+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-21155 | |||||||||
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Title | Cryo-EM structure of F-actin/Plastin2-ABD2 complex | |||||||||
Map data | Cryo-EM structure of F-actin/Plastin2-ABD2 complex | |||||||||
Sample |
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Keywords | F-actin / Plastin 2 / Helical reconstruction / PROTEIN FIBRIL | |||||||||
Function / homology | Function and homology information actin filament network formation / actin crosslink formation / T cell activation involved in immune response / positive regulation of podosome assembly / podosome / cortical actin cytoskeleton organization / cytoskeletal motor activator activity / tropomyosin binding / myosin heavy chain binding / mesenchyme migration ...actin filament network formation / actin crosslink formation / T cell activation involved in immune response / positive regulation of podosome assembly / podosome / cortical actin cytoskeleton organization / cytoskeletal motor activator activity / tropomyosin binding / myosin heavy chain binding / mesenchyme migration / regulation of intracellular protein transport / troponin I binding / filamentous actin / actin filament bundle / skeletal muscle thin filament assembly / actin filament bundle assembly / striated muscle thin filament / glial cell projection / phagocytic cup / skeletal muscle myofibril / actin monomer binding / extracellular matrix disassembly / animal organ regeneration / skeletal muscle fiber development / stress fiber / titin binding / ruffle / protein kinase A signaling / actin filament polymerization / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / filopodium / actin filament / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / ruffle membrane / calcium-dependent protein binding / actin filament binding / actin cytoskeleton / cell migration / integrin binding / cell junction / lamellipodium / GTPase binding / actin binding / cell body / hydrolase activity / protein domain specific binding / focal adhesion / calcium ion binding / positive regulation of gene expression / perinuclear region of cytoplasm / magnesium ion binding / extracellular space / extracellular exosome / ATP binding / identical protein binding / plasma membrane / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | Oryctolagus cuniculus (rabbit) / Homo sapiens (human) | |||||||||
Method | helical reconstruction / cryo EM / Resolution: 3.9 Å | |||||||||
Authors | Zheng W / Kudryashov DS | |||||||||
Funding support | United States, 1 items
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Citation | Journal: Bone Res / Year: 2020 Title: Osteogenesis imperfecta mutations in plastin 3 lead to impaired calcium regulation of actin bundling. Authors: Christopher L Schwebach / Elena Kudryashova / Weili Zheng / Matthew Orchard / Harper Smith / Lucas A Runyan / Edward H Egelman / Dmitri S Kudryashov / Abstract: Mutations in actin-bundling protein plastin 3 (PLS3) emerged as a cause of congenital osteoporosis, but neither the role of PLS3 in bone development nor the mechanisms underlying PLS3-dependent ...Mutations in actin-bundling protein plastin 3 (PLS3) emerged as a cause of congenital osteoporosis, but neither the role of PLS3 in bone development nor the mechanisms underlying PLS3-dependent osteoporosis are understood. Of the over 20 identified osteoporosis-linked PLS3 mutations, we investigated all five that are expected to produce full-length protein. One of the mutations distorted an actin-binding loop in the second actin-binding domain of PLS3 and abolished F-actin bundling as revealed by cryo-EM reconstruction and protein interaction assays. Surprisingly, the remaining four mutants fully retained F-actin bundling ability. However, they displayed defects in Ca sensitivity: two of the mutants lost the ability to be inhibited by Ca, while the other two became hypersensitive to Ca. Each group of the mutants with similar biochemical properties showed highly characteristic cellular behavior. Wild-type PLS3 was distributed between lamellipodia and focal adhesions. In striking contrast, the Ca-hyposensitive mutants were not found at the leading edge but localized exclusively at focal adhesions/stress fibers, which displayed reinforced morphology. Consistently, the Ca-hypersensitive PLS3 mutants were restricted to lamellipodia, while chelation of Ca caused their redistribution to focal adhesions. Finally, the bundling-deficient mutant failed to co-localize with any F-actin structures in cells despite a preserved F-actin binding through a non-mutation-bearing actin-binding domain. Our findings revealed that severe osteoporosis can be caused by a mutational disruption of the Ca-controlled PLS3's cycling between adhesion complexes and the leading edge. Integration of the structural, biochemical, and cell biology insights enabled us to propose a molecular mechanism of plastin activity regulation by Ca. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_21155.map.gz | 59.4 MB | EMDB map data format | |
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Header (meta data) | emd-21155-v30.xml emd-21155.xml | 13.5 KB 13.5 KB | Display Display | EMDB header |
Images | emd_21155.png | 108.9 KB | ||
Filedesc metadata | emd-21155.cif.gz | 6.3 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-21155 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-21155 | HTTPS FTP |
