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Yorodumi- PDB-8ib2: Structure of mammalian spectrin-actin junctional complex of membr... -
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-Basic information
Entry | Database: PDB / ID: 8ib2 | ||||||
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Title | Structure of mammalian spectrin-actin junctional complex of membrane skeleton, Pointed-end segment, headpiece domain of dematin optimized | ||||||
Components |
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Keywords | MEMBRANE PROTEIN / Macrocomplex / membrane skeleton / spectrin-actin junction | ||||||
Function / homology | Function and homology information negative regulation of protein targeting to membrane / Gap junction degradation / Formation of annular gap junctions / Regulation of actin dynamics for phagocytic cup formation / EPHB-mediated forward signaling / Adherens junctions interactions / VEGFA-VEGFR2 Pathway / Cell-extracellular matrix interactions / RHO GTPases Activate WASPs and WAVEs / MAP2K and MAPK activation ...negative regulation of protein targeting to membrane / Gap junction degradation / Formation of annular gap junctions / Regulation of actin dynamics for phagocytic cup formation / EPHB-mediated forward signaling / Adherens junctions interactions / VEGFA-VEGFR2 Pathway / Cell-extracellular matrix interactions / RHO GTPases Activate WASPs and WAVEs / MAP2K and MAPK activation / UCH proteinases / Clathrin-mediated endocytosis / RHOF GTPase cycle / spectrin-associated cytoskeleton / negative regulation of peptidyl-tyrosine phosphorylation / negative regulation of substrate adhesion-dependent cell spreading / platelet dense tubular network membrane / structural constituent of postsynaptic actin cytoskeleton / cell projection membrane / negative regulation of focal adhesion assembly / regulation of filopodium assembly / dense body / positive regulation of fibroblast migration / regulation of lamellipodium assembly / RHO GTPases activate IQGAPs / RHO GTPases Activate Formins / spectrin binding / cortical cytoskeleton / NuA4 histone acetyltransferase complex / negative regulation of peptidyl-threonine phosphorylation / negative regulation of peptidyl-serine phosphorylation / positive regulation of blood coagulation / erythrocyte development / cellular response to cAMP / cellular response to calcium ion / axonogenesis / cell motility / regulation of actin cytoskeleton organization / actin filament / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / actin cytoskeleton / regulation of cell shape / actin binding / actin cytoskeleton organization / cytoplasmic vesicle / protein-containing complex assembly / postsynaptic density / cytoskeleton / hydrolase activity / axon / signaling receptor binding / focal adhesion / synapse / protein kinase binding / perinuclear region of cytoplasm / protein-containing complex / ATP binding / membrane / nucleus / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Sus scrofa (pig) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.8 Å | ||||||
Authors | Li, N. / Chen, S. / Gao, N. | ||||||
Funding support | China, 1items
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Citation | Journal: Cell / Year: 2023 Title: Structural basis of membrane skeleton organization in red blood cells. Authors: Ningning Li / Siyi Chen / Kui Xu / Meng-Ting He / Meng-Qiu Dong / Qiangfeng Cliff Zhang / Ning Gao / Abstract: The spectrin-based membrane skeleton is a ubiquitous membrane-associated two-dimensional cytoskeleton underneath the lipid membrane of metazoan cells. Mutations of skeleton proteins impair the ...The spectrin-based membrane skeleton is a ubiquitous membrane-associated two-dimensional cytoskeleton underneath the lipid membrane of metazoan cells. Mutations of skeleton proteins impair the mechanical strength and functions of the membrane, leading to several different types of human diseases. Here, we report the cryo-EM structures of the native spectrin-actin junctional complex (from porcine erythrocytes), which is a specialized short F-actin acting as the central organizational unit of the membrane skeleton. While an α-/β-adducin hetero-tetramer binds to the barbed end of F-actin as a flexible cap, tropomodulin and SH3BGRL2 together create an absolute cap at the pointed end. The junctional complex is strengthened by ring-like structures of dematin in the middle actin layers and by patterned periodic interactions with tropomyosin over its entire length. This work serves as a structural framework for understanding the assembly and dynamics of membrane skeleton and offers insights into mechanisms of various ubiquitous F-actin-binding factors in other F-actin systems. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8ib2.cif.gz | 336.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8ib2.ent.gz | 275.4 KB | Display | PDB format |
PDBx/mmJSON format | 8ib2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8ib2_validation.pdf.gz | 1.4 MB | Display | wwPDB validaton report |
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Full document | 8ib2_full_validation.pdf.gz | 1.4 MB | Display | |
Data in XML | 8ib2_validation.xml.gz | 58.6 KB | Display | |
Data in CIF | 8ib2_validation.cif.gz | 85 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ib/8ib2 ftp://data.pdbj.org/pub/pdb/validation_reports/ib/8ib2 | HTTPS FTP |
-Related structure data
Related structure data | 35329MC 8iahC 8iaiC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | Mass: 45569.348 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A8D1E7W3 | ||||
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#2: Protein | Mass: 41782.660 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: Q6QAQ1 #3: Chemical | ChemComp-ADP / Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Spectrin-actin junctional complex / Type: COMPLEX / Entity ID: #1 / Source: NATURAL |
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Source (natural) | Organism: Sus scrofa (pig) |
Buffer solution | pH: 7.5 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE / Humidity: 100 % |
-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 / Nominal defocus max: 3000 nm / Nominal defocus min: 2000 nm |
Image recording | Electron dose: 34.4 e/Å2 / Film or detector model: GATAN K2 QUANTUM (4k x 4k) |
-Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
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3D reconstruction | Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 60200 / Symmetry type: POINT |