[English] 日本語
Yorodumi
- PDB-9ibi: Solution NMR study of the titin I-band IgI domain I82 reveals con... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9ibi
TitleSolution NMR study of the titin I-band IgI domain I82 reveals conformational dynamics
ComponentsTitin
KeywordsSTRUCTURAL PROTEIN / muscle scaffold contraction I-band
Function / homology
Function and homology information


heart growth / forward locomotion / striated muscle cell development / regulation of relaxation of cardiac muscle / A band / detection of muscle stretch / muscle myosin complex / ventricular system development / cardiac myofibril assembly / adult heart development ...heart growth / forward locomotion / striated muscle cell development / regulation of relaxation of cardiac muscle / A band / detection of muscle stretch / muscle myosin complex / ventricular system development / cardiac myofibril assembly / adult heart development / cardiac muscle tissue morphogenesis / M band / I band / ankyrin binding / sarcomere organization / somitogenesis / heart morphogenesis / muscle contraction / sarcomere / structural constituent of cytoskeleton / Z disc / heart development / protein tyrosine kinase activity / in utero embryonic development / calmodulin binding / non-specific serine/threonine protein kinase / protein serine kinase activity / protein serine/threonine kinase activity / ATP binding / metal ion binding / nucleus
Similarity search - Function
PPAK motif / PPAK motif / Titin, Z repeat / Titin Z / MyBP-C, tri-helix bundle domain / Tri-helix bundle domain / Immunoglobulin I-set / Immunoglobulin I-set domain / Fibronectin type III domain / Fibronectin type 3 domain ...PPAK motif / PPAK motif / Titin, Z repeat / Titin Z / MyBP-C, tri-helix bundle domain / Tri-helix bundle domain / Immunoglobulin I-set / Immunoglobulin I-set domain / Fibronectin type III domain / Fibronectin type 3 domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Immunoglobulin V-Type / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Tyrosine-protein kinase, active site / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Protein kinase domain / Immunoglobulin-like fold / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
Similarity search - Domain/homology
Biological speciesMus musculus (house mouse)
MethodSOLUTION NMR / molecular dynamics
AuthorsPfuhl, M. / Gage, M.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
British Heart Foundation1827212 United Kingdom
CitationJournal: To Be Published
Title: Solution NMR study of the titin I-band IgI domain I82 reveals conformational dynamics
Authors: Kelly, C.M. / Abukar, S. / Gage, M. / Pfuhl, M.
History
DepositionFeb 12, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 19, 2025Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Titin


Theoretical massNumber of molelcules
Total (without water)11,7151
Polymers11,7151
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: NMR relaxation study, rotational correlation time compatible with monomeric protein
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 50structures with the lowest energy
RepresentativeModel #1lowest energy

-
Components

#1: Protein Titin / Connectin


Mass: 11715.221 Da / Num. of mol.: 1 / Mutation: n.a.
Source method: isolated from a genetically manipulated source
Details: N-terminal 4 amino acids are a cloning artifact / Source: (gene. exp.) Mus musculus (house mouse) / Tissue: muscle / Cell: myocyte / Gene: Ttn / Plasmid: pET-151dTOPO / Production host: Escherichia coli BL21 (bacteria) / Variant (production host): BL21 STAR
References: UniProt: A2ASS6, non-specific serine/threonine protein kinase
Has protein modificationN

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic22D 1H-15N HSQC
121isotropic23D 1H-15N NOESY
131isotropic23D 1H-15N TOCSY
142isotropic12D 1H-13C HSQC
152isotropic12D 1H-13C TROSY aromatic
162isotropic13D 1H-13C NOESY aliphatic
172isotropic13D 1H-13C NOESY aromatic
182isotropic23D HN(CA)CB
1102isotropic33D HNCO
192isotropic33D HN(COC)C(H)
1112isotropic33D HN(COCC)H
1121isotropic23D HNHA

-
Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution10.5 mM [U-95% 15N] Titin, 50.0 mM sodium chloride, 20.0 mM HEPES, 2.0 mM DTT, 0.02 % w/v sodium azide, 95% H2O/5% D2O15N_sample95% H2O/5% D2O
solution20.5 mM [U-95% 13C; U-95% 15N] Titin, 50.0 mM sodium chloride, 20.0 mM HEPES, 2.0 mM DTT, 0.02 % w/v sodium azide, 95% H2O/5% D2O15N_13C_sample95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.5 mMTitin[U-95% 15N]1
50.0 mMsodium chloridenatural abundance1
20.0 mMHEPESnatural abundance1
2.0 mMDTTnatural abundance1
0.02 % w/vsodium azidenatural abundance1
0.5 mMTitin[U-95% 13C; U-95% 15N]2
50.0 mMsodium chloridenatural abundance2
20.0 mMHEPESnatural abundance2
2.0 mMDTTnatural abundance2
0.02 % w/vsodium azidenatural abundance2
Sample conditionsIonic strength: 50.0 mM / Ionic strength err: 1 / Label: condition_1 / pH: 7 / PH err: 0.05 / Pressure: 1 atm / Pressure err: 0.02 / Temperature: 298 K / Temperature err: 0.2

-
NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-IDDetails
Bruker AVANCE III HDBrukerAVANCE III HD9501Crick
Bruker AVANCE NEOBrukerAVANCE NEO8002KCL
Bruker AVANCE IIIBrukerAVANCE III7003KCL

-
Processing

NMR software
NameVersionDeveloperClassification
TopSpin4.3Bruker Biospinprocessing
CcpNmr Analysis2.4.2CCPNchemical shift assignment
CcpNmr Analysis Assign3.2.12CCPNchemical shift assignment
ARIA2.3.3Michael Nilges, Benjamin Bardiauxstructure calculation
RefinementMethod: molecular dynamics / Software ordinal: 4 / Details: standard parameters used
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 50 / 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