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- EMDB-35329: Structure of mammalian spectrin-actin junctional complex of membr... -

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Basic information

Entry
Database: EMDB / ID: EMD-35329
TitleStructure of mammalian spectrin-actin junctional complex of membrane skeleton, Pointed-end segment, headpiece domain of dematin optimized
Map data
Sample
  • Complex: Spectrin-actin junctional complex
    • Protein or peptide: Dematin actin binding protein
  • Protein or peptide: Actin, cytoplasmic 1
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
KeywordsMacrocomplex / membrane skeleton / spectrin-actin junction / MEMBRANE PROTEIN
Function / homology
Function and homology information


endoplasmic reticulum tubular network organization / smooth endoplasmic reticulum calcium ion homeostasis / negative regulation of protein targeting to membrane / 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 ...endoplasmic reticulum tubular network organization / smooth endoplasmic reticulum calcium ion homeostasis / negative regulation of protein targeting to membrane / 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 / RHOF GTPase cycle / Formation of the canonical BAF (cBAF) complex / Formation of the polybromo-BAF (pBAF) complex / Formation of the embryonic stem cell BAF (esBAF) complex / Formation of the non-canonical BAF (ncBAF) complex / GBP-mediated host defense / Platelet degranulation / Gap junction degradation / Formation of annular gap junctions / UCH proteinases / spectrin-associated cytoskeleton / negative regulation of substrate adhesion-dependent cell spreading / Clathrin-mediated endocytosis / Regulation of CDH1 Function / Formation of the dystrophin-glycoprotein complex (DGC) / platelet dense tubular network membrane / cell projection membrane / negative regulation of focal adhesion assembly / regulation of filopodium assembly / cellular response to cytochalasin B / regulation of transepithelial transport / morphogenesis of a polarized epithelium / structural constituent of postsynaptic actin cytoskeleton / protein localization to adherens junction / dense body / regulation of lamellipodium assembly / Tat protein binding / actin filament capping / postsynaptic actin cytoskeleton / positive regulation of fibroblast migration / apical protein localization / adherens junction assembly / RHO GTPases activate IQGAPs / RHO GTPases Activate Formins / tight junction / positive regulation of wound healing / apical junction complex / spectrin binding / erythrocyte development / NuA4 histone acetyltransferase complex / regulation of norepinephrine uptake / transporter regulator activity / smooth endoplasmic reticulum / cortical cytoskeleton / establishment or maintenance of cell polarity / nitric-oxide synthase binding / brush border / regulation of synaptic vesicle endocytosis / kinesin binding / regulation of protein localization to plasma membrane / microtubule-based process / positive regulation of double-strand break repair via homologous recombination / axonogenesis / cellular response to cAMP / calyx of Held / cell motility / nitric-oxide synthase regulator activity / actin filament / adherens junction / Schaffer collateral - CA1 synapse / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / cytoplasmic ribonucleoprotein granule / regulation of cell shape / actin cytoskeleton organization / actin cytoskeleton / lamellipodium / actin binding / protein-containing complex assembly / cytoplasmic vesicle / cytoskeleton / regulation of cell cycle / postsynaptic density / ribonucleoprotein complex / signaling receptor binding / axon / focal adhesion / synapse / protein kinase binding / perinuclear region of cytoplasm / glutamatergic synapse / ATP hydrolysis activity / protein-containing complex / ATP binding / membrane / identical protein binding / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Putative adherens-junction anchoring domain / : / Putative adherens-junction anchoring region of AbLIM / Villin headpiece / Villin headpiece domain superfamily / Villin headpiece domain / Headpiece (HP) domain profile. / Villin headpiece domain / Actins signature 1. / Actin, conserved site ...Putative adherens-junction anchoring domain / : / Putative adherens-junction anchoring region of AbLIM / Villin headpiece / Villin headpiece domain superfamily / Villin headpiece domain / Headpiece (HP) domain profile. / Villin headpiece domain / Actins signature 1. / Actin, conserved site / Actins signature 2. / Actin/actin-like conserved site / Actins and actin-related proteins signature. / Actin / Actin family / Actin / ATPase, nucleotide binding domain
Similarity search - Domain/homology
Dematin / Actin, cytoplasmic 1
Similarity search - Component
Biological speciesSus scrofa (pig)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.8 Å
AuthorsLi N / Chen S / Gao N
Funding support China, 1 items
OrganizationGrant numberCountry
National Science Foundation (NSF, China) China
CitationJournal: 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
DepositionFeb 9, 2023-
Header (metadata) releaseApr 26, 2023-
Map releaseApr 26, 2023-
UpdateJul 3, 2024-
Current statusJul 3, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_35329.png

