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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-adducinADD2
  • 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 / 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 ...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 / spectrin / Clathrin-mediated endocytosis / lens fiber cell development / myofibril assembly / spectrin-associated cytoskeleton / negative regulation of peptidyl-tyrosine phosphorylation / negative regulation of substrate adhesion-dependent cell spreading / cellular response to cytochalasin B / 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 / positive regulation of fibroblast migration / regulation of lamellipodium assembly / tight junction / RHO GTPases activate IQGAPs / RHO GTPases Activate Formins / regulation of norepinephrine uptake / lamellipodium assembly / regulation of synaptic vesicle endocytosis / NuA4 histone acetyltransferase complex / apical junction complex / establishment or maintenance of cell polarity / spectrin binding / cortical cytoskeleton / tropomyosin binding / negative regulation of peptidyl-threonine phosphorylation / nitric-oxide synthase binding / erythrocyte development / kinesin binding / calyx of Held / brush border / striated muscle thin filament / actin filament bundle assembly / : / positive regulation of double-strand break repair via homologous recombination / positive regulation of blood coagulation / regulation of protein localization to plasma membrane / negative regulation of peptidyl-serine phosphorylation / cellular response to cAMP / 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 filament binding / actin cytoskeleton / lamellipodium / actin binding / regulation of cell shape / cytoplasmic vesicle / protein-containing complex assembly / postsynaptic density / cytoskeleton / hydrolase activity / regulation of cell cycle / ribonucleoprotein complex / axon / signaling receptor binding / focal adhesion / glutamatergic synapse / synapse / protein kinase binding / perinuclear region of cytoplasm / protein-containing complex / ATP binding / membrane / identical protein binding / nucleus / plasma membrane
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 / 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 / Leucine-rich repeat domain superfamily / ATPase, nucleotide binding domain / 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 / 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 1.1May 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
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
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 , 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 / ADD2


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 / Adenosine 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

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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 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: 3.5 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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