+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-30085 | |||||||||
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Title | F-actin-Utrophin complex | |||||||||
Map data | F-actin in complex with calponin homology 1 of utrophin actin binding domain | |||||||||
Sample |
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Keywords | Utrophin / N-terminus actin binding domain / calponin homology / F-actin / F-actin marker protein / CONTRACTILE PROTEIN | |||||||||
Function / homology | Function and homology information synaptic signaling / dystrophin-associated glycoprotein complex / regulation of sodium ion transmembrane transporter activity / Striated Muscle Contraction / vinculin binding / EGR2 and SOX10-mediated initiation of Schwann cell myelination / filopodium membrane / muscle organ development / positive regulation of cell-matrix adhesion / skeletal muscle thin filament assembly ...synaptic signaling / dystrophin-associated glycoprotein complex / regulation of sodium ion transmembrane transporter activity / Striated Muscle Contraction / vinculin binding / EGR2 and SOX10-mediated initiation of Schwann cell myelination / filopodium membrane / muscle organ development / positive regulation of cell-matrix adhesion / skeletal muscle thin filament assembly / striated muscle thin filament / skeletal muscle fiber development / stress fiber / muscle contraction / filopodium / actin filament / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / neuromuscular junction / sarcolemma / integrin binding / actin binding / postsynaptic membrane / cytoskeleton / hydrolase activity / protein kinase binding / protein-containing complex / extracellular exosome / zinc ion binding / nucleoplasm / ATP binding / membrane / plasma membrane / cytoplasm Similarity search - Function | |||||||||
Biological species | Gallus gallus (chicken) / Homo sapiens (human) | |||||||||
Method | helical reconstruction / cryo EM / Resolution: 3.6 Å | |||||||||
Authors | Kumari A / Ragunath VK | |||||||||
Funding support | India, 2 items
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Citation | Journal: 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 |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_30085.map.gz | 59.1 MB | EMDB map data format | |
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Header (meta data) | emd-30085-v30.xml emd-30085.xml | 16 KB 16 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_30085_fsc.xml | 9.1 KB | Display | FSC data file |
Images | emd_30085.png | 141.3 KB | ||
Filedesc metadata | emd-30085.cif.gz | 6.6 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-30085 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-30085 | HTTPS FTP |
-Validation report
Summary document | emd_30085_validation.pdf.gz | 598.5 KB | Display | EMDB validaton report |
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Full document | emd_30085_full_validation.pdf.gz | 598.1 KB | Display | |
Data in XML | emd_30085_validation.xml.gz | 10.8 KB | Display | |
Data in CIF | emd_30085_validation.cif.gz | 14.3 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-30085 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-30085 | HTTPS FTP |
-Related structure data
Related structure data | 6m5gMC 7bt7C 7bteC 7btiC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_30085.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | F-actin in complex with calponin homology 1 of utrophin actin binding domain | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.38 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : Filamentous actin in ADP state
Entire | Name: Filamentous actin in ADP state |
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Components |
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-Supramolecule #1: Filamentous actin in ADP state
Supramolecule | Name: Filamentous actin in ADP state / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2 |
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Source (natural) | Organism: Gallus gallus (chicken) |
-Supramolecule #2: Actin
Supramolecule | Name: Actin / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1 / Details: Filamentous actin |
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-Supramolecule #3: utrophin
Supramolecule | Name: 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
Macromolecule | Name: Actin, alpha skeletal muscle / type: protein_or_peptide / ID: 1 / Number of copies: 5 / Enantiomer: LEVO |
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Source (natural) | Organism: Gallus gallus (chicken) |
Molecular weight | Theoretical: 42.096953 KDa |
Sequence | String: 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 |
-Macromolecule #2: Utrophin
Macromolecule | Name: Utrophin / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 30.771949 KDa |
Recombinant expression | Organism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) |
Sequence | String: 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 |
-Macromolecule #3: MAGNESIUM ION
Macromolecule | Name: MAGNESIUM ION / type: ligand / ID: 3 / Number of copies: 5 / Formula: MG |
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Molecular weight | Theoretical: 24.305 Da |
-Macromolecule #4: ADENOSINE-5'-DIPHOSPHATE
Macromolecule | Name: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 4 / Number of copies: 5 / Formula: ADP |
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Molecular weight | Theoretical: 427.201 Da |
Chemical component information | ChemComp-ADP: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | helical reconstruction |
Aggregation state | filament |
-Sample preparation
Concentration | 0.0002 mg/mL |
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Buffer | pH: 8 |
Grid | Model: 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 |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 293 K / Instrument: FEI VITROBOT MARK I / Details: blot for 3 seconds. |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Temperature | Min: 100.0 K / Max: 120.0 K |
Image recording | Film 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 beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 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 stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |