[English] 日本語
Yorodumi
- PDB-1ozs: C-domain of human cardiac troponin C in complex with the inhibito... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1ozs
TitleC-domain of human cardiac troponin C in complex with the inhibitory region of human cardiac troponin I
Components
  • Troponin C, slow skeletal and cardiac muscles
  • Troponin I, cardiac muscle
KeywordsSTRUCTURAL PROTEIN / EF-Hand
Function / homology
Function and homology information


regulation of systemic arterial blood pressure by ischemic conditions / troponin C binding / diaphragm contraction / regulation of ATP-dependent activity / regulation of muscle filament sliding speed / troponin T binding / cardiac myofibril / cardiac Troponin complex / troponin complex / regulation of muscle contraction ...regulation of systemic arterial blood pressure by ischemic conditions / troponin C binding / diaphragm contraction / regulation of ATP-dependent activity / regulation of muscle filament sliding speed / troponin T binding / cardiac myofibril / cardiac Troponin complex / troponin complex / regulation of muscle contraction / regulation of smooth muscle contraction / negative regulation of ATP-dependent activity / transition between fast and slow fiber / Striated Muscle Contraction / muscle filament sliding / response to metal ion / regulation of cardiac muscle contraction by calcium ion signaling / ventricular cardiac muscle tissue morphogenesis / heart contraction / troponin I binding / skeletal muscle contraction / calcium channel inhibitor activity / vasculogenesis / Ion homeostasis / cardiac muscle contraction / 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 / EF-hand domain pair / EF-hand / : ...Troponin I residues 1-32 / Troponin I residues 1-32 / : / Troponin / Troponin domain superfamily / Troponin / EF hand domain / 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 / 100 structures calculated using CNS simulated annealing protocol starting from extended structures
AuthorsLindhout, D.A. / Sykes, B.D.
CitationJournal: J.Biol.Chem. / Year: 2003
Title: Structure and dynamics of the C-domain of human cardiac troponin C in complex with the inhibitory region of human cardiac troponin I.
Authors: Lindhout, D.A. / Sykes, B.D.
History
DepositionApr 9, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 16, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly ...database_2 / pdbx_struct_assembly / pdbx_struct_conn_angle / pdbx_struct_oper_list / struct_conn / 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 / _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.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.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

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


Theoretical massNumber of molelcules
Total (without water)11,1174
Polymers11,0362
Non-polymers802
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)30 / 100structures with the lowest energy
Representative

-
Components

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


Mass: 8512.409 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TNNC1 OR TNNC / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3 (pLysS) / References: UniProt: P63316
#2: Protein/peptide Troponin I, cardiac muscle / cIp


Mass: 2524.066 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TNNI3 OR TNNC1 / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3 (pLysS) / References: UniProt: P19429
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 13C-separated NOESY
121HNHA
1313D 15N-separated NOESY
1413D 13C-TOCSY
1513D 15N-TOCSY

-
Sample preparation

DetailsContents: 13C/15N-cCTnC in complex with 13C/15N-cIp
Solvent system: 100 mM KCl, 10 mM Imidazole, 20mM CaCl2, 1mM DSS, pH 6.7
Sample conditionsIonic strength: 0.1 / pH: 6.7 / Pressure: 1 atm / Temperature: 303 K
Crystal grow
*PLUS
Method: other / Details: NMR

-
NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA8001
Varian INOVAVarianINOVA5002
Varian UNITYVarianUNITY6003

-
Processing

NMR software
NameVersionDeveloperClassification
VNMR6.1bvarian inc.collection
CNS1.1Brungerstructure solution
NMRPipe1Delaglioprocessing
CNS1.1Brungerrefinement
RefinementMethod: 100 structures calculated using CNS simulated annealing protocol starting from extended structures
Software ordinal: 1
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 30

+
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