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- EMDB-5170: Binding of alpha-actinin CH1 to F-actin -

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Basic information

Entry
Database: EMDB / ID: EMD-5170
TitleBinding of alpha-actinin CH1 to F-actin
Map datareconstructed volume of F-actin decorated with alpha-actinin ABD (CH1 and CH2)
Sample
  • Sample: F-actin decorated with alpha-actinin ABD (containing CH1 and CH2)
  • Protein or peptide: F-actin
Keywordshelical filaments / calponin homology domains
Function / homology
Function and homology information


positive regulation of glucose catabolic process to lactate via pyruvate / negative regulation of relaxation of muscle / skeletal muscle atrophy / regulation of the force of skeletal muscle contraction / positive regulation of skeletal muscle tissue growth / positive regulation of skeletal muscle fiber development / response to denervation involved in regulation of muscle adaptation / positive regulation of fast-twitch skeletal muscle fiber contraction / positive regulation of norepinephrine uptake / positive regulation of bone mineralization involved in bone maturation ...positive regulation of glucose catabolic process to lactate via pyruvate / negative regulation of relaxation of muscle / skeletal muscle atrophy / regulation of the force of skeletal muscle contraction / positive regulation of skeletal muscle tissue growth / positive regulation of skeletal muscle fiber development / response to denervation involved in regulation of muscle adaptation / positive regulation of fast-twitch skeletal muscle fiber contraction / positive regulation of norepinephrine uptake / positive regulation of bone mineralization involved in bone maturation / cellular response to cytochalasin B / bBAF complex / npBAF complex / nBAF complex / brahma complex / regulation of transepithelial transport / Formation of annular gap junctions / morphogenesis of a polarized epithelium / Formation of the dystrophin-glycoprotein complex (DGC) / structural constituent of postsynaptic actin cytoskeleton / GBAF complex / Gap junction degradation / Folding of actin by CCT/TriC / focal adhesion assembly / regulation of G0 to G1 transition / protein localization to adherens junction / Cell-extracellular matrix interactions / transition between fast and slow fiber / dense body / postsynaptic actin cytoskeleton / Tat protein binding / muscle cell development / negative regulation of oxidative phosphorylation / Prefoldin mediated transfer of substrate to CCT/TriC / RSC-type complex / Striated Muscle Contraction / regulation of double-strand break repair / bone morphogenesis / regulation of nucleotide-excision repair / negative regulation of glycolytic process / Adherens junctions interactions / Nephrin family interactions / RHOF GTPase cycle / adherens junction assembly / apical protein localization / Sensory processing of sound by outer hair cells of the cochlea / Interaction between L1 and Ankyrins / negative regulation of calcineurin-NFAT signaling cascade / tight junction / structural constituent of muscle / SWI/SNF complex / negative regulation of cold-induced thermogenesis / regulation of mitotic metaphase/anaphase transition / Sensory processing of sound by inner hair cells of the cochlea / regulation of aerobic respiration / positive regulation of T cell differentiation / apical junction complex / cortical actin cytoskeleton / regulation of norepinephrine uptake / positive regulation of double-strand break repair / transporter regulator activity / maintenance of blood-brain barrier / nitric-oxide synthase binding / cortical cytoskeleton / NuA4 histone acetyltransferase complex / pseudopodium / establishment or maintenance of cell polarity / positive regulation of stem cell population maintenance / Regulation of MITF-M-dependent genes involved in pigmentation / Recycling pathway of L1 / brush border / regulation of G1/S transition of mitotic cell cycle / kinesin binding / EPH-ephrin mediated repulsion of cells / negative regulation of cell differentiation / RHO GTPases Activate WASPs and WAVEs / regulation of synaptic vesicle endocytosis / positive regulation of myoblast differentiation / RHO GTPases activate IQGAPs / regulation of protein localization to plasma membrane / positive regulation of double-strand break repair via homologous recombination / EPHB-mediated forward signaling / cytoskeleton organization / substantia nigra development / axonogenesis / calyx of Held / nitric-oxide synthase regulator activity / cell projection / Translocation of SLC2A4 (GLUT4) to the plasma membrane / FCGR3A-mediated phagocytosis / actin filament / adherens junction / positive regulation of cell differentiation / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / cell motility / RHO GTPases Activate Formins / Signaling by high-kinase activity BRAF mutants / MAP2K and MAPK activation / DNA Damage Recognition in GG-NER / kinetochore
Similarity search - Function
EF-hand, Ca insensitive / Ca2+ insensitive EF hand / Ca2+ insensitive EF hand / Spectrin repeat / Spectrin repeat / Actinin-type actin-binding domain signature 1. / Actinin-type actin-binding domain signature 2. / Actinin-type actin-binding domain, conserved site / Spectrin/alpha-actinin / Spectrin repeats ...EF-hand, Ca insensitive / Ca2+ insensitive EF hand / Ca2+ insensitive EF hand / Spectrin repeat / Spectrin repeat / Actinin-type actin-binding domain signature 1. / Actinin-type actin-binding domain signature 2. / Actinin-type actin-binding domain, conserved site / Spectrin/alpha-actinin / Spectrin repeats / Calponin homology domain / Calponin homology (CH) domain / Calponin homology domain / CH domain superfamily / Calponin homology (CH) domain profile. / Actins signature 1. / Actin, conserved site / Actins signature 2. / Actin/actin-like conserved site / Actins and actin-related proteins signature. / Actin / Actin family / Actin / EF-hand, calcium binding motif / ATPase, nucleotide binding domain / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair
Similarity search - Domain/homology
Actin, cytoplasmic 1 / Alpha-actinin-3
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodhelical reconstruction / cryo EM / Resolution: 15.0 Å
AuthorsGalkin VE / Orlova A / Salmazo A / Djinovic-Carugo K / Egelman EH
CitationJournal: Nat Struct Mol Biol / Year: 2010
Title: Opening of tandem calponin homology domains regulates their affinity for F-actin.
Authors: Vitold E Galkin / Albina Orlova / Anita Salmazo / Kristina Djinovic-Carugo / Edward H Egelman /
Abstract: Many actin-binding proteins contain calponin homology (CH) domains, but the manner in which these domains interact with F-actin has been controversial. Crystal structures have shown the tandem CH ...Many actin-binding proteins contain calponin homology (CH) domains, but the manner in which these domains interact with F-actin has been controversial. Crystal structures have shown the tandem CH domains of alpha-actinin to be in a compact, closed conformation, but the interpretations of complexes of such tandem CH domains with F-actin have been ambiguous. We show that the tandem CH domains of alpha-actinin bind F-actin in an open conformation, explaining mutations that cause human diseases and suggesting that the opening of these domains may be one of the main regulatory mechanisms for proteins with tandem CH domains.
History
DepositionFeb 17, 2010-
Header (metadata) releaseFeb 23, 2010-
Map releaseApr 20, 2010-
UpdateSep 23, 2011-
Current statusSep 23, 2011Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.61
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.61
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-3lue
  • Surface level: 0.61
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_5170_1.jpg

