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- EMDB-28936: Cryo-EM structure of the Tropomodulin-capped pointed end of F-actin -
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Open data
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Basic information
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Title | Cryo-EM structure of the Tropomodulin-capped pointed end of F-actin | ||||||||||||
![]() | Final map of the Tropomodulin-bound actin filament pointed end. | ||||||||||||
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![]() | Actin cytoskeleton / filament / Tmod / STRUCTURAL PROTEIN | ||||||||||||
Function / homology | ![]() pointed-end actin filament capping / lens fiber cell development / myofibril assembly / Striated Muscle Contraction / cytoskeletal motor activator activity / myofibril / cortical cytoskeleton / tropomyosin binding / mesenchyme migration / troponin I binding ...pointed-end actin filament capping / lens fiber cell development / myofibril assembly / Striated Muscle Contraction / cytoskeletal motor activator activity / myofibril / cortical cytoskeleton / tropomyosin binding / mesenchyme migration / troponin I binding / myosin heavy chain binding / filamentous actin / actin filament bundle / skeletal muscle thin filament assembly / striated muscle thin filament / actin filament bundle assembly / skeletal muscle myofibril / actin monomer binding / skeletal muscle fiber development / muscle contraction / stress fiber / titin binding / actin filament polymerization / sarcomere / adult locomotory behavior / filopodium / actin filament organization / actin filament / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / calcium-dependent protein binding / lamellipodium / actin binding / cell body / cytoskeleton / hydrolase activity / protein domain specific binding / calcium ion binding / positive regulation of gene expression / magnesium ion binding / ATP binding / identical protein binding / membrane / cytoplasm / cytosol Similarity search - Function | ||||||||||||
Biological species | ![]() ![]() ![]() ![]() ![]() | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.26 Å | ||||||||||||
![]() | Carman PJ / Barrie KR / Dominguez R | ||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Structures of the free and capped ends of the actin filament. Authors: Peter J Carman / Kyle R Barrie / Grzegorz Rebowski / Roberto Dominguez / ![]() Abstract: The barbed and pointed ends of the actin filament (F-actin) are the sites of growth and shrinkage and the targets of capping proteins that block subunit exchange, including CapZ at the barbed end and ...The barbed and pointed ends of the actin filament (F-actin) are the sites of growth and shrinkage and the targets of capping proteins that block subunit exchange, including CapZ at the barbed end and tropomodulin at the pointed end. We describe cryo-electron microscopy structures of the free and capped ends of F-actin. Terminal subunits at the free barbed end adopt a "flat" F-actin conformation. CapZ binds with minor changes to the barbed end but with major changes to itself. By contrast, subunits at the free pointed end adopt a "twisted" monomeric actin (G-actin) conformation. Tropomodulin binding forces the second subunit into an F-actin conformation. The structures reveal how the ends differ from the middle in F-actin and how these differences control subunit addition, dissociation, capping, and interactions with end-binding proteins. | ||||||||||||
History |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 123 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 22.1 KB 22.1 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 13.2 KB | Display | ![]() |
Images | ![]() | 1.4 MB | ||
Others | ![]() ![]() ![]() | 205.7 MB 226.9 MB 226.9 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8f8tMC ![]() 8f8pC ![]() 8f8qC ![]() 8f8rC ![]() 8f8sC C: citing same article ( M: atomic model generated by this map |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
File | ![]() | ||||||||||||||||||||
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Annotation | Final map of the Tropomodulin-bound actin filament pointed end. | ||||||||||||||||||||
Voxel size | X=Y=Z: 1.08 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Additional map: Sharpened final map of the Tropomodulin-bound actin filament...
File | emd_28936_additional_1.map | ||||||||||||
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Annotation | Sharpened final map of the Tropomodulin-bound actin filament pointed end. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half-map B of the Tropomodulin-bound actin filament pointed end.
File | emd_28936_half_map_1.map | ||||||||||||
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Annotation | Half-map B of the Tropomodulin-bound actin filament pointed end. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half-map A of the Tropomodulin-bound actin filament pointed end.
