[English] 日本語
Yorodumi- EMDB-8918: Cryo-EM structure of FLNa ABD-E254K bound to phalloidin-stabilize... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-8918 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Cryo-EM structure of FLNa ABD-E254K bound to phalloidin-stabilized F-actin, collected on a FEI Tecnai F20 microscope | |||||||||
Map data | Symmetrized FLNa-ABD-E254K bound to F-actin stabilized by phalloidin. Low-pass filtered to 7.4 Angstrom with a B-factor of -500. | |||||||||
Sample |
| |||||||||
Biological species | Homo sapiens (human) / Gallus gallus (chicken) | |||||||||
Method | helical reconstruction / cryo EM / Resolution: 7.4 Å | |||||||||
Authors | Iwamoto DV / Huehn AR / Simon B / Huet-Calderwoot C / Baldassarre M / Sindelar CV / Calderwood DA | |||||||||
Citation | Journal: 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 |
|
-Structure visualization
Movie |
Movie viewer |
---|---|
Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_8918.map.gz | 22.1 MB | EMDB map data format | |
---|---|---|---|---|
Header (meta data) | emd-8918-v30.xml emd-8918.xml | 13.9 KB 13.9 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_8918_fsc.xml | 13.9 KB | Display | FSC data file |
Images | emd_8918.png | 34.3 KB | ||
Masks | emd_8918_msk_1.map | 226.3 MB | Mask map | |
Others | emd_8918_half_map_1.map.gz emd_8918_half_map_2.map.gz | 32.6 MB 32.6 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-8918 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-8918 | HTTPS FTP |
-Validation report
Summary document | emd_8918_validation.pdf.gz | 79 KB | Display | EMDB validaton report |
---|---|---|---|---|
Full document | emd_8918_full_validation.pdf.gz | 78.1 KB | Display | |
Data in XML | emd_8918_validation.xml.gz | 495 B | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-8918 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-8918 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
---|
-Map
File | Download / File: emd_8918.map.gz / Format: CCP4 / Size: 226.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Symmetrized FLNa-ABD-E254K bound to F-actin stabilized by phalloidin. Low-pass filtered to 7.4 Angstrom with a B-factor of -500. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.247 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
|
-Supplemental data
-Mask #1
File | emd_8918_msk_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & Slices |
| ||||||||||||
Density Histograms |
-Half map: Symmetrized and unfiltered half map (1) of FLNa-ABD-E254K...
File | emd_8918_half_map_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Symmetrized and unfiltered half map (1) of FLNa-ABD-E254K bound to F-actin stabilized by phalloidin | ||||||||||||
Projections & Slices |
| ||||||||||||
Density Histograms |
-Half map: Symmetrized and unfiltered half map (2) of FLNa-ABD-E254K...
File | emd_8918_half_map_2.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Symmetrized and unfiltered half map (2) of FLNa-ABD-E254K bound to F-actin stabilized by phalloidin | ||||||||||||
Projections & Slices |
| ||||||||||||
Density Histograms |
-Sample components
-Entire : Helical filament of Filamin A actin-binding domain E254K bound to...
Entire | Name: Helical filament of Filamin A actin-binding domain E254K bound to F-actin stabilized by phalloidin |
---|---|
Components |
|
-Supramolecule #1: Helical filament of Filamin A actin-binding domain E254K bound to...
Supramolecule | Name: Helical filament of Filamin A actin-binding domain E254K bound to F-actin stabilized by phalloidin type: complex / ID: 1 / Parent: 0 |
---|
-Supramolecule #2: Filamin A ABD-E254K
Supramolecule | Name: Filamin A ABD-E254K / type: complex / ID: 2 / Parent: 1 |
---|---|
Source (natural) | Organism: Homo sapiens (human) |
Recombinant expression | Organism: Escherichia coli (E. coli) / Recombinant strain: D21 |
-Supramolecule #3: F-actin
Supramolecule | Name: F-actin / type: complex / ID: 3 / Parent: 1 |
---|---|
Source (natural) | Organism: Gallus gallus (chicken) |
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
Processing | helical reconstruction |
Aggregation state | helical array |
-Sample preparation
Buffer | pH: 7 |
---|---|
Vitrification | Cryogen name: ETHANE / Instrument: HOMEMADE PLUNGER |
-Electron microscopy
Microscope | FEI TECNAI F20 |
---|---|
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Tecnai F20 / Image courtesy: FEI Company |