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- PDB-9pqh: NMR Structure of Ca2+/Calmodulin bound to the GluN1 C0 domain of ... -

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Basic information

Entry
Database: PDB / ID: 9pqh
TitleNMR Structure of Ca2+/Calmodulin bound to the GluN1 C0 domain of the NMDA receptor
Components
  • Calmodulin-1
  • Glutamate receptor ionotropic, NMDA 1
KeywordsMETAL BINDING PROTEIN
Function / homology
Function and homology information


glycine-gated cation channel activity / excitatory chemical synaptic transmission / Synaptic adhesion-like molecules / response to glycine / propylene metabolic process / Assembly and cell surface presentation of NMDA receptors / regulation of monoatomic cation transmembrane transport / NMDA glutamate receptor activity / Neurexins and neuroligins / CaM pathway ...glycine-gated cation channel activity / excitatory chemical synaptic transmission / Synaptic adhesion-like molecules / response to glycine / propylene metabolic process / Assembly and cell surface presentation of NMDA receptors / regulation of monoatomic cation transmembrane transport / NMDA glutamate receptor activity / Neurexins and neuroligins / CaM pathway / NMDA selective glutamate receptor complex / Cam-PDE 1 activation / glutamate binding / Sodium/Calcium exchangers / Calmodulin induced events / neurotransmitter receptor complex / ligand-gated sodium channel activity / Reduction of cytosolic Ca++ levels / Activation of Ca-permeable Kainate Receptor / CREB1 phosphorylation through the activation of CaMKII/CaMKK/CaMKIV cascasde / Loss of phosphorylation of MECP2 at T308 / CREB1 phosphorylation through the activation of Adenylate Cyclase / negative regulation of high voltage-gated calcium channel activity / PKA activation / calcium ion transmembrane import into cytosol / CaMK IV-mediated phosphorylation of CREB / Glycogen breakdown (glycogenolysis) / protein heterotetramerization / CLEC7A (Dectin-1) induces NFAT activation / Activation of RAC1 downstream of NMDARs / negative regulation of ryanodine-sensitive calcium-release channel activity / organelle localization by membrane tethering / mitochondrion-endoplasmic reticulum membrane tethering / glycine binding / autophagosome membrane docking / negative regulation of calcium ion export across plasma membrane / regulation of cardiac muscle cell action potential / presynaptic endocytosis / Synthesis of IP3 and IP4 in the cytosol / positive regulation of reactive oxygen species biosynthetic process / regulation of cell communication by electrical coupling involved in cardiac conduction / Phase 0 - rapid depolarisation / calcineurin-mediated signaling / Negative regulation of NMDA receptor-mediated neuronal transmission / monoatomic cation transmembrane transport / Unblocking of NMDA receptors, glutamate binding and activation / RHO GTPases activate PAKs / positive regulation of calcium ion transport into cytosol / Ion transport by P-type ATPases / Uptake and function of anthrax toxins / regulation of ryanodine-sensitive calcium-release channel activity / Long-term potentiation / protein phosphatase activator activity / Calcineurin activates NFAT / Regulation of MECP2 expression and activity / monoatomic ion channel complex / regulation of neuronal synaptic plasticity / monoatomic cation transport / DARPP-32 events / Smooth Muscle Contraction / detection of calcium ion / regulation of cardiac muscle contraction / synaptic cleft / catalytic complex / positive regulation of synaptic transmission, glutamatergic / RHO GTPases activate IQGAPs / regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion / calcium ion homeostasis / calcium channel inhibitor activity / Activation of AMPK downstream of NMDARs / presynaptic cytosol / cellular response to interferon-beta / Protein methylation / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / titin binding / eNOS activation / Ion homeostasis / Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / glutamate-gated calcium ion channel activity / regulation of calcium-mediated signaling / voltage-gated potassium channel complex / EPHB-mediated forward signaling / excitatory synapse / FCERI mediated Ca+2 mobilization / calcium channel complex / ionotropic glutamate receptor signaling pathway / substantia nigra development / positive regulation of excitatory postsynaptic potential / regulation of heart rate / Ras activation upon Ca2+ influx through NMDA receptor / FCGR3A-mediated IL10 synthesis / sodium ion transmembrane transport / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / synaptic membrane / calyx of Held / adenylate cyclase activator activity / protein serine/threonine kinase activator activity / sarcomere / VEGFR2 mediated cell proliferation / VEGFR2 mediated vascular permeability
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 ...: / : / : / 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 / EF-hand domain pair / EF-hand, calcium binding motif / Periplasmic binding protein-like I / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair
Similarity search - Domain/homology
Calmodulin-1 / Glutamate receptor ionotropic, NMDA 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsBej, A. / Ames, J.B.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Eye Institute (NIH/NEI)NIH R01 EY012347 United States
CitationJournal: J.Biol.Chem. / Year: 2026
Title: Structural Basis and Functional Analysis of NMDA Receptor Regulation by Calmodulin.
Authors: Bej, A. / Erickson-Oberg, M.Q. / Nigam, A. / Yu, I. / Hell, J.W. / Johnson, J.W. / Ames, J.B.
History
DepositionJul 22, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 21, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)122,5236
Polymers122,3622
Non-polymers1604
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: NMR Distance Restraints, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Calmodulin-1


