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- PDB-5j7j: NMR Derived Structure of Ca2+ Calmodulin bound to Phosphorylated ... -

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Basic information

Entry
Database: PDB / ID: 5j7j
TitleNMR Derived Structure of Ca2+ Calmodulin bound to Phosphorylated PSD-95
Components
  • Calmodulin
  • Disks large homolog 4
KeywordsMETAL BINDING PROTEIN / phosphorylated / calmodulin / PSD-95 / Voltage-Gated Channel
Function / homology
Function and homology information


LGI-ADAM interactions / P2Y1 nucleotide receptor binding / beta-1 adrenergic receptor binding / neuroligin family protein binding / regulation of grooming behavior / NrCAM interactions / synaptic vesicle maturation / positive regulation of neuron projection arborization / receptor localization to synapse / vocalization behavior ...LGI-ADAM interactions / P2Y1 nucleotide receptor binding / beta-1 adrenergic receptor binding / neuroligin family protein binding / regulation of grooming behavior / NrCAM interactions / synaptic vesicle maturation / positive regulation of neuron projection arborization / receptor localization to synapse / vocalization behavior / neuron spine / cerebellar mossy fiber / AMPA glutamate receptor clustering / Synaptic adhesion-like molecules / protein localization to synapse / establishment or maintenance of epithelial cell apical/basal polarity / Trafficking of AMPA receptors / dendritic spine morphogenesis / negative regulation of receptor internalization / neuron projection terminus / juxtaparanode region of axon / acetylcholine receptor binding / RHO GTPases activate CIT / cellular response to potassium ion / Assembly and cell surface presentation of NMDA receptors / myosin II complex / NMDA selective glutamate receptor signaling pathway / Neurexins and neuroligins / Activation of Ca-permeable Kainate Receptor / neuromuscular process controlling balance / neurotransmitter receptor localization to postsynaptic specialization membrane / cortical cytoskeleton / Negative regulation of NMDA receptor-mediated neuronal transmission / Unblocking of NMDA receptors, glutamate binding and activation / locomotory exploration behavior / AMPA glutamate receptor complex / Signaling by ERBB4 / Long-term potentiation / excitatory synapse / social behavior / positive regulation of excitatory postsynaptic potential / positive regulation of synaptic transmission / D1 dopamine receptor binding / regulation of postsynaptic membrane neurotransmitter receptor levels / ionotropic glutamate receptor binding / dendrite cytoplasm / Ras activation upon Ca2+ influx through NMDA receptor / synaptic membrane / learning / PDZ domain binding / adherens junction / neuromuscular junction / establishment of protein localization / cell-cell adhesion / regulation of long-term neuronal synaptic plasticity / postsynaptic density membrane / kinase binding / synaptic vesicle / endocytic vesicle membrane / cell junction / nervous system development / positive regulation of cytosolic calcium ion concentration / RAF/MAP kinase cascade / protein-containing complex assembly / scaffold protein binding / protein phosphatase binding / dendritic spine / chemical synaptic transmission / postsynaptic membrane / neuron projection / postsynaptic density / signaling receptor binding / calcium ion binding / synapse / protein kinase binding / protein-containing complex binding / glutamatergic synapse / endoplasmic reticulum / signal transduction / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Polyubiquitination (PEST) N-terminal domain of MAGUK / Disks large homologue 1, N-terminal PEST domain / Polyubiquitination (PEST) N-terminal domain of MAGUK / PDZ-associated domain of NMDA receptors / PDZ-associated domain of NMDA receptors / Disks large 1-like / : / Guanylate kinase, conserved site / Guanylate kinase-like signature. / Guanylate kinase-like domain profile. ...Polyubiquitination (PEST) N-terminal domain of MAGUK / Disks large homologue 1, N-terminal PEST domain / Polyubiquitination (PEST) N-terminal domain of MAGUK / PDZ-associated domain of NMDA receptors / PDZ-associated domain of NMDA receptors / Disks large 1-like / : / Guanylate kinase, conserved site / Guanylate kinase-like signature. / Guanylate kinase-like domain profile. / Guanylate kinase-like domain / Guanylate kinase/L-type calcium channel beta subunit / Guanylate kinase / Guanylate kinase homologues. / : / PDZ domain / SH3 domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily / EF-hand domain pair / EF-hand, calcium binding motif / Src homology 3 domains / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Calmodulin-1 / Calmodulin-2 B / Disks large homolog 4
Similarity search - Component
Biological speciesXenopus laevis (African clawed frog)
Homo sapiens (human)
MethodSOLUTION NMR / molecular dynamics
AuthorsTurner, M.L. / Ames, J.B. / Anderson, D.E.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Mental Health (NIH/NIMH)MH097887 United States
National Institutes of Health/National Eye Institute (NIH/NEI)EY012347 United States
CitationJournal: Embo J. / Year: 2018
Title: Ca2+/calmodulin binding to PSD-95 mediates homeostatic synaptic scaling down.
Authors: Chowdhury, D. / Turner, M. / Patriarchi, T. / Hergarden, A.C. / Anderson, D. / Zhang, Y. / Sun, J. / Chen, C.Y. / Ames, J.B. / Hell, J.W.
History
DepositionApr 6, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 25, 2017Provider: repository / Type: Initial release
Revision 1.1May 8, 2019Group: Data collection / Database references / Category: citation / citation_author / pdbx_nmr_software
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _pdbx_nmr_software.name
Revision 1.2Nov 27, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / pdbx_nmr_spectrometer
Item: _pdbx_audit_support.funding_organization / _pdbx_nmr_spectrometer.model
Revision 1.3Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Calmodulin
B: Disks large homolog 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,2906
Polymers19,1302
Non-polymers1604
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area2750 Å2
ΔGint-52 kcal/mol
Surface area9290 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)4 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Calmodulin / CaM


