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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-1088 | |||||||||
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Title | Structure of the acrosomal bundle. | |||||||||
![]() | One unit cell of the acrosomal bundle, pseudo-centered to provide a orthogonal map from the pseudo-hexagonal packing | |||||||||
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Function / homology | ![]() cytoskeletal motor activator activity / 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 ...cytoskeletal motor activator activity / 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 / stress fiber / titin binding / actin filament polymerization / filopodium / actin filament / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / calcium-dependent protein binding / lamellipodium / 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 / cytoplasm Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | helical reconstruction / cryo EM / Resolution: 9.5 Å | |||||||||
![]() | Schmid MF / Sherman MB / Matsudaira P / Chiu W | |||||||||
![]() | ![]() Title: Structure of the acrosomal bundle. Authors: Michael F Schmid / Michael B Sherman / Paul Matsudaira / Wah Chiu / ![]() Abstract: In the unactivated Limulus sperm, a 60- micro m-long bundle of actin filaments crosslinked by the protein scruin is bent and twisted into a coil around the base of the nucleus. At fertilization, the ...In the unactivated Limulus sperm, a 60- micro m-long bundle of actin filaments crosslinked by the protein scruin is bent and twisted into a coil around the base of the nucleus. At fertilization, the bundle uncoils and fully extends in five seconds to support a finger of membrane known as the acrosomal process. This biological spring is powered by stored elastic energy and does not require the action of motor proteins or actin polymerization. In a 9.5-A electron cryomicroscopic structure of the extended bundle, we show that twist, tilt and rotation of actin-scruin subunits deviate widely from a 'standard' F-actin filament. This variability in structural organization allows filaments to pack into a highly ordered and rigid bundle in the extended state and suggests a mechanism for storing and releasing energy between coiled and extended states without disassembly. | |||||||||
History |
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Structure visualization
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 43.6 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 12.6 KB 12.6 KB | Display Display | ![]() |
Images | ![]() | 13.6 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Annotation | One unit cell of the acrosomal bundle, pseudo-centered to provide a orthogonal map from the pseudo-hexagonal packing | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X: 1.33333 Å / Y: 1.32143 Å / Z: 1.32951 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
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Sample components
-Entire : Acrosomal bundle from Limulus sperm
Entire | Name: Acrosomal bundle from Limulus sperm |
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Components |
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-Supramolecule #1000: Acrosomal bundle from Limulus sperm
Supramolecule | Name: Acrosomal bundle from Limulus sperm / type: sample / ID: 1000 Oligomeric state: helix of actin and scruin in a 1 to 1 stoichiometry Number unique components: 2 |
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Molecular weight | Experimental: 4.2 MDa / Theoretical: 4.2 MDa / Method: calculated from molecular weight |
-Macromolecule #1: actin
Macromolecule | Name: actin / type: protein_or_peptide / ID: 1 / Name.synonym: F-actin / Details: 28 of these per unit cell / Number of copies: 28 / Oligomeric state: helical / Recombinant expression: No / Database: NCBI |
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Source (natural) | Organism: ![]() |
Molecular weight | Experimental: 1.176 MDa / Theoretical: 1.176 MDa |
-Macromolecule #2: scruin
Macromolecule | Name: scruin / type: protein_or_peptide / ID: 2 / Name.synonym: scruin / Details: 28 of these per unit cell / Number of copies: 28 / Oligomeric state: helical / Recombinant expression: No / Database: NCBI |
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Source (natural) | Organism: ![]() |
Molecular weight | Experimental: 3.08 MDa / Theoretical: 3.08 MDa |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | helical reconstruction |
Aggregation state | 2D array |
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Sample preparation
Concentration | 10 mg/mL |
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Buffer | pH: 7.4 / Details: see J Mol Biol, 221: 711-725 (1991) |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 90 K / Instrument: HOMEMADE PLUNGER / Details: Vitrification instrument: homemade guillotine |
Details | naturally occurring intracellular ordered array. Space group is P2sub1 or P1 21 1. P 1 21 refers to a 2-fold screw axis in the plane of the 2D crystal, whereas I have defined the 2-fold screw along z (second setting monoclinic). |
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Electron microscopy
Microscope | JEOL 4000EX |
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Temperature | Average: 90 K |
Image recording | Category: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: ZEISS SCAI / Digitization - Sampling interval: 7 µm / Number real images: 90 / Average electron dose: 15 e/Å2 / Details: 153 bundles selected / Od range: 1.5 |
Electron beam | Acceleration voltage: 400 kV / Electron source: LAB6 |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 40000 |
Sample stage | Specimen holder: side entry / Specimen holder model: GATAN LIQUID NITROGEN |
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Image processing
Final reconstruction | Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 9.5 Å / Resolution method: OTHER / Software - Name: MRC, CCP4, homemade Details: 1000 2 unit cell segments from 153 bundles (ref:Schmid, MF, J,. Struct Biol. 2003, 144:195-208. |
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CTF correction | Details: each bundle |
Crystal parameters | Unit cell - A: 145 Å / Unit cell - B: 145 Å / Unit cell - C: 765 Å / Unit cell - γ: 120 ° / Unit cell - α: 90 ° / Unit cell - β: 90 ° / Plane group: P 1 21 |
-Atomic model buiding 1
Initial model | PDB ID: |
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Software | Name: foldhunter and homemade software |
Details | Protocol: cross-correlation. each of the 28 actins was fitted and averaged, scruin was density-correlated and averaged because there is no crystal structure. overall B is the NEGATIVE B factor applied as a high-pass filter in the calculation of the map (-500). |
Refinement | Space: REAL / Overall B value: -500 / Target criteria: cross-correlation |
Output model | ![]() PDB-3b5u: ![]() PDB-3b63: |