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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
TitleStructure of mammalian spectrin-actin junctional complex of membrane skeleton, State II, Global map
Components
  • Actin, cytoplasmic 1
  • Adducin 1
  • Beta-adducin
  • Dematin actin binding protein
  • SH3 domain-binding glutamic acid-rich-like protein
  • Spectrin beta chain
  • Tropomodulin-1
  • Tropomyosin 3
  • Tropomyosin-1.9
KeywordsMEMBRANE PROTEIN / Macrocomplex / membrane skeleton / spectrin-actin junction
Function / homology
Function and homology information


negative regulation of protein targeting to membrane / endoplasmic reticulum tubular network organization / pointed-end actin filament capping / 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 / endoplasmic reticulum tubular network organization / pointed-end actin filament capping / 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 / spectrin / Gap junction degradation / Formation of annular gap junctions / RHOF GTPase cycle / Clathrin-mediated endocytosis / Formation of the dystrophin-glycoprotein complex (DGC) / lens fiber cell development / myofibril assembly / spectrin-associated cytoskeleton / negative regulation of substrate adhesion-dependent cell spreading / platelet dense tubular network membrane / cellular response to cytochalasin B / negative regulation of focal adhesion assembly / regulation of transepithelial transport / morphogenesis of a polarized epithelium / regulation of filopodium assembly / cell projection membrane / protein localization to adherens junction / postsynaptic actin cytoskeleton / structural constituent of postsynaptic actin cytoskeleton / Tat protein binding / COP9 signalosome / dense body / actin filament capping / apical protein localization / regulation of lamellipodium assembly / adherens junction assembly / positive regulation of fibroblast migration / RHO GTPases activate IQGAPs / RHO GTPases Activate Formins / tight junction / smooth endoplasmic reticulum calcium ion homeostasis / regulation of norepinephrine uptake / transporter regulator activity / apical junction complex / nitric-oxide synthase binding / positive regulation of wound healing / spectrin binding / tropomyosin binding / NuA4 histone acetyltransferase complex / establishment or maintenance of cell polarity / cortical cytoskeleton / myofibril / regulation of synaptic vesicle endocytosis / brush border / kinesin binding / striated muscle thin filament / erythrocyte development / smooth endoplasmic reticulum / positive regulation of double-strand break repair via homologous recombination / regulation of protein localization to plasma membrane / cellular response to cAMP / muscle contraction / calyx of Held / axonogenesis / adult locomotory behavior / actin filament organization / adherens junction / actin filament / regulation of actin cytoskeleton organization / cell motility / Schaffer collateral - CA1 synapse / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / SH3 domain binding / structural constituent of cytoskeleton / cytoplasmic ribonucleoprotein granule / nucleosome / lamellipodium / actin cytoskeleton / regulation of cell shape / actin binding / actin cytoskeleton organization / protein-containing complex assembly / cytoplasmic vesicle / cytoskeleton / regulation of cell cycle / postsynaptic density / axon / ribonucleoprotein complex / signaling receptor binding / focal adhesion / synapse / protein kinase binding / perinuclear region of cytoplasm / glutamatergic synapse / protein-containing complex / ATP hydrolysis activity / ATP binding / identical protein binding
Similarity search - Function
: / SH3-binding, glutamic acid-rich protein / : / SH3-binding, glutamic acid-rich protein / Putative adherens-junction anchoring domain / : / Putative adherens-junction anchoring region of AbLIM / Tropomodulin / Tropomodulin / Spectrin, beta subunit ...: / SH3-binding, glutamic acid-rich protein / : / SH3-binding, glutamic acid-rich protein / Putative adherens-junction anchoring domain / : / Putative adherens-junction anchoring region of AbLIM / Tropomodulin / Tropomodulin / Spectrin, beta subunit / Class II aldolase/adducin N-terminal / Villin headpiece / Villin headpiece domain superfamily / Class II Aldolase and Adducin N-terminal domain / Villin headpiece domain / Headpiece (HP) domain profile. / Villin headpiece domain / Class II Aldolase and Adducin N-terminal domain / Class II aldolase/adducin N-terminal domain superfamily / Tropomyosins signature. / Tropomyosin / Tropomyosin / Spectrin repeat / Spectrin repeat / DNA repair protein XRCC4-like, C-terminal / Spectrin/alpha-actinin / Spectrin repeats / Actinin-type actin-binding domain signature 1. / Actinin-type actin-binding domain signature 2. / Actinin-type actin-binding domain, conserved site / Calponin homology domain / Calponin homology (CH) domain / Calponin homology domain / CH domain superfamily / Calponin homology (CH) domain profile. / ATPase, substrate binding domain, subdomain 4 / Actin; Chain A, domain 4 / Actins signature 1. / Actin, conserved site / Actins signature 2. / Actin/actin-like conserved site / Actins and actin-related proteins signature. / Actin / Actin family / Actin / Leucine-rich repeat domain superfamily / ATPase, nucleotide binding domain / Thioredoxin-like superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / Tropomodulin-1 / Spectrin beta chain / Beta-adducin / SH3 domain-binding glutamic acid-rich-like protein / Dematin actin binding protein / Adducin 1 / Tropomyosin 3 / Actin, cytoplasmic 1
Similarity search - Component
Biological speciesSus scrofa (pig)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsLi, N. / Chen, S. / Gao, N.
Funding support China, 1items
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 8, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 3, 2023Provider: repository / Type: Initial release
Revision 1.0May 3, 2023Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0May 3, 2023Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0May 3, 2023Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
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Revision 1.0May 3, 2023Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
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Revision 1.0May 3, 2023Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0May 3, 2023Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
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Revision 1.0May 3, 2023Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.0May 3, 2023Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0May 3, 2023Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
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Revision 1.0May 3, 2023Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0May 3, 2023Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1May 10, 2023Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Jul 3, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond / em_admin / Item: _em_admin.last_update
Revision 1.3Jun 18, 2025Group: Data collection / Structure summary / Category: em_admin / em_software / pdbx_entry_details
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Revision 1.1Jun 18, 2025Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Data processing / Experimental summary / Data content type: EM metadata / EM metadata / Category: em_admin / em_software / Data content type: EM metadata / EM metadata / Item: _em_admin.last_update / _em_software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
1: Adducin 1
2: Adducin 1
3: Beta-adducin
4: Beta-adducin
5: Dematin actin binding protein
6: Dematin actin binding protein
7: Dematin actin binding protein
9: Adducin 1
A: Actin, cytoplasmic 1
B: Actin, cytoplasmic 1
C: Actin, cytoplasmic 1
D: Actin, cytoplasmic 1
E: Actin, cytoplasmic 1
F: Actin, cytoplasmic 1
G: Actin, cytoplasmic 1
H: Actin, cytoplasmic 1
I: Actin, cytoplasmic 1
J: Actin, cytoplasmic 1
K: Actin, cytoplasmic 1
M: Spectrin beta chain
N: Spectrin beta chain
O: Spectrin beta chain
P: Spectrin beta chain
Q: Spectrin beta chain
R: Spectrin beta chain
S: Spectrin beta chain
T: Spectrin beta chain
U: Tropomyosin-1.9
V: Tropomyosin 3
Y: Tropomodulin-1
Z: SH3 domain-binding glutamic acid-rich-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,105,11642
Polymers3,100,41731
Non-polymers4,69911
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Protein , 9 types, 31 molecules 12934567ABCDEFGHIJKMNOPQRSTUVYZ

