[English] 日本語
- PDB-5mva: Structure of the thin filament at high calcium concentration -

Open data

ID or keywords:


no data

Basic information

Database: PDB / ID: 5mva
TitleStructure of the thin filament at high calcium concentration
ComponentsActin, alpha skeletal muscle
KeywordsSTRUCTURAL PROTEIN / Thin filament / troponin / actin / tropomyosin / Structural protein
Specimen sourceOryctolagus cuniculus / mammal / Rabbit /
MethodElectron microscopy (27.7 Å resolution / Filament / Single particle) / Transmission electron microscopy
AuthorsPaul, D.M. / Squire, J.M. / Morris, E.P.
CitationJ. Struct. Biol., 2017, 197, 365-371

J. Struct. Biol., 2017, 197, 365-371 Yorodumi Papers
Relaxed and active thin filament structures; a new structural basis for the regulatory mechanism.
Danielle M Paul / John M Squire / Edward P Morris

Validation Report
SummaryFull reportAbout validation report
DateDeposition: Jan 16, 2017 / Release: Nov 29, 2017

Structure visualization

  • Deposited structure unit
  • Imaged by Jmol
  • Download
3D viewer

Downloads & links


Deposited unit
A: Actin, alpha skeletal muscle
B: Actin, alpha skeletal muscle
C: Actin, alpha skeletal muscle
D: Actin, alpha skeletal muscle
E: Actin, alpha skeletal muscle
F: Actin, alpha skeletal muscle
G: Actin, alpha skeletal muscle
H: Actin, alpha skeletal muscle
I: Actin, alpha skeletal muscle
J: Actin, alpha skeletal muscle
K: Actin, alpha skeletal muscle
L: Actin, alpha skeletal muscle
M: Actin, alpha skeletal muscle
N: Actin, alpha skeletal muscle
O: Actin, alpha skeletal muscle
P: Actin, alpha skeletal muscle
Q: Actin, alpha skeletal muscle
R: Actin, alpha skeletal muscle
S: Actin, alpha skeletal muscle
T: Actin, alpha skeletal muscle
U: Actin, alpha skeletal muscle
V: Actin, alpha skeletal muscle
W: Actin, alpha skeletal muscle
hetero molecules

Theoretical massNumber of molelcules
Total (without water)972,96546

TypeNameSymmetry operationNumber
identity operation1_5551
Buried area (Å2)69640
ΔGint (kcal/M)-425
Surface area (Å2)371690


#1: Protein/peptide ...
Actin, alpha skeletal muscle / Alpha-actin-1

Mass: 41875.633 Da / Num. of mol.: 23
Source: (natural) Oryctolagus cuniculus / mammal / Rabbit /
References: UniProt: P68135
#2: Chemical...
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Alpha-actin-1

Mass: 427.201 Da / Num. of mol.: 23 / Formula: C10H15N5O10P2 / : Adenosine diphosphate / Comment: ADP (energy-carrying molecule) *YM

Experimental details


EM experimentAggregation state: FILAMENT / Reconstruction method: SINGLE PARTICLE

Sample preparation

ComponentName: Thin filament at high calcium concentration / Type: COMPLEX / Entity ID: 1 / Source: NATURAL
Source (natural)Organism: Oryctolagus cuniculus
Buffer solutionpH: 7
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: YES / Vitrification applied: NO
EM stainingType: NEGATIVE / Material: Uranyl Acetate

Electron microscopy imaging

MicroscopyMicroscope model: FEI/PHILIPS CM12
Electron gunElectron source: LAB6 / Accelerating voltage: 120 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD
Image recordingElectron dose: 12 e/Å2 / Film or detector model: AGFA SCIENTA FILM
Image scansScanner model: ZEISS SCAI


CTF correctionType: NONE
3D reconstructionResolution: 27.7 Å / Resolution method: FSC 0.5 CUT-OFF / Number of particles: 1680 / Symmetry type: POINT

About Yorodumi


Oct 4, 2017. Three pioneers of this field were awarded Nobel Prize in Chemistry 2017

Three pioneers of this field were awarded Nobel Prize in Chemistry 2017

  • Jacques Dubochet (University of Lausanne, Switzerland) is a pioneer of ice-embedding method of EM specimen (as known as cryo-EM), Most of 3DEM structures in EMDB and PDB are obtained using his method.
  • Joachim Frank (Columbia University, New York, USA) is a pioneer of single particle reconstruction, which is the most used reconstruction method for 3DEM structures in EMDB and EM entries in PDB. And also, he is a develper of Spider, which is one of the most famous software in this field, and is used for some EM Navigor data (e.g. map projection/slice images).
  • Richard Henderson (MRC Laboratory of Molecular Biology, Cambridge, UK) was determined the first biomolecule structure by EM. The first EM entry in PDB, PDB-1brd is determinedby him.

External links: The 2017 Nobel Prize in Chemistry - Press Release

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. See below links for details.
  • 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

Jun 16, 2017. Omokage search with filter

Omokage search with filter

  • Result of Omokage search can be filtered by keywords and the database types

Related info.: Omokage search

Sep 15, 2016. EM Navigator & Yorodumi renewed

EM Navigator & Yorodumi renewed

  • New versions of EM Navigator and Yorodumi started

Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator (legacy version) / Yorodumi (legacy version)

Aug 31, 2016. New EM Navigator & Yorodumi

New EM Navigator & Yorodumi

  • In 15th Sep 2016, the development versions of EM Navigator and Yorodumi will replace the official versions.
  • Current version will continue as 'legacy version' for some time.

Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator / Yorodumi / EM Navigator (legacy version) / Yorodumi (legacy version)

Read more


Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • All the functionalities will be ported from the levgacy version.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.

Related info.: Yorodumi (legacy version) / EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Yorodumi Papers / Jmol/JSmol / Changes in new EM Navigator and Yorodumi

Read more