[English] 日本語
Yorodumi
- PDB-2kgb: NMR solution of the regulatory domain cardiac F77W-Troponin C in ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2kgb
TitleNMR solution of the regulatory domain cardiac F77W-Troponin C in complex with the cardiac Troponin I 144-163 switch peptide
Components
  • Troponin C, slow skeletal and cardiac muscles
  • Troponin I, cardiac muscle
KeywordsCONTRACTILE PROTEIN/CA BINDING PROTEIN / TROPONIN C / TROPONIN I / switch peptide / cNTnC / TnI144-163 / TFE / Acetylation / Calcium / Cardiomyopathy / Disease mutation / Muscle protein / Polymorphism / Actin-binding / Phosphoprotein / CONTRACTILE PROTEIN-CA BINDING PROTEIN COMPLEX
Function / homology
Function and homology information


regulation of systemic arterial blood pressure by ischemic conditions / regulation of muscle filament sliding speed / troponin T binding / diaphragm contraction / troponin C binding / regulation of ATP-dependent activity / cardiac Troponin complex / cardiac myofibril / regulation of smooth muscle contraction / troponin complex ...regulation of systemic arterial blood pressure by ischemic conditions / regulation of muscle filament sliding speed / troponin T binding / diaphragm contraction / troponin C binding / regulation of ATP-dependent activity / cardiac Troponin complex / cardiac myofibril / regulation of smooth muscle contraction / troponin complex / regulation of muscle contraction / transition between fast and slow fiber / negative regulation of ATP-dependent activity / Striated Muscle Contraction / regulation of cardiac muscle contraction by calcium ion signaling / response to metal ion / ventricular cardiac muscle tissue morphogenesis / myosin II complex / heart contraction / troponin I binding / skeletal muscle contraction / calcium channel inhibitor activity / vasculogenesis / cardiac muscle contraction / Ion homeostasis / sarcomere / intracellular calcium ion homeostasis / calcium-dependent protein binding / actin filament binding / actin binding / heart development / protein domain specific binding / calcium ion binding / protein kinase binding / protein homodimerization activity / cytosol
Similarity search - Function
Troponin I residues 1-32 / Troponin I residues 1-32 / Troponin / Troponin domain superfamily / Troponin / EF-hand domain pair / EF-hand / Recoverin; domain 1 / EF-hand domain pair / EF-hand, calcium binding motif ...Troponin I residues 1-32 / Troponin I residues 1-32 / Troponin / Troponin domain superfamily / Troponin / EF-hand domain pair / EF-hand / Recoverin; domain 1 / 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 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Troponin I, cardiac muscle / Troponin C, slow skeletal and cardiac muscles
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsMercier, P. / Julien, O. / Crane, M.L. / Sykes, B.D.
CitationJournal: Protein Sci. / Year: 2009
Title: The effect of the cosolvent trifluoroethanol on a tryptophan side chain orientation in the hydrophobic core of troponin C.
Authors: Julien, O. / Mercier, P. / Crane, M.L. / Sykes, B.D.
History
DepositionMar 7, 2009Deposition site: BMRB / Processing site: RCSB
Revision 1.0Mar 24, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly ...database_2 / pdbx_struct_assembly / pdbx_struct_oper_list / 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 1.3May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
C: Troponin C, slow skeletal and cardiac muscles
I: Troponin I, cardiac muscle
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,3693
Polymers12,3292
Non-polymers401
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100target function
RepresentativeModel #1fewest violations

-
Components

#1: Protein Troponin C, slow skeletal and cardiac muscles / TN-C


Mass: 10109.339 Da / Num. of mol.: 1 / Fragment: regulatory domain / Mutation: F77W
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TNNC1, TNNC / Plasmid: PET3D / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) PLYSS / References: UniProt: P63316
#2: Protein/peptide Troponin I, cardiac muscle / Cardiac troponin I


Mass: 2219.701 Da / Num. of mol.: 1 / Source method: obtained synthetically / References: UniProt: P19429
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1123D 1H-15N NOESY
1213D 1H-13C NOESY
1323D HNHA
1422D 1H-15N HSQC
1512D 1H-13C HSQC
1613D CBCA(CO)NH
1713D HN(CA)CB
1813D H(CCO)NH
1913D (H)CCH-TOCSY
11013D C(CO)NH

-
Sample preparation

Details
Solution-IDContentsSolvent system
1~1 mM [U-99% 13C; U-99% 15N] Protein, 6 mM CALCIUM ION, 15 mM DTT, 100 mM potassium chloride, 10 mM imidazole, ~2 mM Troponin I, 0.03 % sodium azide, 0.3 mM DSS, 90% H2O/10% D2O90% H2O/10% D2O
2~1 mM Protein, 6 mM CALCIUM ION, 15 mM DTT, 0.03 % sodium azide, 0.3 mM DSS, ~2 mM Troponin I, 100 mM potassium chloride, 10 mM imidazole, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMProtein[U-99% 13C; U-99% 15N]1
6 mMCALCIUM ION1
15 mMDTT1
100 mMpotassium chloride1
10 mMimidazole1
2 mMTroponin I1
0.03 %sodium azide1
0.3 mMDSS1
1 mMProtein2
6 mMCALCIUM ION2
15 mMDTT2
0.03 %sodium azide2
0.3 mMDSS2
2 mMTroponin I2
100 mMpotassium chloride2
10 mMimidazole2
Sample conditionsIonic strength: 0.1 / pH: 6.8 / Pressure: ambient / Temperature: 303 K

-
NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA5001
Varian INOVAVarianINOVA6002
Varian INOVAVarianINOVA8003

-
Processing

NMR softwareName: CYANA / Version: 2.1 / Developer: Guntert, P. et al. / Classification: refinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR constraintsNOE constraints total: 1375 / NOE intraresidue total count: 409 / NOE long range total count: 244 / NOE medium range total count: 357 / NOE sequential total count: 365 / Protein chi angle constraints total count: 486 / Protein phi angle constraints total count: 98 / Protein psi angle constraints total count: 294
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20 / Maximum lower distance constraint violation: 1.8 Å / Maximum upper distance constraint violation: 6 Å

+
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://pdbjlvh1.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