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- EMDB-8918: Cryo-EM structure of FLNa ABD-E254K bound to phalloidin-stabilize... -

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Basic information

Entry
Database: EMDB / ID: EMD-8918
TitleCryo-EM structure of FLNa ABD-E254K bound to phalloidin-stabilized F-actin, collected on a FEI Tecnai F20 microscope
Map dataSymmetrized FLNa-ABD-E254K bound to F-actin stabilized by phalloidin. Low-pass filtered to 7.4 Angstrom with a B-factor of -500.
Sample
  • Complex: Helical filament of Filamin A actin-binding domain E254K bound to F-actin stabilized by phalloidin
    • Complex: Filamin A ABD-E254K
    • Complex: F-actin
Biological speciesHomo sapiens (human) / Gallus gallus (chicken)
Methodhelical reconstruction / cryo EM / Resolution: 7.4 Å
AuthorsIwamoto DV / Huehn AR / Simon B / Huet-Calderwoot C / Baldassarre M / Sindelar CV / Calderwood DA
CitationJournal: Nat Struct Mol Biol / Year: 2018
Title: Structural basis of the filamin A actin-binding domain interaction with F-actin.
Authors: Daniel V Iwamoto / Andrew Huehn / Bertrand Simon / Clotilde Huet-Calderwood / Massimiliano Baldassarre / Charles V Sindelar / David A Calderwood /
Abstract: Actin-cross-linking proteins assemble actin filaments into higher-order structures essential for orchestrating cell shape, adhesion, and motility. Missense mutations in the tandem calponin homology ...Actin-cross-linking proteins assemble actin filaments into higher-order structures essential for orchestrating cell shape, adhesion, and motility. Missense mutations in the tandem calponin homology domains of their actin-binding domains (ABDs) underlie numerous genetic diseases, but a molecular understanding of these pathologies is hampered by the lack of high-resolution structures of any actin-cross-linking protein bound to F-actin. Here, taking advantage of a high-affinity, disease-associated mutant of the human filamin A (FLNa) ABD, we combine cryo-electron microscopy and functional studies to reveal at near-atomic resolution how the first calponin homology domain (CH1) and residues immediately N-terminal to it engage actin. We further show that reorientation of CH2 relative to CH1 is required to avoid clashes with actin and to expose F-actin-binding residues on CH1. Our data explain localization of disease-associated loss-of-function mutations to FLNaCH1 and gain-of-function mutations to the regulatory FLNaCH2. Sequence conservation argues that this provides a general model for ABD-F-actin binding.
History
DepositionJun 25, 2018-
Header (metadata) releaseJul 25, 2018-
Map releaseSep 19, 2018-
UpdateOct 17, 2018-
Current statusOct 17, 2018Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.04
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.04
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_8918.png

Downloads & links

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Map

FileDownload / File: emd_8918.map.gz / Format: CCP4 / Size: 226.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSymmetrized FLNa-ABD-E254K bound to F-actin stabilized by phalloidin. Low-pass filtered to 7.4 Angstrom with a B-factor of -500.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.25 Å/pix.
x 390 pix.
= 486.33 Å		1.25 Å/pix.
x 390 pix.
= 486.33 Å		1.25 Å/pix.
x 390 pix.
= 486.33 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.247 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.04 / Movie #1: 0.04
Minimum - Maximum-0.05315499 - 0.15708916
Average (Standard dev.)0.00065655244 (±0.005579334)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions390390390
Spacing390390390
CellA=B=C: 486.33 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.2471.2471.247
M x/y/z390390390
origin x/y/z0.0000.0000.000
length x/y/z486.330486.330486.330
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ450450450
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS390390390
D min/max/mean-0.0530.1570.001

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Supplemental data

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Mask #1

Fileemd_8918_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Symmetrized and unfiltered half map (1) of FLNa-ABD-E254K...

Fileemd_8918_half_map_1.map
AnnotationSymmetrized and unfiltered half map (1) of FLNa-ABD-E254K bound to F-actin stabilized by phalloidin
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Symmetrized and unfiltered half map (2) of FLNa-ABD-E254K...

Fileemd_8918_half_map_2.map
AnnotationSymmetrized and unfiltered half map (2) of FLNa-ABD-E254K bound to F-actin stabilized by phalloidin
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Helical filament of Filamin A actin-binding domain E254K bound to...

EntireName: Helical filament of Filamin A actin-binding domain E254K bound to F-actin stabilized by phalloidin
Components
  • Complex: Helical filament of Filamin A actin-binding domain E254K bound to F-actin stabilized by phalloidin
    • Complex: Filamin A ABD-E254K
    • Complex: F-actin

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Supramolecule #1: Helical filament of Filamin A actin-binding domain E254K bound to...

SupramoleculeName: Helical filament of Filamin A actin-binding domain E254K bound to F-actin stabilized by phalloidin
type: complex / ID: 1 / Parent: 0

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Supramolecule #2: Filamin A ABD-E254K

SupramoleculeName: Filamin A ABD-E254K / type: complex / ID: 2 / Parent: 1
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Escherichia coli (E. coli) / Recombinant strain: D21

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Supramolecule #3: F-actin

SupramoleculeName: F-actin / type: complex / ID: 3 / Parent: 1
Source (natural)Organism: Gallus gallus (chicken)

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statehelical array

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Sample preparation

BufferpH: 7
VitrificationCryogen name: ETHANE / Instrument: HOMEMADE PLUNGER

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Electron microscopy

MicroscopeFEI TECNAI F20
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 27.67 Å
Applied symmetry - Helical parameters - Δ&Phi: -166.89 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 7.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 30000
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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