Mass: 16721.350 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Xenopus laevis Calmodulin / Source: (gene. exp.) Xenopus laevis (African clawed frog) / Gene: calm1, calm2 / Production host: Escherichia coli (E. coli) / References: UniProt: P62155, UniProt: P0DP33*PLUS
#2: Protein/peptide Disks large homolog 4 / Postsynaptic density protein 95 / PSD-95 / Synapse-associated protein 90 / SAP90


Mass: 2408.641 Da / Num. of mol.: 1 / Fragment: UNP residues 1-19 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P78352
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
Has protein modificationY

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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
121anisotropic1IPAP HSQC
131isotropic13D 1H-15N NOESY
141isotropic13D (H)CCH-TOCSY
151isotropic13D CBCA(CO)NH
161isotropic13D HNCO
171isotropic13D HBHA(CO)NH
181isotropic13D 1H-13C NOESY aliphatic
191isotropic12D 1H-13C HSQC aliphatic

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Sample preparation

DetailsType: solution
Contents: 500 uM [U-100% 13C; U-100% 15N] Calmodulin, 750 uM PSD-95 phosphorylated, 90% H2O/10% D2O
Details: 15N, 13C labeled Calmodlin Bound to unlabeled PSD-95
Label: 15N,13C Calmodulin / Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
500 uMCalmodulin[U-100% 13C; U-100% 15N]1
750 uMPSD-95 phosphorylatednatural abundance1
Sample conditionsDetails: 20mM d-11 Tris pH 7.0, 5mM CaCl2, 50mM NaCl, 8% D2O
Ionic strength: 50 mM / Label: CaM Buffer / pH: 7 / Pressure: 1 atm / Temperature: 318 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
SparkyGoddardchemical shift assignment
HADDOCKBonvinstructure calculation
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxchemical shift assignment
SparkyGoddardpeak picking
HADDOCKBonvinrefinement
RefinementMethod: molecular dynamics / Software ordinal: 2
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 4

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