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- EMDB-1497: 2D Arrays of F-actin Cross-linked by Villin -

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Basic information

Entry
Database: EMDB / ID: EMD-1497
Title2D Arrays of F-actin Cross-linked by Villin
Map datatomogram of F-actin crosslinked with villin on a 2D lipid monolayer
Sample
  • Sample: rabbit F-actin cross-linked with chicken villin
  • Organelle or cellular component: cytoskeleton
  • Organelle or cellular component: cytoskeleton
Keywordscytoskeleton / actin / electron tomography / microvilli / image processing / lipid monolayer
Biological speciesOryctolagus cuniculus (rabbit) / Gallus gallus (chicken)
Methodelectron tomography / cryo EM / negative staining / Resolution: 30.0 Å
AuthorsHampton CM / Liu J / Taylor DW / DeRosier DJ / Taylor KA
CitationJournal: Structure / Year: 2008
Title: The 3D structure of villin as an unusual F-Actin crosslinker.
Authors: Cheri M Hampton / Jun Liu / Dianne W Taylor / David J DeRosier / Kenneth A Taylor /
Abstract: Villin is an F-actin nucleating, crosslinking, severing, and capping protein within the gelsolin superfamily. We have used electron tomography of 2D arrays of villin-crosslinked F-actin to generate ...Villin is an F-actin nucleating, crosslinking, severing, and capping protein within the gelsolin superfamily. We have used electron tomography of 2D arrays of villin-crosslinked F-actin to generate 3D images revealing villin's crosslinking structure. In these polar arrays, neighboring filaments are spaced 125.9 +/- 7.1 A apart, offset axially by 17 A, with one villin crosslink per actin crossover. More than 6500 subvolumes containing a single villin crosslink and the neighboring actin filaments were aligned and classified to produce 3D subvolume averages. Placement of a complete villin homology model into the average density reveals that full-length villin binds to different sites on F-actin from those used by other actin-binding proteins and villin's close homolog gelsolin.
History
DepositionMar 13, 2008-
Header (metadata) releaseMar 14, 2008-
Map releaseMay 29, 2009-
UpdateMar 27, 2013-
Current statusMar 27, 2013Processing site: PDBe / Status: Released

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Structure visualization

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Structure viewerEM map:
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Supplemental images

1497.gif

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Map

FileDownload / File: emd_1497.map.gz / Format: CCP4 / Size: 822.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationtomogram of F-actin crosslinked with villin on a 2D lipid monolayer
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
5.76 Å/pix.
x 60 pix.
= 345.6 Å		5.76 Å/pix.
x 1840 pix.
= 11520. Å		5.76 Å/pix.
x 2000 pix.
= 10598.4 Å

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

generated in cubic-lattice coordinate

Voxel sizeX=Y=Z: 5.76 Å
Density

Histogram

Histogram (log scale)
Minimum - Maximum-8.51751 - 9.68876
Average (Standard dev.)0.00000000632091 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-1000-920-30
Dimensions1840200060
Spacing1840200060
CellA: 10598.4 Å / B: 11520 Å / C: 345.6 Å
α=β=γ: 90 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z5.765.765.76
M x/y/z1840200060
origin x/y/z0.0000.0000.000
length x/y/z10598.40011520.000345.600
α/β/γ90.00090.00090.000
start NX/NY/NZ-55-55-55
NX/NY/NZ111111111
MAP C/R/S123
start NC/NR/NS-920-1000-30
NC/NR/NS2000184060
D min/max/mean-8.5189.6890.000

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Supplemental data

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Sample components

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Entire : rabbit F-actin cross-linked with chicken villin

EntireName: rabbit F-actin cross-linked with chicken villin
Components
  • Sample: rabbit F-actin cross-linked with chicken villin
  • Organelle or cellular component: cytoskeleton
  • Organelle or cellular component: cytoskeleton

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Supramolecule #1000: rabbit F-actin cross-linked with chicken villin

SupramoleculeName: rabbit F-actin cross-linked with chicken villin / type: sample / ID: 1000 / Details: 2D rafts are formed on a lipid monolayer / Number unique components: 2

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Supramolecule #1: cytoskeleton

SupramoleculeName: cytoskeleton / type: organelle_or_cellular_component / ID: 1 / Name.synonym: actin / Recombinant expression: No / Database: NCBI
Source (natural)Organism: Oryctolagus cuniculus (rabbit) / synonym: Rabbit / Tissue: psoas muscle
Molecular weightExperimental: 42 MDa

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Supramolecule #2: cytoskeleton

SupramoleculeName: cytoskeleton / type: organelle_or_cellular_component / ID: 2 / Name.synonym: villin / Oligomeric state: monomer / Recombinant expression: No / Database: NCBI
Source (natural)Organism: Gallus gallus (chicken) / synonym: chicken / Tissue: intestinal epithelium / Organelle: microvillus
Molecular weightExperimental: 95 MDa

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Experimental details

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Structure determination

Methodnegative staining, cryo EM
Processingelectron tomography
Aggregation state2D array

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Sample preparation

StainingType: NEGATIVE / Details: uranyl acetate
GridDetails: 200 mesh holey carbon film
VitrificationCryogen name: ETHANE / Instrument: HOMEMADE PLUNGER / Details: Vitrification instrument: plunge freeze
Detailscrystals grown on a lipid-monolayer

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Electron microscopy

MicroscopeFEI/PHILIPS CM300FEG/T
DateMay 19, 2005
Image recordingCategory: CCD / Film or detector model: GENERIC CCD (2k x 2k)
Electron beamAcceleration voltage: 300 kV / Electron source: LAB6
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Cs: 2.0 mm / Nominal magnification: 24000
Sample stageSpecimen holder: high tilt / Specimen holder model: OTHER

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Image processing

Final reconstructionAlgorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 30.0 Å / Resolution method: OTHER / Software - Name: protomo / Details: tomogram is from a single tilt series / Number images used: 60
Crystal parametersPlane group: P 2

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