[English] 日本語
Yorodumi
- PDB-8iah: Structure of mammalian spectrin-actin junctional complex of membr... -

+
Open data


ID or keywords:

Loading...

-
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-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 / regulation of cellular component size / RAF/MAP kinase cascade / pointed-end actin filament capping / endoplasmic reticulum tubular network organization / 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 ...NCAM signaling for neurite out-growth / regulation of cellular component size / RAF/MAP kinase cascade / pointed-end actin filament capping / endoplasmic reticulum tubular network organization / 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 / lymphocyte homeostasis / UCH proteinases / lens fiber cell development / Gap junction degradation / Formation of annular gap junctions / RHOF GTPase cycle / Clathrin-mediated endocytosis / Formation of the dystrophin-glycoprotein complex (DGC) / spectrin-associated cytoskeleton / porphyrin-containing compound biosynthetic process / negative regulation of substrate adhesion-dependent cell spreading / cuticular plate / myofibril assembly / smooth endoplasmic reticulum calcium ion homeostasis / positive regulation of cellular component organization / platelet dense tubular network membrane / plasma membrane organization / negative regulation of focal adhesion assembly / regulation of filopodium assembly / cell projection membrane / cellular response to cytochalasin B / regulation of transepithelial transport / morphogenesis of a polarized epithelium / COP9 signalosome / structural constituent of postsynaptic actin cytoskeleton / protein localization to adherens junction / dense body / actin filament capping / Tat protein binding / postsynaptic actin cytoskeleton / regulation of lamellipodium assembly / adherens junction assembly / apical protein localization / RHO GTPases activate IQGAPs / RHO GTPases Activate Formins / positive regulation of fibroblast migration / tight junction / ankyrin binding / COPI-mediated anterograde transport / apical junction complex / positive regulation of wound healing / cortical actin cytoskeleton / spectrin binding / tropomyosin binding / regulation of norepinephrine uptake / erythrocyte development / nitric-oxide synthase binding / transporter regulator activity / cortical cytoskeleton / myofibril / establishment or maintenance of cell polarity / NuA4 histone acetyltransferase complex / smooth endoplasmic reticulum / brush border / hemopoiesis / striated muscle thin filament / kinesin binding / regulation of synaptic vesicle endocytosis / regulation of protein localization to plasma membrane / positive regulation of double-strand break repair via homologous recombination / positive regulation of T cell proliferation / cytoskeleton organization / axonogenesis / actin filament organization / muscle contraction / cellular response to cAMP / calyx of Held / nitric-oxide synthase regulator activity / adult locomotory behavior / cell projection / adherens junction / actin filament / cell motility / synapse organization / structural constituent of cytoskeleton / SH3 domain binding / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / Schaffer collateral - CA1 synapse / cytoplasmic ribonucleoprotein granule / actin filament binding / cell junction / nucleosome / regulation of cell shape / actin cytoskeleton
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 / Class II Aldolase and Adducin N-terminal domain / Class II Aldolase and Adducin N-terminal domain / Class II aldolase/adducin N-terminal domain superfamily / Villin headpiece / Villin headpiece domain superfamily / Villin headpiece domain / Headpiece (HP) domain profile. / Villin headpiece domain / EF-hand, Ca insensitive / Ca2+ insensitive EF hand / Ca2+ insensitive EF hand / Tropomyosins signature. / Tropomyosin / Tropomyosin / Spectrin repeat / Spectrin repeat / DNA repair protein XRCC4-like, C-terminal / Actinin-type actin-binding domain signature 1. / Actinin-type actin-binding domain signature 2. / Spectrin/alpha-actinin / Spectrin repeats / Actinin-type actin-binding domain, conserved site / Calponin homology domain / Leucine-rich repeat, LRR (right-handed beta-alpha superhelix) / Ribonuclease Inhibitor / Calponin homology (CH) domain / ATPase, substrate binding domain, subdomain 4 / Calponin homology domain / CH domain superfamily / Calponin homology (CH) domain profile. / Alpha-Beta Horseshoe / 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
Revision 1.0May 3, 2023Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0May 3, 2023Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
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 1.0May 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
Revision 1.0May 3, 2023Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
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 1.0May 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
Revision 1.0May 3, 2023Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
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 1.3Jul 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
Components

-
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

-
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

-
Details

Has ligand of interestY
Has protein modificationN

-
Experimental details

-
Experiment

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

-
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 %

-
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)

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more