[English] 日本語
Yorodumi
- PDB-9mo8: Structure of native murine cardiac thin filament at pCa=5.8 in Ca... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9mo8
TitleStructure of native murine cardiac thin filament at pCa=5.8 in Ca2+-free state (upper strand)
Components
  • Actin, alpha cardiac muscle 1
  • Isoform A2 of Troponin T, cardiac muscle
  • Tropomyosin alpha-1 chain
  • Troponin C, slow skeletal and cardiac muscles
  • Troponin I, cardiac muscle
KeywordsMOTOR PROTEIN / thin filament / cryo-EM / troponin / tropomyosin / muscle structure
Function / homology
Function and homology information


atrial cardiac muscle tissue morphogenesis / actin-mediated cell contraction / positive regulation of heart rate by epinephrine / muscle thin filament tropomyosin / RHOB GTPase cycle / Formation of the dystrophin-glycoprotein complex (DGC) / regulation of systemic arterial blood pressure by ischemic conditions / Striated Muscle Contraction / troponin C binding / diaphragm contraction ...atrial cardiac muscle tissue morphogenesis / actin-mediated cell contraction / positive regulation of heart rate by epinephrine / muscle thin filament tropomyosin / RHOB GTPase cycle / Formation of the dystrophin-glycoprotein complex (DGC) / regulation of systemic arterial blood pressure by ischemic conditions / Striated Muscle Contraction / troponin C binding / diaphragm contraction / RHOA GTPase cycle / regulation of ATP-dependent activity / regulation of muscle filament sliding speed / troponin T binding / Smooth Muscle Contraction / cardiac myofibril / cardiac Troponin complex / troponin complex / actin-myosin filament sliding / regulation of muscle contraction / cardiac myofibril assembly / regulation of smooth muscle contraction / negative regulation of ATP-dependent activity / transition between fast and slow fiber / Ion homeostasis / cardiac muscle tissue morphogenesis / positive regulation of ATP-dependent activity / actomyosin structure organization / muscle filament sliding / response to metal ion / I band / regulation of cardiac muscle contraction by calcium ion signaling / sarcomere organization / ventricular cardiac muscle tissue morphogenesis / microfilament motor activity / myosin binding / regulation of heart contraction / tropomyosin binding / troponin I binding / myofibril / mesenchyme migration / striated muscle thin filament / sarcoplasm / skeletal muscle thin filament assembly / calcium channel inhibitor activity / vasculogenesis / striated muscle contraction / cardiac muscle contraction / muscle contraction / sarcomere / filopodium / actin filament / response to bacterium / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / structural constituent of cytoskeleton / response to calcium ion / intracellular calcium ion homeostasis / calcium-dependent protein binding / actin filament binding / lamellipodium / actin cytoskeleton / actin binding / heart development / cell body / in utero embryonic development / response to ethanol / hydrolase activity / protein domain specific binding / protein heterodimerization activity / response to xenobiotic stimulus / synapse / calcium ion binding / positive regulation of gene expression / negative regulation of apoptotic process / protein kinase binding / glutamatergic synapse / protein homodimerization activity / ATP binding / identical protein binding / cytoplasm
Similarity search - Function
Troponin T / Troponin I residues 1-32 / Troponin I residues 1-32 / : / Troponin / Troponin domain superfamily / Troponin / Tropomyosins signature. / Tropomyosin / Tropomyosin ...Troponin T / Troponin I residues 1-32 / Troponin I residues 1-32 / : / Troponin / Troponin domain superfamily / Troponin / Tropomyosins signature. / Tropomyosin / Tropomyosin / EF-hand domain pair / : / Actins signature 1. / Actin, conserved site / Actins signature 2. / Actin/actin-like conserved site / Actins and actin-related proteins signature. / Actin / Actin family / Actin / EF-hand domain pair / EF-hand, calcium binding motif / ATPase, nucleotide binding domain / 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
ADENOSINE-5'-DIPHOSPHATE / Troponin C, slow skeletal and cardiac muscles / Troponin I, cardiac muscle / Troponin T, cardiac muscle / Tropomyosin alpha-1 chain / Actin, alpha cardiac muscle 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 5.2 Å
AuthorsRisi, C.M. / Galkin, V.E.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)R01 HL160966 United States
CitationJournal: To Be Published
Title: Structure of native murine cardiac thin filament at pCa=5.8 in Ca2+-free state (upper strand)
Authors: Risi, C.M. / Galkin, V.E.
History
DepositionDec 25, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 28, 2025Provider: repository / Type: Initial release
Revision 1.0May 28, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0May 28, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0May 28, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0May 28, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0May 28, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0May 28, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Actin, alpha cardiac muscle 1
B: Actin, alpha cardiac muscle 1
C: Actin, alpha cardiac muscle 1
D: Actin, alpha cardiac muscle 1
E: Actin, alpha cardiac muscle 1
F: Actin, alpha cardiac muscle 1
G: Actin, alpha cardiac muscle 1
H: Troponin C, slow skeletal and cardiac muscles
I: Troponin I, cardiac muscle
J: Isoform A2 of Troponin T, cardiac muscle
K: Isoform A2 of Troponin T, cardiac muscle
L: Tropomyosin alpha-1 chain
M: Tropomyosin alpha-1 chain
N: Tropomyosin alpha-1 chain
O: Tropomyosin alpha-1 chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)540,53629
Polymers537,37615
Non-polymers3,16114
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

-
Components

-
Protein , 5 types, 15 molecules ABCDEFGHIJKLMNO

#1: Protein
Actin, alpha cardiac muscle 1 / Alpha-cardiac actin


Mass: 42064.891 Da / Num. of mol.: 7 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
References: UniProt: P68033, Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement
#2: Protein Troponin C, slow skeletal and cardiac muscles / TN-C


Mass: 18437.520 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P19123
#3: Protein Troponin I, cardiac muscle / Cardiac troponin I


Mass: 24308.908 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P48787
#4: Protein Isoform A2 of Troponin T, cardiac muscle / TnTc / Cardiac muscle troponin T / cTnT


Mass: 34616.367 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P50752
#5: Protein
Tropomyosin alpha-1 chain / Alpha-tropomyosin / Tropomyosin-1


Mass: 32735.609 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P58771

-
Non-polymers , 2 types, 14 molecules

#6: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#7: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Mg

-
Details

Has ligand of interestN
Has protein modificationN

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: FILAMENT / 3D reconstruction method: single particle reconstruction

-
Sample preparation

ComponentName: Native murine cardiac thin filament at pCa=5.8 / Type: COMPLEX / Entity ID: #1-#5 / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Mus musculus (house mouse)
Buffer solutionpH: 7
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: EMS Lacey Carbon
VitrificationCryogen name: ETHANE

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 3500 nm / Nominal defocus min: 500 nm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 34 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of real images: 21091

-
Processing

EM software
IDNameCategory
1RELIONparticle selection
2EPUimage acquisition
4RELIONCTF correction
7PHENIXmodel fitting
9PHENIXmodel refinement
10RELIONinitial Euler assignment
11RELIONfinal Euler assignment
12RELIONclassification
13RELION3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 7120025
3D reconstructionResolution: 5.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 58500 / Algorithm: BACK PROJECTION / Details: filtered to 7 Angstroms / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL
Atomic model building
IDPDB-ID 3D fitting-IDAccession codeInitial refinement model-IDSource nameType
17KO4

7ko4

17KO41PDBexperimental model
27UTL

7utl

17UTL2PDBexperimental model
38DD0

8dd0

18DD03PDBexperimental model
48UWW

8uww

18UWW4PDBexperimental model

+
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