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- PDB-2l7l: Solution structure of Ca2+/calmodulin complexed with a peptide re... -

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Basic information

Entry
Database: PDB / ID: 2l7l
TitleSolution structure of Ca2+/calmodulin complexed with a peptide representing the calmodulin-binding domain of calmodulin kinase I
Components
  • Calcium/calmodulin-dependent protein kinase type 1
  • Calmodulin
KeywordsMetal Binding Protein/Transferase / Calmodulin complex / calmodulin-peptide complex / CaMKI / Metal Binding Protein-Transferase complex
Function / homology
Function and homology information


Activation of RAC1 downstream of NMDARs / positive regulation of syncytium formation by plasma membrane fusion / regulation of high voltage-gated calcium channel activity / positive regulation of synapse structural plasticity / regulation of muscle cell differentiation / : / Ca2+/calmodulin-dependent protein kinase / regulation of protein binding / establishment of protein localization to mitochondrial membrane / type 3 metabotropic glutamate receptor binding ...Activation of RAC1 downstream of NMDARs / positive regulation of syncytium formation by plasma membrane fusion / regulation of high voltage-gated calcium channel activity / positive regulation of synapse structural plasticity / regulation of muscle cell differentiation / : / Ca2+/calmodulin-dependent protein kinase / regulation of protein binding / establishment of protein localization to mitochondrial membrane / type 3 metabotropic glutamate receptor binding / CaM pathway / Cam-PDE 1 activation / Sodium/Calcium exchangers / nucleocytoplasmic transport / regulation of synaptic vesicle endocytosis / Calmodulin induced events / Reduction of cytosolic Ca++ levels / CREB1 phosphorylation through the activation of CaMKII/CaMKK/CaMKIV cascasde / Activation of Ca-permeable Kainate Receptor / Loss of phosphorylation of MECP2 at T308 / CREB1 phosphorylation through the activation of Adenylate Cyclase / PKA activation / negative regulation of high voltage-gated calcium channel activity / calmodulin-dependent protein kinase activity / CaMK IV-mediated phosphorylation of CREB / Glycogen breakdown (glycogenolysis) / positive regulation of cyclic-nucleotide phosphodiesterase activity / organelle localization by membrane tethering / negative regulation of calcium ion export across plasma membrane / regulation of synaptic vesicle exocytosis / CLEC7A (Dectin-1) induces NFAT activation / regulation of cardiac muscle cell action potential / mitochondrion-endoplasmic reticulum membrane tethering / autophagosome membrane docking / Activation of RAC1 downstream of NMDARs / response to corticosterone / positive regulation of dendritic spine development / regulation of synapse organization / positive regulation of muscle cell differentiation / nitric-oxide synthase binding / positive regulation of ryanodine-sensitive calcium-release channel activity / regulation of cell communication by electrical coupling involved in cardiac conduction / Negative regulation of NMDA receptor-mediated neuronal transmission / negative regulation of peptidyl-threonine phosphorylation / Synthesis of IP3 and IP4 in the cytosol / Unblocking of NMDA receptors, glutamate binding and activation / Phase 0 - rapid depolarisation / protein phosphatase activator activity / RHO GTPases activate PAKs / positive regulation of phosphoprotein phosphatase activity / Ion transport by P-type ATPases / Long-term potentiation / Uptake and function of anthrax toxins / Calcineurin activates NFAT / Regulation of MECP2 expression and activity / adenylate cyclase binding / catalytic complex / DARPP-32 events / detection of calcium ion / regulation of cardiac muscle contraction / negative regulation of ryanodine-sensitive calcium-release channel activity / Smooth Muscle Contraction / RHO GTPases activate IQGAPs / calcium channel inhibitor activity / cellular response to interferon-beta / positive regulation of DNA binding / regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion / Protein methylation / phosphatidylinositol 3-kinase binding / eNOS activation / Activation of AMPK downstream of NMDARs / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / positive regulation of protein dephosphorylation / Ion homeostasis / regulation of calcium-mediated signaling / regulation of ryanodine-sensitive calcium-release channel activity / titin binding / positive regulation of protein autophosphorylation / voltage-gated potassium channel complex / sperm midpiece / calcium channel complex / response to amphetamine / activation of adenylate cyclase activity / substantia nigra development / adenylate cyclase activator activity / Ras activation upon Ca2+ influx through NMDA receptor / nitric-oxide synthase regulator activity / regulation of heart rate / sarcomere / protein serine/threonine kinase activator activity / FCERI mediated Ca+2 mobilization / FCGR3A-mediated IL10 synthesis / positive regulation of protein export from nucleus / VEGFR2 mediated vascular permeability / positive regulation of peptidyl-threonine phosphorylation / regulation of cytokinesis / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / VEGFR2 mediated cell proliferation / positive regulation of nitric-oxide synthase activity
Similarity search - Function
Calmodulin / EF-hand domain pair / EF-hand, calcium binding motif / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. ...Calmodulin / EF-hand domain pair / EF-hand, calcium binding motif / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
Similarity search - Domain/homology
Calmodulin / Calmodulin-1 / Calcium/calmodulin-dependent protein kinase type 1
Similarity search - Component
Biological speciesHomo sapiens (human)
Rattus norvegicus (Norway rat)
MethodSOLUTION NMR / torsion angle dynamics, simulated annealing
Model detailslowest energy, model 1
AuthorsGifford, J.L. / Ishida, H. / Vogel, H.J.
CitationJournal: J.Biomol.Nmr / Year: 2011
Title: Fast methionine-based solution structure determination of calcium-calmodulin complexes.
Authors: Gifford, J.L. / Ishida, H. / Vogel, H.J.
History
DepositionDec 13, 2010Deposition site: BMRB / Processing site: RCSB
Revision 1.0May 18, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jun 14, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Calmodulin
B: Calcium/calmodulin-dependent protein kinase type 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,4886
Polymers19,3272
Non-polymers1604
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)1 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Calmodulin / Phosphorylase kinase delta / isoform CRA_a / Calmodulin 3 / Phosphorylase kinase delta / isoform ...Phosphorylase kinase delta / isoform CRA_a / Calmodulin 3 / Phosphorylase kinase delta / isoform CRA_b / cDNA FLJ61744