Downloads & links

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Map

FileDownload / File: emd_5170.map.gz / Format: CCP4 / Size: 3.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationreconstructed volume of F-actin decorated with alpha-actinin ABD (CH1 and CH2)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.38 Å/pix.
x 100 pix.
= 238. Å		2.38 Å/pix.
x 100 pix.
= 238. Å		2.38 Å/pix.
x 100 pix.
= 238. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.38 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.61 / Movie #1: 0.61
Minimum - Maximum-0.683673 - 2.18038
Average (Standard dev.)0.0771251 (±0.294062)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-49-49-49
Dimensions100100100
Spacing100100100
CellA=B=C: 238 Å
α=β=γ: 90 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.382.382.38
M x/y/z100100100
origin x/y/z0.0000.0000.000
length x/y/z238.000238.000238.000
α/β/γ90.00090.00090.000
start NX/NY/NZ-34-26-72
NX/NY/NZ6953145
MAP C/R/S123
start NC/NR/NS-49-49-49
NC/NR/NS100100100
D min/max/mean-0.6842.1800.077

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Supplemental data

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Sample components

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Entire : F-actin decorated with alpha-actinin ABD (containing CH1 and CH2)

EntireName: F-actin decorated with alpha-actinin ABD (containing CH1 and CH2)
Components
  • Sample: F-actin decorated with alpha-actinin ABD (containing CH1 and CH2)
  • Protein or peptide: F-actin

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Supramolecule #1000: F-actin decorated with alpha-actinin ABD (containing CH1 and CH2)

SupramoleculeName: F-actin decorated with alpha-actinin ABD (containing CH1 and CH2)
type: sample / ID: 1000 / Details: none / Oligomeric state: one to one binding / Number unique components: 2

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Macromolecule #1: F-actin

MacromoleculeName: F-actin / type: protein_or_peptide / ID: 1 / Name.synonym: F-actin / Oligomeric state: helical polymer / Recombinant expression: Yes
Source (natural)Organism: Homo sapiens (human) / synonym: Human / Tissue: muscle
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceGO: actin filament binding

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statefilament

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Sample preparation

VitrificationCryogen name: ETHANE / Instrument: OTHER

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Electron microscopy

MicroscopeFEI TECNAI F20
Image recordingCategory: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: NIKON COOLSCAN / Digitization - Sampling interval: 12.7 µm / Bits/pixel: 16
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal magnification: 50000
Sample stageSpecimen holder: Gatan 626 / Specimen holder model: GATAN LIQUID NITROGEN
Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 27.7 Å
Applied symmetry - Helical parameters - Δ&Phi: 166.8 °
Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 15.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: IHRSR

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Atomic model buiding 1

Initial model(PDB ID:

1tjt

,

2btf

)
RefinementSpace: REAL
Output model

PDB-3lue:
Model of alpha-actinin CH1 bound to F-actin

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