#1: Protein Adducin 1 / Alpha-adducin


Mass: 81307.211 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A8D1Q0D0
#2: Protein Beta-adducin


Mass: 80705.914 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A480JMR2
#3: Protein Dematin actin binding protein / Dematin


Mass: 45569.348 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A8D1E7W3
#4: Protein
Actin, cytoplasmic 1


Mass: 41782.660 Da / Num. of mol.: 11 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: Q6QAQ1
#5: Protein
Spectrin beta chain / Spectrin beta chain / erythrocytic


Mass: 248510.672 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A480J001
#6: Protein Tropomyosin-1.9


Mass: 28791.223 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig)
#7: Protein Tropomyosin 3 / Tropomyosin-3.1


Mass: 29080.742 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: Q6QA25
#8: Protein Tropomodulin-1


Mass: 40523.055 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A287BCZ0
#9: Protein SH3 domain-binding glutamic acid-rich-like protein / SH3 domain-binding glutamic acid-rich-like protein 2


Mass: 12285.930 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A4X1V2Q0

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Non-polymers , 1 types, 11 molecules

#10: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM

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Details

Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Spectrin-actin junctional complex / Type: COMPLEX / Entity ID: #1-#9 / Source: NATURAL
Source (natural)Organism: Sus scrofa (pig)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE / Humidity: 100 %

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 3000 nm / Nominal defocus min: 2000 nm
Image recordingElectron dose: 34.4 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 QUANTUM (4k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.19.2_4158: / Classification: refinement
EM softwareName: PHENIX / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 68000 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00361482
ELECTRON MICROSCOPYf_angle_d0.72883150
ELECTRON MICROSCOPYf_dihedral_angle_d6.2268390
ELECTRON MICROSCOPYf_chiral_restr0.0469290
ELECTRON MICROSCOPYf_plane_restr0.00510688

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