Mass: 16721.350 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CALM1, CALM3, hCG_20313, hCG_21749 / Production host: Escherichia coli (E. coli) / References: UniProt: B4DJ51, UniProt: P0DP23*PLUS
#2: Protein/peptide Calcium/calmodulin-dependent protein kinase type 1 / CaM kinase I / CaM-KI / CaM kinase I alpha / CaMKI-alpha


Mass: 2606.121 Da / Num. of mol.: 1 / Fragment: Calmodulin-binding residues 299-320 / Source method: obtained synthetically / Source: (synth.) Rattus norvegicus (Norway rat)
References: UniProt: Q63450, Ca2+/calmodulin-dependent protein kinase
#3: Chemical
ChemComp-CA / CALCIUM ION


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

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1232D 1H-13C HSQC
1322D 1H-1H COSY
1413D CBCA(CO)NH
1513D C(CO)NH
1613D HNCO
1713D HN(CA)CB
1813D HBHA(CO)NH
1913D H(CCO)NH
11033D 1H-13C NOESY
11113D HN(CA)CO
11212D HMBC
11313D LRCH
1142F2-filtered 2D 1H-1H NOESY
21542D 1H-15N IPAP HSQC
21652D 1H-15N IPAP HSQC
NMR detailsText: The structure was determined using a combination of NOE and residual dipolar coupling restraints.

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Sample preparation

Details
Solution-IDContentsSolvent system
10.95 mM [U-13C; U-15N] protein, 1.05 mM peptide, 4 mM CALCIUM ION, 0.5 mM DSS, 100 mM potassium chloride, 20 mM Bis-Tris, 0.03 % sodium azide, 90% H2O/10% D2O90% H2O/10% D2O
20.66 mM [U-2H; U-15N] protein, 0.40 mM peptide, 20 mM Bis-Tris, 100 mM potassium chloride, 4 mM CALCIUM ION, 0.03 % sodium azide, 0.5 mM DSS, 90% H2O/10% D2O90% H2O/10% D2O
30.64 mM 1H/13C-methyl Met; U-2H; U-15N protein, 0.83 mM peptide, 20 mM Bis-Tris, 100 mM potassium chloride, 4 mM CALCIUM ION, 0.03 % sodium azide, 0.5 mM DSS, 100% D2O100% D2O
40.95 mM [U-13C; U-15N] protein, 1.05 mM peptide, 20 mM Bis-Tris, 300 mM potassium chloride, 4 mM CALCIUM ION, 0.03 % sodium azide, 0.5 mM DSS, 90% H2O/10% D2O90% H2O/10% D2O
50.95 mM [U-13C; U-15N] protein, 1.05 mM peptide, 20 mM Bis-Tris, 300 mM potassium chloride, 4 mM CALCIUM ION, 0.03 % sodium azide, 0.5 mM DSS, 16 w/v Pf1 phage, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.95 mMprotein_1-1[U-13C; U-15N]1
1.05 mMprotein_2-21
4 mMCALCIUM ION-31
0.5 mMDSS-41
100 mMpotassium chloride-51
20 mMBis-Tris-61
0.03 %sodium azide-71
0.66 mMprotein_1-8[U-2H; U-15N]2
0.40 mMprotein_2-92
20 mMBis-Tris-102
100 mMpotassium chloride-112
4 mMCALCIUM ION-122
0.03 %sodium azide-132
0.5 mMDSS-142
0.64 mMprotein_1-151H/13C-methyl Met; U-2H; U-15N3
0.83 mMprotein_2-163
20 mMBis-Tris-173
100 mMpotassium chloride-183
4 mMCALCIUM ION-193
0.03 %sodium azide-203
0.5 mMDSS-213
0.95 mMprotein_1-22[U-13C; U-15N]4
1.05 mMprotein_2-234
20 mMBis-Tris-244
300 mMpotassium chloride-254
4 mMCALCIUM ION-264
0.03 %sodium azide-274
0.5 mMDSS-284
0.95 mMprotein_1-29[U-13C; U-15N]5
1.05 mMprotein_2-305
20 mMBis-Tris-315
300 mMpotassium chloride-325
4 mMCALCIUM ION-335
0.03 %sodium azide-345
0.5 mMDSS-355
16 w/vPf1 phage-365
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
10.1 6.8 ambient 303 K
20.3 6.8 ambient 303 K

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NMR measurement

NMR spectrometerType: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 500 MHz

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Processing

NMR software
NameDeveloperClassification
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRViewJohnson, One Moon Scientificchemical shift assignment
NMRViewJohnson, One Moon Scientificpeak picking
CYANAGuntert, Mumenthaler and Wuthrichchemical shift assignment
CYANAGuntert, Mumenthaler and Wuthrichstructure solution
CYANAGuntert, Mumenthaler and Wuthrichrefinement
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure solution
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
ProcheckNMRLaskowski and MacArthurdata analysis
TALOSCornilescu, Delaglio and Baxdata analysis
MOLMOLKoradi, Billeter and Wuthrichdata analysis
XwinNMRBruker Biospincollection
RefinementMethod: torsion angle dynamics, simulated annealing / Software ordinal: 1
NMR constraintsNOE constraints total: 528
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 1

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