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- EMDB-30085: F-actin-Utrophin complex -

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Basic information

Entry
Database: EMDB / ID: EMD-30085
TitleF-actin-Utrophin complex
Map dataF-actin in complex with calponin homology 1 of utrophin actin binding domain
Sample
  • Complex: Filamentous actin in ADP state
    • Complex: Actin
      • Protein or peptide: Actin, alpha skeletal muscle
    • Complex: utrophin
      • Protein or peptide: Utrophin
  • Ligand: MAGNESIUM ION
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
KeywordsUtrophin / N-terminus actin binding domain / calponin homology / F-actin / F-actin marker protein / CONTRACTILE PROTEIN
Function / homology
Function and homology information


regulation of sodium ion transmembrane transporter activity / synaptic signaling / dystrophin-associated glycoprotein complex / Striated Muscle Contraction / Formation of the dystrophin-glycoprotein complex (DGC) / vinculin binding / EGR2 and SOX10-mediated initiation of Schwann cell myelination / filopodium membrane / positive regulation of cell-matrix adhesion / muscle organ development ...regulation of sodium ion transmembrane transporter activity / synaptic signaling / dystrophin-associated glycoprotein complex / Striated Muscle Contraction / Formation of the dystrophin-glycoprotein complex (DGC) / vinculin binding / EGR2 and SOX10-mediated initiation of Schwann cell myelination / filopodium membrane / positive regulation of cell-matrix adhesion / muscle organ development / striated muscle thin filament / skeletal muscle thin filament assembly / stress fiber / skeletal muscle fiber development / muscle contraction / filopodium / actin filament / sarcolemma / neuromuscular junction / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / integrin binding / actin cytoskeleton / actin binding / postsynaptic membrane / cytoskeleton / hydrolase activity / ciliary basal body / cilium / protein kinase binding / protein-containing complex / extracellular exosome / zinc ion binding / nucleoplasm / ATP binding / membrane / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Dystrophin/utrophin / EF-hand domain, type 1 / EF-hand domain, type 2 / EF hand / EF-hand / : / Spectrin repeat / Spectrin repeat / Spectrin/alpha-actinin / Spectrin repeats ...Dystrophin/utrophin / EF-hand domain, type 1 / EF-hand domain, type 2 / EF hand / EF-hand / : / Spectrin repeat / Spectrin repeat / Spectrin/alpha-actinin / Spectrin repeats / Actinin-type actin-binding domain signature 1. / Actinin-type actin-binding domain signature 2. / Actinin-type actin-binding domain, conserved site / Calponin homology domain / Zinc finger ZZ-type signature. / Zinc-binding domain, present in Dystrophin, CREB-binding protein. / Calponin homology (CH) domain / Zinc finger, ZZ type / Zinc finger, ZZ-type / Zinc finger, ZZ-type superfamily / Zinc finger ZZ-type profile. / Calponin homology domain / CH domain superfamily / Calponin homology (CH) domain profile. / WW/rsp5/WWP domain signature. / WW domain superfamily / WW/rsp5/WWP domain profile. / Domain with 2 conserved Trp (W) residues / WW domain / Actins signature 1. / Actin, conserved site / Actins signature 2. / Actin/actin-like conserved site / Actins and actin-related proteins signature. / Actin / Actin family / Actin / ATPase, nucleotide binding domain / EF-hand domain pair
Similarity search - Domain/homology
Utrophin / Actin, alpha skeletal muscle
Similarity search - Component
Biological speciesGallus gallus (chicken) / Homo sapiens (human)
Methodhelical reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsKumari A / Ragunath VK
Funding support India, 2 items
OrganizationGrant numberCountry
Department of Biotechnology (DBT, India)IA/I/14/2/501533 India
Department of Biotechnology (DBT, India)DBT/PR12422/MED/31/287/2014 India
CitationJournal: EMBO J / Year: 2020
Title: Structural insights into actin filament recognition by commonly used cellular actin markers.
Authors: Archana Kumari / Shubham Kesarwani / Manjunath G Javoor / Kutti R Vinothkumar / Minhajuddin Sirajuddin /
Abstract: Cellular studies of filamentous actin (F-actin) processes commonly utilize fluorescent versions of toxins, peptides, and proteins that bind actin. While the choice of these markers has been largely ...Cellular studies of filamentous actin (F-actin) processes commonly utilize fluorescent versions of toxins, peptides, and proteins that bind actin. While the choice of these markers has been largely based on availability and ease, there is a severe dearth of structural data for an informed judgment in employing suitable F-actin markers for a particular requirement. Here, we describe the electron cryomicroscopy structures of phalloidin, lifeAct, and utrophin bound to F-actin, providing a comprehensive high-resolution structural comparison of widely used actin markers and their influence towards F-actin. Our results show that phalloidin binding does not induce specific conformational change and lifeAct specifically recognizes closed D-loop conformation, i.e., ADP-Pi or ADP states of F-actin. The structural models aided designing of minimal utrophin and a shorter lifeAct, which can be utilized as F-actin marker. Together, our study provides a structural perspective, where the binding sites of utrophin and lifeAct overlap with majority of actin-binding proteins and thus offering an invaluable resource for researchers in choosing appropriate actin markers and generating new marker variants.
History
DepositionMar 10, 2020-
Header (metadata) releaseMay 20, 2020-
Map releaseMay 20, 2020-
UpdateMar 27, 2024-
Current statusMar 27, 2024Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0464
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.0464
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6m5g
  • Surface level: 0.0464
  • Imaged by UCSF Chimera
  • Download
  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6m5g
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_30085.png