File | emd_28936_half_map_2.map | ||||||||||||
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Annotation | Half-map A of the Tropomodulin-bound actin filament pointed end. | ||||||||||||
Projections & Slices |
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Density Histograms |
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Sample components
-Entire : Tropomodulin-capped pointed end of F-actin
Entire | Name: Tropomodulin-capped pointed end of F-actin |
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Components |
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-Supramolecule #1: Tropomodulin-capped pointed end of F-actin
Supramolecule | Name: Tropomodulin-capped pointed end of F-actin / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2 |
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-Supramolecule #2: Tropomodulin (Tmod)
Supramolecule | Name: Tropomodulin (Tmod) / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #2 |
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Source (natural) | Organism: ![]() |
-Supramolecule #3: Actin filament
Supramolecule | Name: Actin filament / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #1 |
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Source (natural) | Organism: ![]() ![]() |
-Macromolecule #1: Actin, alpha skeletal muscle
Macromolecule | Name: Actin, alpha skeletal muscle / type: protein_or_peptide / ID: 1 / Number of copies: 7 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 42.109973 KDa |
Sequence | String: MCDEDETTAL VCDNGSGLVK AGFAGDDAPR AVFPSIVGRP RHQGVMVGMG QKDSYVGDEA QSKRGILTLK YPIE(HIC)G IIT NWDDMEKIWH HTFYNELRVA PEEHPTLLTE APLNPKANRE KMTQIMFETF NVPAMYVAIQ AVLSLYASGR TTGIVLD SG DGVTHNVPIY ...String: MCDEDETTAL VCDNGSGLVK AGFAGDDAPR AVFPSIVGRP RHQGVMVGMG QKDSYVGDEA QSKRGILTLK YPIE(HIC)G IIT NWDDMEKIWH HTFYNELRVA PEEHPTLLTE APLNPKANRE KMTQIMFETF NVPAMYVAIQ AVLSLYASGR TTGIVLD SG DGVTHNVPIY EGYALPHAIM RLDLAGRDLT DYLMKILTER GYSFVTTAER EIVRDIKEKL CYVALDFENE MATAASSS S LEKSYELPDG QVITIGNERF RCPETLFQPS FIGMESAGIH ETTYNSIMKC DIDIRKDLYA NNVMSGGTTM YPGIADRMQ KEITALAPST MKIKIIAPPE RKYSVWIGGS ILASLSTFQQ MWITKQEYDE AGPSIVHRKC F |
-Macromolecule #2: Tropomodulin-1
Macromolecule | Name: Tropomodulin-1 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 40.619078 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: MSYRRELEKY RDLDEDEILG ALTEEELRTL ENELDELDPD NALLPAGLRQ KDQTTKAPTG PFKREELLDH LEKQAKEFKD REDLVPYTG EKRGKVWVPK QKPLDPVLES VTLEPELEEA LANASDAELC DIAAILGMHT LMSNQQYYQA LSSSSIMNKE G LNSVIKPT ...String: MSYRRELEKY RDLDEDEILG ALTEEELRTL ENELDELDPD NALLPAGLRQ KDQTTKAPTG PFKREELLDH LEKQAKEFKD REDLVPYTG EKRGKVWVPK QKPLDPVLES VTLEPELEEA LANASDAELC DIAAILGMHT LMSNQQYYQA LSSSSIMNKE G LNSVIKPT QYKPVPDEEP NSTDVEETLE RIKNNDPKLE EVNLNNIRNI PIPTLKAYAE ALKENSYVKK FSIVGTRSND PV AYALAEM LKENKVLKTL NVESNFISGA GILRLVEALP YNTSLVEMKI DNQSQPLGNK VEMEIVSMLE KNATLLKFGY HFT QQGPRL RASNAMMNNN DLVRKRRLAD LTGPIIPKCR SGV |
-Macromolecule #3: ADENOSINE-5'-DIPHOSPHATE
Macromolecule | Name: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 3 / Number of copies: 7 / Formula: ADP |
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Molecular weight | Theoretical: 427.201 Da |
Chemical component information | ![]() ChemComp-ADP: |
-Macromolecule #4: MAGNESIUM ION
Macromolecule | Name: MAGNESIUM ION / type: ligand / ID: 4 / Number of copies: 7 / Formula: MG |
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Molecular weight | Theoretical: 24.305 Da |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 1.05 mg/mL |
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Buffer | pH: 7.5 |
Grid | Model: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. / Pretreatment - Atmosphere: AIR |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 278 K / Instrument: FEI VITROBOT MARK IV / Details: Blot force 0 Blot time 2.5 s. |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 44.7 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 81000 |
Sample stage | Specimen 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
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: RIGID BODY FIT / Target criteria: Cross-correlation coefficient |
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Output model | ![]() PDB-8f8t: |