[English] 日本語
Yorodumi
- PDB-3lue: Model of alpha-actinin CH1 bound to F-actin -

+
Open data


ID or keywords:

Loading...

no data

-
Basic information

Entry
Database: PDB / ID: 3lue
TitleModel of alpha-actinin CH1 bound to F-actin
DescriptorActin, cytoplasmic 1, Alpha-actinin-3
KeywordsSTRUCTURAL PROTEIN / calponin homology domains / Acetylation / ATP-binding / Cytoplasm / Cytoskeleton / Methylation / Nucleotide-binding / Phosphoprotein / Actin-binding / Calcium / Polymorphism / Deafness / Disease mutation / Dystonia
Specimen sourceHomo sapiens / human
MethodElectron microscopy (15 Å resolution / Filament / Helical)
AuthorsGalkin, V.E. / Orlova, A. / Salmazo, A. / Djinovic-Carugo, K. / Egelman, E.H.
CitationNat. Struct. Mol. Biol., 2010, 17, 614-616

Nat. Struct. Mol. Biol., 2010, 17, 614-616 Yorodumi Papers
Opening of tandem calponin homology domains regulates their affinity for F-actin.
Vitold E Galkin / Albina Orlova / Anita Salmazo / Kristina Djinovic-Carugo / Edward H Egelman

Validation Report
SummaryFull reportAbout validation report
DateDeposition: Feb 17, 2010 / Release: Apr 28, 2010
RevisionDateData content typeGroupProviderType
1.0Apr 28, 2010Structure modelrepositoryInitial release
1.1Jul 13, 2011Structure modelVersion format compliance

-
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, cytoplasmic 1
B: Actin, cytoplasmic 1
C: Actin, cytoplasmic 1
D: Actin, cytoplasmic 1
E: Actin, cytoplasmic 1
F: Actin, cytoplasmic 1
G: Actin, cytoplasmic 1
H: Actin, cytoplasmic 1
I: Actin, cytoplasmic 1
J: Actin, cytoplasmic 1
K: Alpha-actinin-3
M: Alpha-actinin-3
L: Alpha-actinin-3
O: Alpha-actinin-3
N: Alpha-actinin-3
Q: Alpha-actinin-3
P: Alpha-actinin-3
S: Alpha-actinin-3
R: Alpha-actinin-3
T: Alpha-actinin-3


Theoretical massNumber of molelcules
Total (without water)541,23220
Polyers541,23220
Non-polymers00
Water0
#1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
DetailsAuthors state that the model is from a continuous helix where the rotation per subunit is -167.2 degrees and the rise per subunit is 26.6 Angstroms.

-
Components

#1: Polypeptide(L)
Actin, cytoplasmic 1 / Beta-actin / Actin / cytoplasmic 1 / N-terminally processed


Mass: 41651.465 Da / Num. of mol.: 10 / Source: (gene. exp.) Homo sapiens / human / References: UniProt: P60709

Cellular component

Molecular function

Biological process

#2: Polypeptide(L)
Alpha-actinin-3 / Alpha-actinin skeletal muscle isoform 3 / F-actin cross-linking protein


Mass: 12471.712 Da / Num. of mol.: 10 / Source: (gene. exp.) Homo sapiens / human / References: UniProt: Q08043

Cellular component

Molecular function

Biological process

  • focal adhesion assembly (GO: 0048041)
  • muscle filament sliding (GO: 0030049)
  • negative regulation of calcineurin-NFAT signaling cascade (GO: 0070885)
  • negative regulation of glycolytic process (GO: 0045820)
  • negative regulation of oxidative phosphorylation (GO: 0090324)
  • positive regulation of glucose catabolic process to lactate via pyruvate (GO: 1904025)
  • positive regulation of skeletal muscle tissue growth (GO: 0048633)
  • regulation of aerobic respiration (GO: 1903715)
  • regulation of apoptotic process (GO: 0042981)
  • regulation of the force of skeletal muscle contraction (GO: 0014728)
  • response to denervation involved in regulation of muscle adaptation (GO: 0014894)
  • skeletal muscle atrophy (GO: 0014732)
  • transition between fast and slow fiber (GO: 0014883)

-
Experimental details

-
Experiment

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

-
Sample preparation

Component
IDNameTypeDetailsParent IDSynonym
1F-actin decorated with alpha-actinin ABD (containing CH1 and CH2)COMPLEXone to one binding0
2F-actinhelical polymer1F-actin
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

-
Electron microscopy imaging

Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company
MicroscopyMicroscope model: FEI TECNAI F20
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 50000 / Camera length: 0 mm
Specimen holderSpecimen holder model: GATAN LIQUID NITROGEN / Specimen holder type: gatan 626 / Tilt angle max: 0 deg. / Tilt angle min: 0 deg.
Image recordingFilm or detector model: KODAK SO-163 FILM
Image scansSampling size: 12.7 microns / Scanner model: NIKON COOLSCAN

-
Processing

EM software
IDNameCategory
1UCSF ChimeraMODEL FITTING
2UCSF ChimeraMODEL FITTING
3IHRSRRECONSTRUCTION
CTF correctionDetails: Weiner filter
Helical symmertyAngular rotation/subunit: 166.8 deg. / Axial rise/subunit: 27.7 Å / Axial symmetry: C1
3D reconstructionMethod: back projection / Resolution: 15 Å / Resolution method: FSC 0.5 CUT-OFF / Nominal pixel size: 2.38 / Actual pixel size: 2.38
Details: AUTHORS STATE THAT THE STRANGE C-N BONDS WERE THE RESULT OF BREAKING THE CHAINS AT THESE POINTS TO DO RIGID BODY FITTING OF THE SUBDOMAINS.
Symmetry type: HELICAL
Atomic model buildingDetails: METHOD--both manually and with Chimera DETAILS--AUTHORS STATE THAT THE STRANGE C-N BONDS WERE THE RESULT OF BREAKING THE CHAINS AT THESE POINTS TO DO RIGID BODY FITTING OF THE SUBDOMAINS.
Ref protocol: OTHER / Ref space: REAL
Number of atoms included #LASTProtein: 37910 / Nucleic acid: 0 / Ligand: 0 / Solvent: 0 / Total: 37910

+
About Yorodumi

-
News

-
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

-
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