICALLY REMOVED AND REPLACED WITH A GLY-THR LINKER THEREFORE, THE SEQUENCE MATCHES DISCONTINUOUSLY WITH THE REFERENCE DATABASE (394-544 AND 663-800).

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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: 2.66 Å3/Da / Density % sol: 53.75 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.2 M NaKphosphate, 20% PEG 3350, 2% glycerol, 0.2 M NaCl, 0.01 M Tris, 0.001 M EDTA, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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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 12, 2012 / Details: Double crystal
RadiationMonochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→40 Å / Num. all: 27791 / Num. obs: 27791 / % possible obs: 100 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.8 % / Biso Wilson estimate: 21.2 Å2 / Rmerge(I) obs: 0.078 / Net I/σ(I): 17.6
Reflection shellResolution: 1.9→1.93 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.56 / Mean I/σ(I) obs: 2.5 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine: 1.7.3_928)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1PB7

1pb7


Resolution: 1.894→36.849 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 22.49 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2056 1371 5 %Random
Rwork0.1717 ---
obs0.1735 27414 98.12 %-
all-27414 --
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40.383 Å2 / ksol: 0.359 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--7.91 Å20 Å21.5097 Å2
2---1.9372 Å2-0 Å2
3---9.8471 Å2
Refinement stepCycle: LAST / Resolution: 1.894→36.849 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2215 0 5 223 2443
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0112307
X-RAY DIFFRACTIONf_angle_d1.2873117
X-RAY DIFFRACTIONf_dihedral_angle_d13.122870
X-RAY DIFFRACTIONf_chiral_restr0.075339
X-RAY DIFFRACTIONf_plane_restr0.006401
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8939-1.96160.28741030.23342477X-RAY DIFFRACTION92
1.9616-2.04010.25461280.18992587X-RAY DIFFRACTION98
2.0401-2.1330.21881420.16582586X-RAY DIFFRACTION98
2.133-2.24540.22911410.1642583X-RAY DIFFRACTION99
2.2454-2.38610.25431400.16772609X-RAY DIFFRACTION98
2.3861-2.57020.21471290.1792609X-RAY DIFFRACTION99
2.5702-2.82880.23911300.17392625X-RAY DIFFRACTION99
2.8288-3.23790.20421430.17532646X-RAY DIFFRACTION99
3.2379-4.07860.18991430.172654X-RAY DIFFRACTION100
4.0786-36.85610.17831720.16092667X-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)
13.2615-0.13540.10352.7168-0.0530.97960.32450.4545-0.0828-0.3042-0.21510.30930.1819-0.0219-0.08730.16870.0865-0.05790.1549-0.05050.159711.8126-4.463718.9249
21.7130.17990.68352.25670.28651.06760.1920.60640.2671-0.2584-0.1981-0.1432-0.06550.24130.00280.17120.09070.04130.2850.09130.177427.62653.693718.4467
35.4357-2.8086-1.7753.25692.0442.17160.2760.5478-0.1003-0.3267-0.26090.1948-0.00870.0879-0.01560.24920.1201-0.05860.26710.01220.131737.5662-20.284913.5696
43.3241-0.0507-0.03824.5772-0.31562.97680.205-0.14660.45360.2156-0.1765-0.0001-0.03250.2366-0.060.0869-0.0055-0.00390.1538-0.03120.140327.17342.249830.8081
53.90850.0517-0.85721.99332.38244.0602-0.3363-0.0977-1.16950.35150.1457-0.40560.92210.5021-0.17880.31630.0277-0.00690.14630.03790.388618.86-16.592929.0449
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 5:73)
2X-RAY DIFFRACTION2(chain A and resid 74:145)
3X-RAY DIFFRACTION3(chain A and resid 146:246)
4X-RAY DIFFRACTION4(chain A and resid 247:277)
5X-RAY DIFFRACTION5(chain A and resid 278:290)

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