Downloads & links

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Map

FileDownload / File: emd_35329.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
1.37 Å/pix.
x 240 pix.
= 328.8 Å		1.37 Å/pix.
x 240 pix.
= 328.8 Å		1.37 Å/pix.
x 240 pix.
= 328.8 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.37 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.05
Minimum - Maximum-0.14534168 - 0.29509056
Average (Standard dev.)0.00058229105 (±0.008103737)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions240240240
Spacing240240240
CellA=B=C: 328.8 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_35329_half_map_1.map
Projections & Slices
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Half map: #1

Fileemd_35329_half_map_2.map
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Sample components

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Entire : Spectrin-actin junctional complex

EntireName: Spectrin-actin junctional complex
Components
  • Complex: Spectrin-actin junctional complex
    • Protein or peptide: Dematin actin binding protein
  • Protein or peptide: Actin, cytoplasmic 1
  • Ligand: ADENOSINE-5'-DIPHOSPHATE

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Supramolecule #1: Spectrin-actin junctional complex

SupramoleculeName: Spectrin-actin junctional complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Sus scrofa (pig)

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Macromolecule #1: Dematin actin binding protein

MacromoleculeName: Dematin actin binding protein / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Sus scrofa (pig)
Molecular weightTheoretical: 45.569348 KDa
SequenceString: MERLQKQPLT SPGSVSSSRG SSVPGSPSSI VAKMDNQVLG YKDLAAIPKD KAILDIERPD LMIYEPHFTY SLLEHVELPR SRERSLSPK STSPPPSPEV WAESRSPGTF PQASAPRTTG TPRTSLPHFH HPETTRPDSN IYKKPPIYKQ REPTGGSPQS K HLIEDLII ...String:
MERLQKQPLT SPGSVSSSRG SSVPGSPSSI VAKMDNQVLG YKDLAAIPKD KAILDIERPD LMIYEPHFTY SLLEHVELPR SRERSLSPK STSPPPSPEV WAESRSPGTF PQASAPRTTG TPRTSLPHFH HPETTRPDSN IYKKPPIYKQ REPTGGSPQS K HLIEDLII ESSKFPAAQP PDPNQPAKIE TDYWPCPPSL AVVETEWRKR KASRRGAEEE EEEEDDDSGE EMKALRERQR EE LSKVTSN LGKMILKEEM EKSLPIRRKT RSLPDRTPFH TSLQAGTSKS SSLPAYGRTT LSRLQSTDFS PSGSETESPG LQN GEGQRG RMDRGTSLPC VLEQKIYPYE MLVVTNKGRT KLPPGVDRMR LERHLSAEDF SRVFSMSPEE FGKLALWKRN ELKK KASLF

UniProtKB: Dematin

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Macromolecule #2: Actin, cytoplasmic 1

MacromoleculeName: Actin, cytoplasmic 1 / type: protein_or_peptide / ID: 2 / Number of copies: 5 / Enantiomer: LEVO
Source (natural)Organism: Sus scrofa (pig)
Molecular weightTheoretical: 41.78266 KDa
SequenceString: MDDDIAALVV DNGSGMCKAG FAGDDAPRAV FPSIVGRPRH QGVMVGMGQK DSYVGDEAQS KRGILTLKYP IEHGIVTNWD DMEKIWHHT FYNELRVAPE EHPVLLTEAP LNPKANREKM TQIMFETFNT PAMYVAIQAV LSLYASGRTT GIVMDSGDGV T HTVPIYEG ...String:
MDDDIAALVV DNGSGMCKAG FAGDDAPRAV FPSIVGRPRH QGVMVGMGQK DSYVGDEAQS KRGILTLKYP IEHGIVTNWD DMEKIWHHT FYNELRVAPE EHPVLLTEAP LNPKANREKM TQIMFETFNT PAMYVAIQAV LSLYASGRTT GIVMDSGDGV T HTVPIYEG YALPHAILRL DLAGRDLTDY LMKILTERGY SFTTTAEREI VRDIKEKLCY VALDFEQEMA TAASSSSLEK SY ELPDGQV ITIGNERFRC PEALFQPSFL GMESCGIHET TFNSIMKCDV DIRKDLYANT VLSGGTTMYP GIADRMQKEI TAL APSTMK IKIIAPPERK YSVWIGGSIL ASLSTFQQMW ISKQEYDESG PSIVHRKCF

UniProtKB: Actin, cytoplasmic 1

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Macromolecule #3: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 3 / Number of copies: 5 / Formula: ADP
Molecular weightTheoretical: 427.201 Da
Chemical component information

ChemComp-ADP:
ADENOSINE-5'-DIPHOSPHATE / ADP, energy-carrying molecule*YM

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE / Chamber humidity: 100 %

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 QUANTUM (4k x 4k) / Average electron dose: 34.4 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 2.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 60200
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING

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