[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 / ATP-binding / Cytoskeleton / Methylation / Nucleotide-binding / Phosphoprotein / Actin-binding / Deafness / Disease mutation / Dystonia
Specimen sourceHomo sapiens / human
MethodElectron microscopy (15 A resolution / Helical / Vitreous ice (cryo EM))
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 StrPapers
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

DateDeposition: Feb 17, 2010 / Release: Apr 28, 2010 / Last modification: May 19, 2010

-
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)541,23620
Polyers541,23620
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: 41651.809 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: 12471.813 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 experimentReconstruction method: HELICAL / Specimen type: VITREOUS ICE (CRYO EM)

-
Sample preparation

Assembly of specimenName: F-actin decorated with alpha-actinin ABD (containing CH1 and CH2)
Aggregation state: FILAMENT / Details: none / Composition: one to one binding / Number of components: 2
ComponentName: F-actin / Type: PROTEIN / Ebi expression system: E. coli / Ebi tissue: muscle / Mutant flag: YES / Oligomeric details: helical polymer / Synonym: F-actin
VitrificationCryogen name: ETHANE

-
Electron microscopy imaging

EM imagingCamera length: 0 mm
Electron gunAccelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 50000 X
Specimen holderSpecimen holder model: GATAN LIQUID NITROGEN / Specimen holder type: gatan 626 / Tilt angle max: 0 deg. / Tilt angle min: 0 deg.
CameraType: Kodak SO163
EM image scansSampling size: 12.7 microns / Scanner model: NIKON COOLSCAN
RadiationDiffraction protocol: SINGLE WAVELENGTH / Monochromatic or laue m l: M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1

-
Processing

Image selectionSoftware name: Chimera
EM helical entityAngular rotation per subunit: 166.8 deg. / Axial rise per subunit: 27.7 A
3D reconstructionMethod: back projection / Software: IHRSR / Resolution: 15 A / Resolution method: FSC at 0.5 / Nominal pixel size: 2.38 A/pix / Actual pixel size: 2.38 A/pix / CTF correction method: Weiner filter
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.
Atomic model buildingMethod: both manually and with Chimera / Software name: 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 space: REAL
Number of atoms included #LASTProtein: 37910 / Nucleic acid: 0 / Ligand: 0 / Solvent: 0 / Total: 37910

+
About Yorodumi

-
News

-
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

+
Mar 3, 2016. Presentation (PDF format) at IPR seminar on Feb 19.

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