[English] 日本語
Yorodumi
- PDB-6mv3: NMR structure of the cNTnC-cTnI chimera bound to calcium desensit... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6mv3
TitleNMR structure of the cNTnC-cTnI chimera bound to calcium desensitizer W7
ComponentsTroponin C, slow skeletal and cardiac muscles,Troponin I, cardiac muscle chimera
KeywordsMETAL BINDING PROTEIN / cardiac troponin / calcium binding protein / EF hand / calcium desensitizer / W7
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 domain pair / EF-hand, calcium binding motif / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. ...Troponin I residues 1-32 / Troponin I residues 1-32 / Troponin / Troponin domain superfamily / Troponin / EF-hand domain pair / 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
Similarity search - Domain/homology
Chem-WW7 / Troponin I, cardiac muscle / Troponin C, slow skeletal and cardiac muscles
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsCai, F. / Hwang, P.M. / Sykes, B.D.
Funding support Canada, 1items
OrganizationGrant numberCountry
Other privateB.D.S., G-14-0005884 Canada
CitationJournal: Biochemistry / Year: 2018
Title: Structural Changes Induced by the Binding of the Calcium Desensitizer W7 to Cardiac Troponin.
Authors: Cai, F. / Hwang, P.M. / Sykes, B.D.
History
DepositionOct 24, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 14, 2018Provider: repository / Type: Initial release
Revision 1.1Dec 5, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status / pdbx_nmr_software
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
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: Troponin C, slow skeletal and cardiac muscles,Troponin I, cardiac muscle chimera
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,5673
Polymers14,1861
Non-polymers3812
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area790 Å2
ΔGint-3 kcal/mol
Surface area8520 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

-
Components

#1: Protein Troponin C, slow skeletal and cardiac muscles,Troponin I, cardiac muscle chimera / TN-C / Cardiac troponin I


Mass: 14186.127 Da / Num. of mol.: 1 / Mutation: C35S, C84S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TNNC1, TNNC, TNNI3, TNNC1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P63316, UniProt: P19429
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-WW7 / N-(6-AMINOHEXYL)-5-CHLORO-1-NAPHTHALENESULFONAMIDE


Mass: 340.868 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H21ClN2O2S / Feature type: SUBJECT OF INVESTIGATION

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-15N HSQC
122isotropic12D 1H-13C HSQC
131isotropic13D 1H-15N NOESY
142isotropic13D 1H-13C NOESY
152isotropic12D TOCSY
162isotropic12D 13C,15N-double-filtered NOESY

-
Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution10.5 mM [U-15N] cChimera_protein, 100 mM potassium chloride, 10 mM imidazole, 10 mM calcium chloride, 0.25 mM [U-99% 2H] DSS, 2.5 mM WW7, 1 % [U-99% 2H] DMSO, 95% H2O/5% D2O15N_chimera95% H2O/5% D2O
solution20.5 mM [U-13C; U-15N] cChimera_protein, 100 mM potassium chloride, 10 mM imidazole, 10 mM calcium chloride, 0.25 mM [U-99% 2H] DSS, 2.5 mM WW7, 1 % [U-99% 2H] DMSO, 100% D2O13C_15N_chimera100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.5 mMcChimera_protein[U-15N]1
100 mMpotassium chloridenatural abundance1
10 mMimidazolenatural abundance1
10 mMcalcium chloridenatural abundance1
0.25 mMDSS[U-99% 2H]1
2.5 mMWW7natural abundance1
1 %DMSO[U-99% 2H]1
0.5 mMcChimera_protein[U-13C; U-15N]2
100 mMpotassium chloridenatural abundance2
10 mMimidazolenatural abundance2
10 mMcalcium chloridenatural abundance2
0.25 mMDSS[U-99% 2H]2
2.5 mMWW7natural abundance2
1 %DMSO[U-99% 2H]2
Sample conditionsIonic strength: NA Not defined / Label: NMR_sample / pH: 6.8 / Pressure: ambient atm / Temperature: 303 K

-
NMR measurement

NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 600 MHz

-
Processing

NMR software
NameDeveloperClassification
VnmrJVariancollection
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRViewJJohnson, One Moon Scientificpeak picking
NMRViewJJohnson, One Moon Scientificchemical shift assignment
ARIA2Linge, O'Donoghue and Nilgesdata analysis
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure calculation
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
RefinementMethod: simulated annealing / Software ordinal: 7
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 20

+
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