3D Electron Microscopy (3D-EM) Data Navigator [English / 日本語]
Top Gallery List Diagram Statistics Viewer Documents
Movie pageYodrodumi (structure viewer)
PDBj>EM Navigator>Detail page - PDB-3lue

Model of alpha-actinin CH1 bound to F-actin

by helical reconstruction, at 15 A resolution

Movie

Orientation:

#1: Depositted structure unit, Image by Jmol

#2: Superimposing with EM 3D map: EMDB-5170, Image by UCSF CHIMERA

Entry
Summary
Database / IDPORTEIN DATA BANK (PDB) / 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
AuthorsGalkin, V.E., Orlova, A., Salmazo, A., Djinovic-Carugo, K., Egelman, E.H.
DateDeposition: 2010-02-17, Release: 2010-04-28
PDBj Mine pagesSummary, Structural Details, Experimental Details, Functional Details
Other databasesRCSB-PDB, PDBe, CATH, CE, FSSP, SCOP, VAST
Structure Visualization
MoviesMovie Page

#1: Depositted structure unit, Image by Jmol

#2: Superimposing with EM 3D map: EMDB-5170, Image by UCSF CHIMERA

Structure viewersYorodumi, jV4, Jmol, Biological unit (Images, jV)
Related Structure Data
Related Entries

EMDB-5170

CiteFit

Cite: data citing same article

Fit: target map of fitting

Similar strucutres (beta)
List of similar structure data about Omokage system
Article
Citation - primary
ArticleNat. Struct. Mol. Biol., Vol. 17, Issue 5, Page 614-6, Year 2010
TitleOpening of tandem calponin homology domains regulates their affinity for F-actin.
AuthorsVitold E Galkin, Albina Orlova, Anita Salmazo, Kristina Djinovic-Carugo, Edward H Egelman
Department of Biochemistry and Molecular Genetics, University of Virginia Medical Center, Charlottesville, Virginia, USA.
KeywordsActinin (chemistry, 11003-00-2), Actins (chemistry), Calcium-Binding Proteins (chemistry), Crystallography, X-Ray, Humans, Microfilament Proteins (chemistry), Models, Molecular, Protein Binding, Protein Conformation, Protein Structure, Tertiary, calponin
LinksDOI: 10.1038/nsmb.1789, PubMed: 20383143, PMC: PMC2921939
Components
ID 1 : Beta-actin, Actin, cytoplasmic 1, N-terminally processed
Image
DescriptionActin, cytoplasmic 1
Typepolypeptide(L)
Formula weight41651.809 Da
Number of molecules10
ID1
SourceMethod: Isolated from a genetically manipulated source
Gene: human, ACTB, ID:9606, Homo sapiens
Host: ID:562, Escherichia coli

LinksUniProt: P60709, Sequence view
ID 2 : Alpha-actinin skeletal muscle isoform 3, F-actin cross-linking protein
Image
DescriptionAlpha-actinin-3
Typepolypeptide(L)
Formula weight12471.813 Da
Number of molecules10
ID2
SourceMethod: Isolated from a genetically manipulated source
Gene: human, ACTN3, ID:9606, Homo sapiens
Host: ID:562, Escherichia coli
LinksUniProt: Q08043, Sequence view
Sample
Assembly
Aggregation stateFILAMENT
Compositionone to one binding
Detailsnone
NameF-actin decorated with alpha-actinin ABD (containing CH1 and CH2)
Num components2
Entity assembly
Assembly-ID1
Ebi expression systemE. coli
Ebi tissuemuscle
Mutant flagYES
NameF-actin
Oligomeric detailshelical polymer
SynonymF-actin
TypePROTEIN
Experiment
Reconstruction methodHELICAL
Specimen typeVITREOUS ICE (CRYO EM)
Vitrification
Cryogen nameETHANE
Experiment
MethodELECTRON MICROSCOPY
Electron Microscopy
Electron gun
Accelerating voltage200 kV
Illumination modeFLOOD BEAM
Lens
ModeBRIGHT FIELD
MagnificationNominal: 50000 X
Detector distance0.0
Specimen holder
Specimen holderModel: GATAN LIQUID NITROGEN, Type: gatan 626
Tilt angleMin: 0.0 degrees, Max: 0.0 degrees
Detector
TypeKodak SO163
Image scans
Sampling size12.7
Scanner modelNIKON COOLSCAN
Processing
2D projection selection
Software nameChimera
Helical entity
Angular rotation per subunit166.8 degrees
Axial rise per subunit27.7 A
3D reconstruction
Actual pixel size2.38 A/pix
CTF correction methodWeiner filter
DetailsAUTHORS 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.
Methodback projection
Nominal pixel size2.38 A/pix
Resolution15.0 A
Resolution methodFSC at 0.5
SoftwareIHRSR
3D fitting
DetailsAUTHORS 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.
Methodboth manually and with Chimera
Refinement SpaceREAL
Software nameChimera
Refine hist
Cycle idLAST
Refine idELECTRON MICROSCOPY
Total atoms37910
Protein atoms37910
Download
PDB format
Allpdb3lue.ent.gz
pdb3lue.ent (uncompressed file)
Header onlypdb3lue.ent.gz
mmCIF format
mmCIF3lue.cif.gz
XML format
All3lue.xml.gz
No-atom3lue-noatom.xml.gz
Ext-atom3lue-extatom.xml.gz
Movie files
movie #1
.mp4 (H.264/MPEG-4 AVC format), 2.5 MB
.webm (WebM/VP8 format), 3.5 MB
movie #2
.mp4 (H.264/MPEG-4 AVC format), 3.7 MB
.webm (WebM/VP8 format), 4.8 MB