[English] 日本語
Yorodumi
- PDB-5noj: Ca2+-induced Movement of Tropomyosin on Native Cardiac Thin Filam... -

+
Open data


ID or keywords:

Loading...

no data

-
Basic information

Entry
Database: PDB / ID: 5noj
TitleCa2+-induced Movement of Tropomyosin on Native Cardiac Thin Filaments - "OPEN" state
DescriptorCardiac muscle alpha actin 1
cardiac alpha tropomyosin
KeywordsMOTOR PROTEIN / F-actin / tropomyosin / motor protein
Specimen sourceSus scrofa / mammal / Pig / イノシシ, いのしし, ニホンイノシシ, ブタ / image: Sus scrofa domestica
MethodElectron microscopy (11 Å resolution / Helical array / Helical)
AuthorsRisi, C. / Eisner, J. / Belknap, B. / Heeley, D.H. / White, H.D. / Schroeder, G.F. / Galkin, V.E.
CitationProc. Natl. Acad. Sci. U.S.A., 2017, 114, 6782-6787

Proc. Natl. Acad. Sci. U.S.A., 2017, 114, 6782-6787 StrPapers
Ca(2+)-induced movement of tropomyosin on native cardiac thin filaments revealed by cryoelectron microscopy.
Cristina Risi / Jamie Eisner / Betty Belknap / David H Heeley / Howard D White / Gunnar F Schröder / Vitold E Galkin

Validation Report
SummaryFull reportAbout validation report
DateDeposition: Apr 12, 2017 / Release: Aug 2, 2017
RevisionDateData content typeGroupCategoryItemProviderType
1.0Aug 2, 2017Structure modelrepositoryInitial release
1.1Aug 9, 2017Structure modelDatabase referencescitation / citation_author_citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name

-
Structure visualization

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


View / / Stereo:
Center
Zoom
Scale
Slabnear <=> far

fix: /
Orientation
Orientation Rotation
Misc. /
Show/hide

Downloads & links

-
Assembly

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: cardiac alpha tropomyosin
H: cardiac alpha tropomyosin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)229,53417
Polyers227,2777
Non-polymers2,25810
Water0
#1


TypeNameSymmetry operationNumber
identity operation1_5551
Buried area (Å2)19430
ΔGint (kcal/M)-208
Surface area (Å2)84260
MethodPISA

-
Components

#1: Polypeptide(L)
Actin, alpha skeletal muscle / Alpha-actin-1


Mass: 40818.477 Da / Num. of mol.: 5
Source: (gene. exp.) Sus scrofa / mammal / イノシシ, いのしし, ニホンイノシシ, ブタ / image: Sus scrofa domestica
References: UniProt: P68137
#2: Polypeptide(L)cardiac alpha tropomyosin


Mass: 11592.281 Da / Num. of mol.: 2
Source: (gene. exp.) Sus scrofa / mammal / イノシシ, いのしし, ニホンイノシシ, ブタ / image: Sus scrofa domestica
#3: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / ADP *YM


Mass: 427.201 Da / Num. of mol.: 5 / Formula: C10H15N5O10P2
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 5 / Formula: Mg

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: HELICAL ARRAY / Reconstruction method: HELICAL

-
Sample preparation

ComponentName: Native Cardiac Thin Filaments / Type: ORGANELLE OR CELLULAR COMPONENT / Details: Sample contains actin, tropomyosin, and troponin. / Entity ID: 1, 2 / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Sus scrofa
Buffer solutionpH: 7
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 95 %

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyMicroscope model: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD
Image recordingElectron dose: 3 e/Å2 / Film or detector model: FEI FALCON II (4k x 4k)

-
Processing

EM software
IDNameVersionCategoryImage processing IDFitting IDDetails
1EMAN2PARTICLE SELECTION1
4CTFFIND3CTF CORRECTION1
7DIREXMODEL FITTING1
13SPIDERRECONSTRUCTION1IHRSR
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: -166.7 deg. / Axial rise/subunit: 27.4 Å / Axial symmetry: C1
3D reconstructionResolution: 11 Å / Resolution method: FSC 0.5 CUT-OFF / Number of particles: 3809 / Symmetry type: HELICAL
Atomic model buildingDetails: Rigid fitting was done with Chimera and then DireX was used for flexible fitting.
Ref protocol: FLEXIBLE FIT / Ref space: REAL / Target criteria: Cross-correlation coefficient

+
About Yorodumi

-
News

-
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)

+
Apr 13, 2016. Omokage search got faster

Omokage search got faster

  • The computation time became ~1/2 compared to the previous version by re-optimization of data accession
  • Enjoy "shape similarity" of biomolecules, more!

Related info.: Omokage search

Read more

-
Yorodumi

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