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- PDB-8iai: Structure of mammalian spectrin-actin junctional complex of membr... -
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Basic information
Entry | Database: PDB / ID: 8iai | ||||||
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Title | Structure of mammalian spectrin-actin junctional complex of membrane skeleton, State II, Global map | ||||||
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![]() | MEMBRANE PROTEIN / Macrocomplex / membrane skeleton / spectrin-actin junction | ||||||
Function / homology | ![]() negative regulation of protein targeting to membrane / pointed-end actin filament capping / 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 ...negative regulation of protein targeting to membrane / pointed-end actin filament capping / 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 / spectrin / RHOF GTPase cycle / lens fiber cell development / myofibril assembly / 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 / negative regulation of focal adhesion assembly / cell projection membrane / dense body / regulation of filopodium assembly / COP9 signalosome / actin filament capping / positive regulation of fibroblast migration / regulation of lamellipodium assembly / RHO GTPases activate IQGAPs / RHO GTPases Activate Formins / lamellipodium assembly / spectrin binding / NuA4 histone acetyltransferase complex / cortical cytoskeleton / tropomyosin binding / negative regulation of peptidyl-threonine phosphorylation / striated muscle thin filament / actin filament bundle assembly / : / positive regulation of blood coagulation / erythrocyte development / negative regulation of peptidyl-serine phosphorylation / cellular response to cAMP / cellular response to calcium ion / adult locomotory behavior / axonogenesis / muscle contraction / cell motility / actin filament / regulation of actin cytoskeleton organization / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / structural constituent of cytoskeleton / : / actin filament binding / actin cytoskeleton / actin binding / regulation of cell shape / 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 | ![]() ![]() | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.5 Å | ||||||
![]() | Li, N. / Chen, S. / Gao, N. | ||||||
Funding support | ![]()
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![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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PDBx/mmCIF format | ![]() | 1.5 MB | Display | ![]() |
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PDB format | ![]() | 1.1 MB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Summary document | ![]() | 2.2 MB | Display | ![]() |
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Full document | ![]() | 2.2 MB | Display | |
Data in XML | ![]() | 192.5 KB | Display | |
Data in CIF | ![]() | 296.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 35302MC ![]() 8iahC ![]() 8ib2C M: map data used to model this data C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Assembly
Deposited unit | ![]()
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Components
-Protein , 9 types, 31 molecules 12934567ABCDEFGHIJKMNOPQRSTUVYZ
#1: Protein | Mass: 81307.211 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #2: Protein | Mass: 80705.914 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #3: Protein | Mass: 45569.348 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #4: Protein | Mass: 41782.660 Da / Num. of mol.: 11 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #5: Protein | Mass: 248510.672 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #6: Protein | | Mass: 28791.223 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #7: Protein | | Mass: 29080.742 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #8: Protein | | Mass: 40523.055 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #9: Protein | | Mass: 12285.930 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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-Non-polymers , 1 types, 11 molecules ![](data/chem/img/ADP.gif)
#10: Chemical | ChemComp-ADP / |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
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Sample preparation
Component | Name: Spectrin-actin junctional complex / Type: COMPLEX / Entity ID: #1-#9 / Source: NATURAL |
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Source (natural) | Organism: ![]() ![]() |
Buffer solution | pH: 7.5 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE / Humidity: 100 % |
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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: ![]() |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 3000 nm / Nominal defocus min: 2000 nm |
Image recording | Electron dose: 34.4 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 QUANTUM (4k x 4k) |
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Processing
Software | Name: PHENIX / Version: 1.19.2_4158: / Classification: refinement | ||||||||||||||||||||||||
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 68000 / Symmetry type: POINT | ||||||||||||||||||||||||
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