+Open data
-Basic information
Entry | Database: PDB / ID: 6vec | ||||||
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Title | Cryo-EM structure of F-actin/Plastin2-ABD2 complex | ||||||
Components |
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Keywords | PROTEIN FIBRIL / F-actin / Plastin 2 / Helical reconstruction | ||||||
Function / homology | Function and homology information actin filament network formation / actin crosslink formation / T cell activation involved in immune response / podosome / positive regulation of podosome assembly / cortical actin cytoskeleton organization / cytoskeletal motor activator activity / tropomyosin binding / mesenchyme migration / regulation of intracellular protein transport ...actin filament network formation / actin crosslink formation / T cell activation involved in immune response / podosome / positive regulation of podosome assembly / cortical actin cytoskeleton organization / cytoskeletal motor activator activity / tropomyosin binding / mesenchyme migration / regulation of intracellular protein transport / troponin I binding / myosin heavy chain binding / filamentous actin / actin filament bundle / skeletal muscle thin filament assembly / glial cell projection / striated muscle thin filament / actin filament bundle assembly / 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 / ruffle membrane / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / actin filament binding / integrin binding / calcium-dependent protein binding / cell junction / actin cytoskeleton / cell migration / 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 / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) Oryctolagus cuniculus (rabbit) | ||||||
Method | ELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 3.9 Å | ||||||
Authors | Zheng, W. / Kudryashov, D.S. / Egelman, E.H. | ||||||
Funding support | United States, 1items
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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 | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 6vec.cif.gz | 1.1 MB | Display | PDBx/mmCIF format |
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PDB format | pdb6vec.ent.gz | 954.3 KB | Display | PDB format |
PDBx/mmJSON format | 6vec.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6vec_validation.pdf.gz | 1.6 MB | Display | wwPDB validaton report |
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Full document | 6vec_full_validation.pdf.gz | 1.7 MB | Display | |
Data in XML | 6vec_validation.xml.gz | 160.8 KB | Display | |
Data in CIF | 6vec_validation.cif.gz | 230.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ve/6vec ftp://data.pdbj.org/pub/pdb/validation_reports/ve/6vec | HTTPS FTP |
-Related structure data
Related structure data | 21155MC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Symmetry | Helical symmetry: (Circular symmetry: 1 / Dyad axis: no / N subunits divisor: 1 / Num. of operations: 11 / Rise per n subunits: 28 Å / Rotation per n subunits: -166.5 °) |
-Components
#1: Protein | Mass: 42096.953 Da / Num. of mol.: 11 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: P68135 #2: Protein | Mass: 47983.633 Da / Num. of mol.: 11 / Fragment: UNP residues 385-625 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: HEL-S-37 Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: V9HWJ7, UniProt: P13796*PLUS #3: Chemical | ChemComp-ADP / #4: Chemical | ChemComp-MG / Has ligand of interest | N | |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: FILAMENT / 3D reconstruction method: helical reconstruction |
-Sample preparation
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Molecular weight | Experimental value: NO | ||||||||||||||||||||||||
Source (natural) |
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Source (recombinant) | Organism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) | ||||||||||||||||||||||||
Buffer solution | pH: 7.5 | ||||||||||||||||||||||||
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||||||
Specimen support | Details: unspecified | ||||||||||||||||||||||||
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD |
Specimen holder | Cryogen: NITROGEN |
Image recording | Electron dose: 20 e/Å2 / Detector mode: INTEGRATING / Film or detector model: FEI FALCON III (4k x 4k) |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||
Helical symmerty | Angular rotation/subunit: -166.5 ° / Axial rise/subunit: 28 Å / Axial symmetry: C1 | ||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 248184 | ||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 124092 / Symmetry type: HELICAL | ||||||||||||||||||||||||||||||||||||
Atomic model building | PDB-ID: 5ONV Accession code: 5ONV / Source name: PDB / Type: experimental model |