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- EMDB-1088: Structure of the acrosomal bundle. -

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Basic information

Entry
Database: EMDB / ID: EMD-1088
TitleStructure of the acrosomal bundle.
Map dataOne unit cell of the acrosomal bundle, pseudo-centered to provide a orthogonal map from the pseudo-hexagonal packing
Sample
  • Sample: Acrosomal bundle from Limulus sperm
  • Protein or peptide: actin
  • Protein or peptide: scruin
Function / homology
Function and homology information


cytoskeletal motor activator activity / myosin heavy chain binding / tropomyosin binding / actin filament bundle / troponin I binding / filamentous actin / mesenchyme migration / actin filament bundle assembly / skeletal muscle myofibril / striated muscle thin filament ...cytoskeletal motor activator activity / myosin heavy chain binding / tropomyosin binding / actin filament bundle / troponin I binding / filamentous actin / mesenchyme migration / actin filament bundle assembly / skeletal muscle myofibril / striated muscle thin filament / skeletal muscle thin filament assembly / actin monomer binding / skeletal muscle fiber development / stress fiber / titin binding / actin filament polymerization / actin filament / filopodium / 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
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
Similarity search - Domain/homology
Actin-3 / Actin, alpha skeletal muscle
Similarity search - Component
Biological speciesLimulus polyphemus (Atlantic horseshoe crab)
Methodhelical reconstruction / cryo EM / Resolution: 9.5 Å
AuthorsSchmid MF / Sherman MB / Matsudaira P / Chiu W
CitationJournal: Nature / Year: 2004
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
DepositionJul 1, 2004-
Header (metadata) releaseJul 7, 2004-
Map releaseSep 7, 2004-
UpdateSep 25, 2013-
Current statusSep 25, 2013Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 340
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 340
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-3b5u
  • Surface level: 340
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-3b63
  • Surface level: 340
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-3b5u
  • Imaged by Jmol
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-3b63
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

1088.gif

Downloads & links

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Map

FileDownload / File: emd_1088.map.gz / Format: CCP4 / Size: 46.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationOne unit cell of the acrosomal bundle, pseudo-centered to provide a orthogonal map from the pseudo-hexagonal packing
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesY (Sec.)X (Row.)Z (Col.)
1.32 Å/pix.
x 112 pix.
= 148. Å		1.33 Å/pix.
x 192 pix.
= 255.999 Å		1.33 Å/pix.
x 576 pix.
= 765.798 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

generated in cubic-lattice coordinate

Voxel sizeX: 1.33333 Å / Y: 1.32143 Å / Z: 1.32951 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 430.0 / Movie #1: 340
Minimum - Maximum-974.402832030000013 - 977.198852539999962
Average (Standard dev.)-0.00000001 (±215.096801760000005)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZXY
Origin-96-288-56
Dimensions192576112
Spacing112192576
CellA: 255.99936 Å / B: 148.00015 Å / C: 765.7977 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.3333281251.32142857142861.3295104166667
M x/y/z192112576
origin x/y/z0.0000.0000.000
length x/y/z255.999148.000765.798
α/β/γ90.00090.00090.000
start NX/NY/NZ-96-56-288
NX/NY/NZ192112576
MAP C/R/S312
start NC/NR/NS-288-96-56
NC/NR/NS576192112
D min/max/mean-974.403977.199-0.000

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Supplemental data

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Sample components

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Entire : Acrosomal bundle from Limulus sperm

EntireName: Acrosomal bundle from Limulus sperm
Components
  • Sample: Acrosomal bundle from Limulus sperm
  • Protein or peptide: actin
  • Protein or peptide: scruin

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Supramolecule #1000: Acrosomal bundle from Limulus sperm

SupramoleculeName: 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
Molecular weightExperimental: 4.2 MDa / Theoretical: 4.2 MDa / Method: calculated from molecular weight

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Macromolecule #1: actin

MacromoleculeName: 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
Source (natural)Organism: Limulus polyphemus (Atlantic horseshoe crab) / synonym: horseshoe crab / Tissue: sperm / Cell: sperm / Organelle: acrosomal process / Location in cell: acrosomal bundle
Molecular weightExperimental: 1.176 MDa / Theoretical: 1.176 MDa

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Macromolecule #2: scruin

MacromoleculeName: 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
Source (natural)Organism: Limulus polyphemus (Atlantic horseshoe crab) / synonym: horseshoe crab / Tissue: sperm / Cell: sperm / Organelle: acrosomal process / Location in cell: acrosomal bundle
Molecular weightExperimental: 3.08 MDa / Theoretical: 3.08 MDa

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation state2D array

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Sample preparation

Concentration10 mg/mL
BufferpH: 7.4 / Details: see J Mol Biol, 221: 711-725 (1991)
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 90 K / Instrument: HOMEMADE PLUNGER / Details: Vitrification instrument: homemade guillotine
Detailsnaturally 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

MicroscopeJEOL 4000EX
TemperatureAverage: 90 K
Image recordingCategory: 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 beamAcceleration voltage: 400 kV / Electron source: LAB6
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 40000
Sample stageSpecimen holder: side entry / Specimen holder model: GATAN LIQUID NITROGEN

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Image processing

Final reconstructionAlgorithm: 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.
CTF correctionDetails: each bundle
Crystal parametersUnit 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

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Atomic model buiding 1

Initial modelPDB ID:

1atn

SoftwareName: foldhunter and homemade software
DetailsProtocol: 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).
RefinementSpace: REAL / Overall B value: -500 / Target criteria: cross-correlation
Output model

PDB-3b5u:
Actin filament model from extended form of acromsomal bundle in the Limulus sperm

PDB-3b63:
Actin filament model in the extended form of acromsomal bundle in the Limulus sperm

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