Downloads & links

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Map

FileDownload / File: emd_30085.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationF-actin in complex with calponin homology 1 of utrophin actin binding domain
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.38 Å/pix.
x 256 pix.
= 353.28 Å		1.38 Å/pix.
x 256 pix.
= 353.28 Å		1.38 Å/pix.
x 256 pix.
= 353.28 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.38 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0464 / Movie #1: 0.0464
Minimum - Maximum-0.11641386 - 0.2835282
Average (Standard dev.)-0.000023684237 (±0.009875082)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 353.28 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.381.381.38
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z353.280353.280353.280
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS256256256
D min/max/mean-0.1160.284-0.000

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Supplemental data

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Sample components

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Entire : Filamentous actin in ADP state

EntireName: Filamentous actin in ADP state
Components
  • Complex: Filamentous actin in ADP state
    • Complex: Actin
      • Protein or peptide: Actin, alpha skeletal muscle
    • Complex: utrophin
      • Protein or peptide: Utrophin
  • Ligand: MAGNESIUM ION
  • Ligand: ADENOSINE-5'-DIPHOSPHATE

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Supramolecule #1: Filamentous actin in ADP state

SupramoleculeName: Filamentous actin in ADP state / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Gallus gallus (chicken)

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Supramolecule #2: Actin

SupramoleculeName: Actin / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1 / Details: Filamentous actin

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Supramolecule #3: utrophin

SupramoleculeName: utrophin / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2 / Details: actin binding domain of utrophin

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Macromolecule #1: Actin, alpha skeletal muscle

