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

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Basic information

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-adducinADD2
  • 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 / 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 / VEGFA-VEGFR2 Pathway / Cell-extracellular matrix interactions ...NCAM signaling for neurite out-growth / RAF/MAP kinase cascade / 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 / VEGFA-VEGFR2 Pathway / Cell-extracellular matrix interactions / RHO GTPases Activate WASPs and WAVEs / MAP2K and MAPK activation / cuticular plate / spectrin / Clathrin-mediated endocytosis / lymphocyte homeostasis / lens fiber cell development / myofibril assembly / spectrin-associated cytoskeleton / negative regulation of peptidyl-tyrosine phosphorylation / negative regulation of substrate adhesion-dependent cell spreading / porphyrin-containing compound biosynthetic process / cellular response to cytochalasin B / plasma membrane organization / platelet dense tubular network membrane / regulation of transepithelial transport / structural constituent of postsynaptic actin cytoskeleton / morphogenesis of a polarized epithelium / negative regulation of focal adhesion assembly / postsynaptic actin cytoskeleton / protein localization to adherens junction / cell projection membrane / dense body / Tat protein binding / regulation of filopodium assembly / COP9 signalosome / apical protein localization / actin filament capping / adherens junction assembly / RHO GTPases activate IQGAPs / RHO GTPases Activate Formins / regulation of lamellipodium assembly / positive regulation of fibroblast migration / tight junction / regulation of norepinephrine uptake / COPI-mediated anterograde transport / NuA4 histone acetyltransferase complex / regulation of synaptic vesicle endocytosis / apical junction complex / erythrocyte development / establishment or maintenance of cell polarity / spectrin binding / tropomyosin binding / positive regulation of double-strand break repair via homologous recombination / cortical cytoskeleton / negative regulation of peptidyl-threonine phosphorylation / nitric-oxide synthase binding / brush border / calyx of Held / striated muscle thin filament / kinesin binding / hemopoiesis / : / positive regulation of blood coagulation / regulation of protein localization to plasma membrane / negative regulation of peptidyl-serine phosphorylation / cellular response to cAMP / positive regulation of T cell proliferation / cellular response to calcium ion / axonogenesis / adult locomotory behavior / muscle contraction / cell motility / actin filament / regulation of actin cytoskeleton organization / adherens junction / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / Schaffer collateral - CA1 synapse / structural constituent of cytoskeleton / cytoplasmic ribonucleoprotein granule / : / nucleosome / actin cytoskeleton / positive regulation of protein binding / lamellipodium / actin binding / regulation of cell shape / cytoplasmic vesicle / actin cytoskeleton organization / protein-containing complex assembly / postsynaptic density / cytoskeleton / regulation of cell cycle / hydrolase activity / ribonucleoprotein complex / axon / signaling receptor binding / focal adhesion / synapse / glutamatergic synapse
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 / Villin headpiece / Villin headpiece domain superfamily / Villin headpiece domain ...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 / Villin headpiece / Villin headpiece domain superfamily / Villin headpiece domain / Headpiece (HP) domain profile. / Villin headpiece domain / Class II aldolase/adducin N-terminal / Class II Aldolase and Adducin N-terminal domain / Class II Aldolase and Adducin N-terminal domain / Class II aldolase/adducin N-terminal domain superfamily / Tropomyosins signature. / Tropomyosin / Tropomyosin / EF-hand, Ca insensitive / Ca2+ insensitive EF hand / Ca2+ insensitive EF hand / DNA repair protein XRCC4-like, C-terminal / Spectrin repeat / Spectrin repeat / Spectrin/alpha-actinin / Actinin-type actin-binding domain signature 1. / Actinin-type actin-binding domain signature 2. / Spectrin repeats / 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. / 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 / ATPase, nucleotide binding domain / Src homology 3 domains / EF-hand calcium-binding domain profile. / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / EF-hand domain / EF-hand domain pair / Thioredoxin-like superfamily
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / Tropomodulin-1 / Spectrin beta chain / Beta-adducin / SH3 domain-binding glutamic acid-rich-like protein / Spectrin alpha, erythrocytic 1 / 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: 3.6 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 1.1May 10, 2023Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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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
Water0
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 / ADD2


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 / Adenosine 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

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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 FIELDBright-field microscopy / 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
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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