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- PDB-8iah: Structure of mammalian spectrin-actin junctional complex of membr... -

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Entry
Database: PDB / ID: 8iah
TitleStructure of mammalian spectrin-actin junctional complex of membrane skeleton, State I, Global map
Components
  • Actin, cytoplasmic 1
  • Adducin 1
  • Beta-adducin
  • Dematin actin binding protein
  • SH3 domain-binding glutamic acid-rich-like protein
  • Spectrin alpha, erythrocytic 1
  • Spectrin beta chain
  • Tropomodulin-1
  • Tropomyosin 3
  • Tropomyosin-1.9
KeywordsMEMBRANE PROTEIN / Macrocomplex / membrane skeleton / spectrin-actin junction
Function / homology
Function and homology information


NCAM signaling for neurite out-growth / RAF/MAP kinase cascade / regulation of cellular component size / lens fiber cell development / endoplasmic reticulum tubular network organization / smooth endoplasmic reticulum calcium ion homeostasis / pointed-end actin filament capping / negative regulation of protein targeting to membrane / regulation of multicellular organismal development / positive regulation of developmental process ...NCAM signaling for neurite out-growth / RAF/MAP kinase cascade / regulation of cellular component size / lens fiber cell development / endoplasmic reticulum tubular network organization / smooth endoplasmic reticulum calcium ion homeostasis / pointed-end actin filament capping / negative regulation of protein targeting to membrane / regulation of multicellular organismal development / positive regulation of developmental process / spectrin / 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 / Striated Muscle Contraction / Gap junction degradation / Formation of annular gap junctions / UCH proteinases / spectrin-associated cytoskeleton / negative regulation of substrate adhesion-dependent cell spreading / Clathrin-mediated endocytosis / cuticular plate / Regulation of CDH1 Function / Formation of the dystrophin-glycoprotein complex (DGC) / myofibril assembly / positive regulation of cellular component organization / platelet dense tubular network membrane / cell projection membrane / negative regulation of focal adhesion assembly / regulation of filopodium assembly / cellular response to cytochalasin B / COP9 signalosome / 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 / COPI-mediated anterograde transport / ankyrin binding / cortical actin cytoskeleton / positive regulation of wound healing / apical junction complex / spectrin binding / tropomyosin 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 / myofibril / nitric-oxide synthase binding / striated muscle thin filament / 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 / cytoskeleton organization / cell projection / muscle contraction / cellular response to cAMP / calyx of Held / cell motility / nitric-oxide synthase regulator activity / actin filament organization / actin filament / adherens junction / SH3 domain binding / synapse organization / cell junction / Schaffer collateral - CA1 synapse / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / structural constituent of cytoskeleton / cytoplasmic ribonucleoprotein granule / regulation of cell shape
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 / Spectrin, beta subunit / Tropomodulin ...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 / Spectrin, beta subunit / Tropomodulin / TMOD/LMOD Leucine-rich domain / Class II aldolase/adducin N-terminal / Class II Aldolase and Adducin N-terminal domain / Class II Aldolase and Adducin N-terminal domain / Villin headpiece / Villin headpiece domain superfamily / Villin headpiece domain / Headpiece (HP) domain profile. / Villin headpiece domain / Class II aldolase/adducin N-terminal domain superfamily / EF-hand, Ca insensitive / Ca2+ insensitive EF hand / Ca2+ insensitive EF hand / Tropomyosins signature. / Tropomyosin / Tropomyosin / Spectrin repeat / Spectrin repeat / Spectrin/alpha-actinin / Spectrin repeats / DNA repair protein XRCC4-like, C-terminal / Actinin-type actin-binding domain signature 1. / Actinin-type actin-binding domain signature 2. / Actinin-type actin-binding domain, conserved site / Leucine-rich repeat, LRR (right-handed beta-alpha superhelix) / Ribonuclease Inhibitor / Calponin homology domain / Calponin homology (CH) domain / ATPase, substrate binding domain, subdomain 4 / Alpha-Beta Horseshoe / Calponin homology domain / CH domain superfamily / Calponin homology (CH) domain profile. / 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 / SH3 domain / Leucine-rich repeat domain superfamily / Src homology 3 domains / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / ATPase, nucleotide binding domain / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair / 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 / Spectrin alpha chain, erythrocytic 1 / Dematin / Alpha-adducin / Tropomyosin alpha-4 chain / Actin, cytoplasmic 1
Similarity search - Component
Biological speciesSus scrofa (pig)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.6 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
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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: 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 1.3Jul 2, 2025Group: Data collection / Structure summary / Category: em_admin / em_software / pdbx_entry_details
Item: _em_admin.last_update / _em_software.name / _pdbx_entry_details.has_protein_modification
Revision 1.1Jul 2, 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
0: Adducin 1
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
8: Spectrin alpha, erythrocytic 1
9: Beta-adducin
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
L: 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
W: Tropomyosin 3
X: Tropomyosin 3
Y: Tropomodulin-1
Z: SH3 domain-binding glutamic acid-rich-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,567,55548
Polymers3,562,42836
Non-polymers5,12612
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 , 10 types, 36 molecules 0123495678ABCDEFGHIJKLMNOPQRST...

#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.: 3 / 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 Spectrin alpha, erythrocytic 1


Mass: 281361.031 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A5G2R924
#5: Protein
Actin, cytoplasmic 1


Mass: 41782.660 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: Q6QAQ1
#6: 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
#7: Protein Tropomyosin-1.9


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


Mass: 29080.742 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: Q6QA25
#9: 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
#10: 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, 12 molecules

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


Mass: 427.201 Da / Num. of mol.: 12 / 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-#10 / 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: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 43000 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00575690
ELECTRON MICROSCOPYf_angle_d0.868102304
ELECTRON MICROSCOPYf_dihedral_angle_d6.210324
ELECTRON MICROSCOPYf_chiral_restr0.04911438
ELECTRON MICROSCOPYf_plane_restr0.00613212

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