[English] 日本語
Yorodumi
- PDB-2l98: Structure of trans-Resveratrol in complex with the cardiac regula... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2l98
TitleStructure of trans-Resveratrol in complex with the cardiac regulatory protein Troponin C
ComponentsTroponin C, slow skeletal and cardiac muscles
KeywordsCONTRACTILE PROTEIN / structural protein / metal binding protein / antioxidant
Function / homology
Function and homology information


diaphragm contraction / regulation of ATP-dependent activity / regulation of muscle filament sliding speed / troponin T binding / cardiac Troponin complex / troponin complex / regulation of muscle contraction / transition between fast and slow fiber / Striated Muscle Contraction / response to metal ion ...diaphragm contraction / regulation of ATP-dependent activity / regulation of muscle filament sliding speed / troponin T binding / cardiac Troponin complex / troponin complex / regulation of muscle contraction / transition between fast and slow fiber / Striated Muscle Contraction / response to metal ion / ventricular cardiac muscle tissue morphogenesis / troponin I binding / skeletal muscle contraction / cardiac muscle contraction / calcium-dependent protein binding / actin filament binding / calcium ion binding / protein homodimerization activity / cytosol
Similarity search - Function
EF hand / 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 / 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
RESVERATROL / Troponin C, slow skeletal and cardiac muscles
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / water refinement
Model detailslowest energy, model 1
AuthorsSykes, B.D. / Pineda-Sanabria, S.E. / Robertson, I.M.
CitationJournal: Biochemistry / Year: 2011
Title: Structure of trans-Resveratrol in Complex with the Cardiac Regulatory Protein Troponin C.
Authors: Pineda-Sanabria, S.E. / Robertson, I.M. / Sykes, B.D.
History
DepositionFeb 2, 2011Deposition site: BMRB / Processing site: RCSB
Revision 1.0Mar 30, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2May 1, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software / pdbx_struct_conn_angle / 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_nmr_software.name / _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.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

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


Theoretical massNumber of molelcules
Total (without water)8,6784
Polymers8,3691
Non-polymers3083
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

-
Components

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


Mass: 8369.205 Da / Num. of mol.: 1 / Fragment: EF-hand domains 3 and 4, residues 91-161
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TNNC, TNNC1 / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21 (de3) Plyss / References: UniProt: P63316
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-STL / RESVERATROL / Resveratrol


Mass: 228.243 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H12O3

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1111D 1H
1212D 1H-15N HSQC
1312D 1H-13C HSQC aliphatic
1422D 1H-1H NOESY
1522D 1H-1H ROESY
1612D 13C-15N filtered NOESY
1712D 13C edited/filtered NOESY-HSQC
2813D 13C edited/filtered HMQC-NOESY
1922D 1H-1H NOESY

-
Sample preparation

Details
Solution-IDContentsSolvent system
10.5 mM [U-100% 13C; U-100% 15N] CcTnC, 2.0 mM RESVERATROL, 10.0 mM CALCIUM ION, 6-8 mM TCEP, 0.5 mM [U-99% 2H] DSS, 100 mM potassium chloride, 10 mM imidazole, 100% H2O100% H2O
20.5 mM [U-100% 13C; U-100% 15N] CcTnC, 2.0 mM RESVERATROL, 10.0 mM CALCIUM ION, 6-8 mM TCEP, 0.5 mM [U-99% 2H] DSS, 100 mM potassium chloride, 8 mM imidazole, 2 mM [U-2H] imidazole, 100% D2O100% D2O
Sample
Conc. (mg/ml)UnitsComponentIsotopic labelingConc. range (mg/ml)Solution-ID
0.5 mMCcTnC-1[U-100% 13C; U-100% 15N]1
2.0 mMRESVERATROL-21
10.0 mMCALCIUM ION-31
mMTCEP-46-81
0.5 mMDSS-5[U-99% 2H]1
100 mMpotassium chloride-61
10 mMimidazole-71
0.5 mMCcTnC-8[U-100% 13C; U-100% 15N]2
2.0 mMRESVERATROL-92
10.0 mMCALCIUM ION-102
mMTCEP-116-82
0.5 mMDSS-12[U-99% 2H]2
100 mMpotassium chloride-132
8 mMimidazole-142
2 mMimidazole-15[U-2H]2
Sample conditions
Conditions-IDpHPressure (kPa)Temperature (K)
16.9 ambient 303 K
26.9 ambient 298 K

-
NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA5001
Varian UnityVarianUNITY6002
Varian INOVAVarianINOVA8003

-
Processing

NMR software
NameDeveloperClassification
VnmrJVariancollection
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRViewJohnson, One Moon Scientificdata analysis
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure solution
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
RefinementMethod: water refinement / Software ordinal: 1
Details: Refinement in explicit solvent with a water box edge length of 18.8 and inclusion of atomic charges
NMR constraintsNOE constraints total: 28 / NOE long range total count: 23 / NOE medium range total count: 5
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / 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://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