[English] 日本語
Yorodumi
- PDB-2l7l: Solution structure of Ca2+/calmodulin complexed with a peptide re... -

+
Open data


ID or keywords:

Loading...

-
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 / positive regulation of synapse structural plasticity / regulation of muscle cell differentiation / regulation of protein binding / Ca2+/calmodulin-dependent protein kinase / calcium/calmodulin-dependent protein kinase activity / CaM pathway / Cam-PDE 1 activation / Sodium/Calcium exchangers ...Activation of RAC1 downstream of NMDARs / positive regulation of syncytium formation by plasma membrane fusion / positive regulation of synapse structural plasticity / regulation of muscle cell differentiation / regulation of protein binding / Ca2+/calmodulin-dependent protein kinase / calcium/calmodulin-dependent protein kinase activity / CaM pathway / Cam-PDE 1 activation / Sodium/Calcium exchangers / Reduction of cytosolic Ca++ levels / Calmodulin induced events / nucleocytoplasmic transport / 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 / organelle localization by membrane tethering / negative regulation of high voltage-gated calcium channel activity / CaMK IV-mediated phosphorylation of CREB / autophagosome membrane docking / mitochondrion-endoplasmic reticulum membrane tethering / Glycogen breakdown (glycogenolysis) / positive regulation of cyclic-nucleotide phosphodiesterase activity / negative regulation of calcium ion export across plasma membrane / CLEC7A (Dectin-1) induces NFAT activation / Activation of RAC1 downstream of NMDARs / regulation of cardiac muscle cell action potential / positive regulation of muscle cell differentiation / positive regulation of dendritic spine development / regulation of synapse organization / positive regulation of ryanodine-sensitive calcium-release channel activity / regulation of cell communication by electrical coupling involved in cardiac conduction / Synthesis of IP3 and IP4 in the cytosol / negative regulation of peptidyl-threonine phosphorylation / Negative regulation of NMDA receptor-mediated neuronal transmission / Phase 0 - rapid depolarisation / Unblocking of NMDA receptors, glutamate binding and activation / negative regulation of ryanodine-sensitive calcium-release channel activity / adenylate cyclase activator activity / protein phosphatase activator activity / RHO GTPases activate PAKs / Ion transport by P-type ATPases / : / Uptake and function of anthrax toxins / Long-term potentiation / Regulation of MECP2 expression and activity / Calcineurin activates NFAT / catalytic complex / DARPP-32 events / regulation of cardiac muscle contraction / detection of calcium ion / Smooth Muscle Contraction / regulation of ryanodine-sensitive calcium-release channel activity / cellular response to interferon-beta / RHO GTPases activate IQGAPs / calcium channel inhibitor activity / regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion / eNOS activation / Protein methylation / voltage-gated potassium channel complex / enzyme regulator activity / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / Activation of AMPK downstream of NMDARs / Ion homeostasis / Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / : / titin binding / positive regulation of protein autophosphorylation / regulation of calcium-mediated signaling / sperm midpiece / calcium channel complex / substantia nigra development / Ras activation upon Ca2+ influx through NMDA receptor / sarcomere / regulation of heart rate / FCERI mediated Ca+2 mobilization / FCGR3A-mediated IL10 synthesis / protein serine/threonine kinase activator activity / VEGFR2 mediated vascular permeability / positive regulation of protein export from nucleus / regulation of cytokinesis / VEGFR2 mediated cell proliferation / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / positive regulation of peptidyl-threonine phosphorylation / spindle microtubule / Translocation of SLC2A4 (GLUT4) to the plasma membrane / positive regulation of receptor signaling pathway via JAK-STAT / RAF activation / Transcriptional activation of mitochondrial biogenesis / positive regulation of protein serine/threonine kinase activity / Stimuli-sensing channels / cellular response to type II interferon / positive regulation of neuron projection development / spindle pole / response to calcium ion / RAS processing / Signaling by RAF1 mutants / Signaling by moderate kinase activity BRAF mutants
Similarity search - Function
: / 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. ...: / 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 1 (Phosphorylase kinase, delta), isoform CRA_a / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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

-
Experimental details

-
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.

-
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)
10.16.8ambient 303 K
20.36.8ambient 303 K

-
NMR measurement

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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more