-Validation report
Summary document | emd_21155_validation.pdf.gz | 617.2 KB | Display | EMDB validaton report |
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Full document | emd_21155_full_validation.pdf.gz | 616.8 KB | Display | |
Data in XML | emd_21155_validation.xml.gz | 6.1 KB | Display | |
Data in CIF | emd_21155_validation.cif.gz | 6.9 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-21155 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-21155 | HTTPS FTP |
-Related structure data
Related structure data | 6vecMC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_21155.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Cryo-EM structure of F-actin/Plastin2-ABD2 complex | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.4 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : Complex of Plastin2-ABD2 with F-actin
Entire | Name: Complex of Plastin2-ABD2 with F-actin |
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Components |
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-Supramolecule #1: Complex of Plastin2-ABD2 with F-actin
Supramolecule | Name: Complex of Plastin2-ABD2 with F-actin / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2 |
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-Supramolecule #2: F-actin
Supramolecule | Name: F-actin / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1 |
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Source (natural) | Organism: Oryctolagus cuniculus (rabbit) |
-Supramolecule #3: Plastin2-ABD2
Supramolecule | Name: Plastin2-ABD2 / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2 |
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Source (natural) | Organism: Homo sapiens (human) |
-Macromolecule #1: Actin, alpha skeletal muscle
Macromolecule | Name: Actin, alpha skeletal muscle / type: protein_or_peptide / ID: 1 / Number of copies: 11 / Enantiomer: LEVO |
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Source (natural) | Organism: Oryctolagus cuniculus (rabbit) |
Molecular weight | Theoretical: 42.096953 KDa |
Sequence | String: MCDEDETTAL VCDNGSGLVK AGFAGDDAPR AVFPSIVGRP RHQGVMVGMG QKDSYVGDEA QSKRGILTLK YPIEHGIITN WDDMEKIWH HTFYNELRVA PEEHPTLLTE APLNPKANRE KMTQIMFETF NVPAMYVAIQ AVLSLYASGR TTGIVLDSGD G VTHNVPIY ...String: MCDEDETTAL VCDNGSGLVK AGFAGDDAPR AVFPSIVGRP RHQGVMVGMG QKDSYVGDEA QSKRGILTLK YPIEHGIITN WDDMEKIWH HTFYNELRVA PEEHPTLLTE APLNPKANRE KMTQIMFETF NVPAMYVAIQ AVLSLYASGR TTGIVLDSGD G VTHNVPIY EGYALPHAIM RLDLAGRDLT DYLMKILTER GYSFVTTAER EIVRDIKEKL CYVALDFENE MATAASSSSL EK SYELPDG QVITIGNERF RCPETLFQPS FIGMESAGIH ETTYNSIMKC DIDIRKDLYA NNVMSGGTTM YPGIADRMQK EIT ALAPST MKIKIIAPPE RKYSVWIGGS ILASLSTFQQ MWITKQEYDE AGPSIVHRKC F UniProtKB: Actin, alpha skeletal muscle |
-Macromolecule #2: LCP1
Macromolecule | Name: LCP1 / type: protein_or_peptide / ID: 2 / Number of copies: 11 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 47.983633 KDa |
Recombinant expression | Organism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) |
Sequence | String: MNHKVHHHHH HIEGRHMELG TLEENLYFQG ELADIELSRN EALIALLREG ESLEDLMKLS PEELLLRWAN YHLENAGCNK IGNFSTDIK DSKAYYHLLE QVAPKGDEEG VPAVVIDMSG LREKDDIQRA ECMLQQAERL GCRQFVTATD VVRGNPKLNL A FIANLFNR ...String: MNHKVHHHHH HIEGRHMELG TLEENLYFQG ELADIELSRN EALIALLREG ESLEDLMKLS PEELLLRWAN YHLENAGCNK IGNFSTDIK DSKAYYHLLE QVAPKGDEEG VPAVVIDMSG LREKDDIQRA ECMLQQAERL GCRQFVTATD VVRGNPKLNL A FIANLFNR YPALHKPENQ DIDWGALEGE TREERTFRNW MNSLGVNPRV NHLYSDLSDA LVIFQLYEKI KVPVDWNRVN KP PYPKLGG NMKKLENCNY AVELGKNQAK FSLVGIGGQD LNEGNRTLTL ALIWQLMRRY TLNILEEIGG GQKVNDDIIV NWV NETLRE AEKSSSISSF KDPKISTSLP VLDLIDAIQP GSINYDLLKT ENLNDDEKLN NAKYAISMAR KIGARVYALP EDLV EVNPK MVMTVFACLM GKGMKRV UniProtKB: Epididymis secretory protein Li 37 |
-Macromolecule #3: ADENOSINE-5'-DIPHOSPHATE
Macromolecule | Name: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 3 / Number of copies: 11 / Formula: ADP |
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Molecular weight | Theoretical: 427.201 Da |
Chemical component information | ChemComp-ADP: |
-Macromolecule #4: MAGNESIUM ION
Macromolecule | Name: MAGNESIUM ION / type: ligand / ID: 4 / Number of copies: 11 / Formula: MG |
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Molecular weight | Theoretical: 24.305 Da |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | helical reconstruction |
Aggregation state | filament |
-Sample preparation
Buffer | pH: 7.5 |
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Grid | Pretreatment - Type: PLASMA CLEANING / Details: unspecified |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: FEI FALCON III (4k x 4k) / Detector mode: INTEGRATING / Average electron dose: 20.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Sample stage | Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Final reconstruction | Applied symmetry - Helical parameters - Δz: 28.0 Å Applied symmetry - Helical parameters - Δ&Phi: -166.5 ° Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric) Resolution.type: BY AUTHOR / Resolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 124092 |
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Segment selection | Number selected: 248184 / Software - Name: EMAN2 |
Startup model | Type of model: OTHER |
Final angle assignment | Type: NOT APPLICABLE |