MacromoleculeName: Actin, alpha skeletal muscle / type: protein_or_peptide / ID: 1 / Number of copies: 5 / Enantiomer: LEVO
Source (natural)Organism: Gallus gallus (chicken)
Molecular weightTheoretical: 42.096953 KDa
SequenceString: MCDEDETTAL VCDNGSGLVK AGFAGDDAPR AVFPSIVGRP RHQGVMVGMG QKDSYVGDEA QSKRGILTLK YPIEHGIITN WDDMEKIWH HTFYNELRVA PEEHPTLLTE APLNPKANRE KMTQIMFETF NVPAMYVAIQ AVLSLYASGR TTGIVLDSGD G VTHNVPIY ...String:
MCDEDETTAL VCDNGSGLVK AGFAGDDAPR AVFPSIVGRP RHQGVMVGMG QKDSYVGDEA QSKRGILTLK YPIEHGIITN WDDMEKIWH HTFYNELRVA PEEHPTLLTE APLNPKANRE KMTQIMFETF NVPAMYVAIQ AVLSLYASGR TTGIVLDSGD G VTHNVPIY EGYALPHAIM RLDLAGRDLT DYLMKILTER GYSFVTTAER EIVRDIKEKL CYVALDFENE MATAASSSSL EK SYELPDG QVITIGNERF RCPETLFQPS FIGMESAGIH ETTYNSIMKC DIDIRKDLYA NNVMSGGTTM YPGIADRMQK EIT ALAPST MKIKIIAPPE RKYSVWIGGS ILASLSTFQQ MWITKQEYDE AGPSIVHRKC F

UniProtKB: Actin, alpha skeletal muscle

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Macromolecule #2: Utrophin

MacromoleculeName: Utrophin / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 30.771949 KDa
Recombinant expressionOrganism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
SequenceString: HHHHHHGSMA KYGEHEASPD NGQNEFSDII KSRSDEHNDV QKKTFTKWIN ARFSKSGKPP INDMFTDLKD GRKLLDLLEG LTGTSLPKE RGSTRVHALN NVNRVLQVLH QNNVELVNIG GTDIVDGNHK LTLGLLWSII LHWQVKDVMK DVMSDLQQTN S EKILLSWV ...String:
HHHHHHGSMA KYGEHEASPD NGQNEFSDII KSRSDEHNDV QKKTFTKWIN ARFSKSGKPP INDMFTDLKD GRKLLDLLEG LTGTSLPKE RGSTRVHALN NVNRVLQVLH QNNVELVNIG GTDIVDGNHK LTLGLLWSII LHWQVKDVMK DVMSDLQQTN S EKILLSWV RQTTRPYSQV NVLNFTTSWT DGLAFNAVLH RHKPDLFSWD KVVKMSPIER LEHAFSKAQT YLGIEKLLDP ED VAVQLPD KKSIIMYLTS LFEVLPQQVT ID

UniProtKB: Utrophin

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Macromolecule #3: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 3 / Number of copies: 5 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #4: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 4 / Number of copies: 5 / Formula: ADP
Molecular weightTheoretical: 427.201 Da
Chemical component information

ChemComp-ADP:
ADENOSINE-5'-DIPHOSPHATE / ADP, energy-carrying molecule*YM

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statefilament

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Sample preparation

Concentration0.0002 mg/mL
BufferpH: 8
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Support film - Film thickness: 50 / Pretreatment - Type: PLASMA CLEANING / Pretreatment - Time: 60 sec. / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 0.025 kPa
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 293 K / Instrument: FEI VITROBOT MARK I / Details: blot for 3 seconds.

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Electron microscopy

MicroscopeFEI TITAN KRIOS
TemperatureMin: 100.0 K / Max: 120.0 K
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Detector mode: INTEGRATING / Number grids imaged: 1 / Number real images: 765 / Average exposure time: 2.0 sec. / Average electron dose: 42.6 e/Å2 / Details: 20
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: OTHER / Imaging mode: OTHER / Cs: 2.7 mm / Nominal defocus max: 4.735 µm / Nominal defocus min: 1.25 µm / Nominal magnification: 59000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 27.5 Å
Applied symmetry - Helical parameters - Δ&Phi: -166.6 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0) / Number images used: 149660
Segment selectionNumber selected: 259938
Startup modelType of model: INSILICO MODEL / In silico model: cylinder / Details: generated in relion image handler
Final angle assignmentType: NOT APPLICABLE / Software - Name: RELION (ver. 3.0)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

5onv


Chain - Chain ID: A / Chain - Residue range: 6-373 / Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL / Protocol: RIGID BODY FIT / Overall B value: 177
Output model

PDB-6m5g:
F-actin-Utrophin complex

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