Mass: 16852.545 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CALM1, CALM, CAM, CAM1 / Production host: Escherichia coli (E. coli) / References: UniProt: P0DP23
#2: Protein Glutamate receptor ionotropic, NMDA 1 / GluN1 / Glutamate [NMDA] receptor subunit zeta-1 / N-methyl-D-aspartate receptor subunit NR1 / NMD-R1 / hNR1


Mass: 105509.789 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q05586
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-15N HSQC
121isotropic13D HN(CA)CB
131isotropic13D HN(COCA)CB
141isotropic13D HNCO
151isotropic13D HBHANH
161isotropic13D HBHA(CO)NH
171isotropic13D C(CO)NH
181isotropic13D H(CCO)NH
192isotropic12D 1H-13C HSQC
1102isotropic12D 1H-13C HSQC aromatic
1112isotropic13D 13C-edited NOESY
1122isotropic13D 13-filtered NOESY
1132isotropic12D 13-filtered NOESY

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution10.4 mM [U-99% 13C; U-99% 15N] Calmodulin, 1.0 mM GluN1 C0, 1 mM Calcium chloride, 20 mM [U-99% 2H] TRIS, 93 % H2O, 7 % [U-2H] D2O, 93% H2O/7% D2OH2O93% H2O/7% D2O
solution20.4 mM [U-99% 13C; U-99% 15N] Calmodulin, 1.0 mM GluN1 C0, 1 mM Calcium chloride, 20 mM [U-99% 2H] TRIS, 100 % [U-2H] D2O, 100% D2OD2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.4 mMCalmodulin[U-99% 13C; U-99% 15N]1
1.0 mMGluN1 C0natural abundance1
1 mMCalcium chloridenatural abundance1
20 mMTRIS[U-99% 2H]1
93 %H2Onatural abundance1
7 %D2O[U-2H]1
0.4 mMCalmodulin[U-99% 13C; U-99% 15N]2
1.0 mMGluN1 C0natural abundance2
1 mMCalcium chloridenatural abundance2
20 mMTRIS[U-99% 2H]2
100 %D2O[U-2H]2
Sample conditionsIonic strength: 1 mM / Label: pH7_308K / pH: 7 / Pressure: 1 atm / Temperature: 308 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE III / Manufacturer: Bruker / Model: AVANCE III / Field strength: 800 MHz

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Processing

NMR software
NameDeveloperClassification
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
SparkyGoddardpeak picking
SparkyGoddardchemical shift assignment
HADDOCKBonvinstructure calculation
HADDOCKBonvinrefinement
RefinementMethod: simulated annealing / Software ordinal: 5
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 10

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