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- PDB-7sxa: T-Plastin-F-actin complex, pre-bundling intermediate state -

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Basic information

Entry
Database: PDB / ID: 7sxa
TitleT-Plastin-F-actin complex, pre-bundling intermediate state
Components
  • Actin, alpha skeletal muscle
  • Plastin-3
KeywordsSTRUCTURAL PROTEIN / T-plastin / plastin / actin / filopodium / cytoskeleton / cell protrusion
Function / homology
Function and homology information


structural constituent of presynaptic actin cytoskeleton / actin filament network formation / Striated Muscle Contraction / regulation of synaptic vesicle cycle / actin filament bundle / actin filament bundle assembly / striated muscle thin filament / skeletal muscle thin filament assembly / skeletal muscle fiber development / stress fiber ...structural constituent of presynaptic actin cytoskeleton / actin filament network formation / Striated Muscle Contraction / regulation of synaptic vesicle cycle / actin filament bundle / actin filament bundle assembly / striated muscle thin filament / skeletal muscle thin filament assembly / skeletal muscle fiber development / stress fiber / actin filament / neuromuscular junction / bone development / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / actin filament binding / actin cytoskeleton / hydrolase activity / calcium ion binding / ATP binding / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Fimbrin/Plastin / 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. / Actins signature 1. ...Fimbrin/Plastin / 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. / Actins signature 1. / Actin, conserved site / Actins signature 2. / Actin/actin-like conserved site / Actins and actin-related proteins signature. / Actin / Actin family / Actin / EF-hand domain pair / EF-hand, calcium binding motif / EF-Hand 1, calcium-binding site / ATPase, nucleotide binding domain / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / Plastin-3 / Actin, alpha skeletal muscle
Similarity search - Component
Biological speciesHomo sapiens (human)
Gallus gallus (chicken)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 6.87 Å
AuthorsMei, L. / Reynolds, M.J. / Alushin, G.M.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Dental and Craniofacial Research (NIH/NIDCR)5DP5OD017885 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM141044 United States
CitationJournal: Proc Natl Acad Sci U S A / Year: 2022
Title: Structural mechanism for bidirectional actin cross-linking by T-plastin.
Authors: Lin Mei / Matthew J Reynolds / Damien Garbett / Rui Gong / Tobias Meyer / Gregory M Alushin /
Abstract: To orchestrate cell mechanics, trafficking, and motility, cytoskeletal filaments must assemble into higher-order networks whose local subcellular architecture and composition specify their functions. ...To orchestrate cell mechanics, trafficking, and motility, cytoskeletal filaments must assemble into higher-order networks whose local subcellular architecture and composition specify their functions. Cross-linking proteins bridge filaments at the nanoscale to control a network's μm-scale geometry, thereby conferring its mechanical properties and functional dynamics. While these interfilament linkages are key determinants of cytoskeletal function, their structural mechanisms remain poorly understood. Plastins/fimbrins are an evolutionarily ancient family of tandem calponin-homology domain (CHD) proteins required to construct multiple classes of actin networks, which feature diverse geometries specialized to power cytokinesis, microvilli and stereocilia biogenesis, and persistent cell migration. Here, we focus on the structural basis of actin network assembly by human T-plastin, a ubiquitously expressed isoform necessary for the maintenance of stable cellular protrusions generated by actin polymerization forces. By implementing a machine-learning-enabled cryo-electron microscopy pipeline for visualizing cross-linkers bridging multiple filaments, we uncover a sequential bundling mechanism enabling T-plastin to bridge pairs of actin filaments in both parallel and antiparallel orientations. T-plastin populates distinct structural landscapes in these two bridging orientations that are selectively compatible with actin networks featuring divergent architectures and functions. Our structural, biochemical, and cell biological data highlight inter-CHD linkers as key structural elements underlying flexible but stable cross-linking that are likely to be disrupted by T-plastin mutations that cause hereditary bone diseases.
History
DepositionNov 22, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 31, 2022Provider: repository / Type: Initial release
Revision 1.1Sep 21, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Plastin-3
C: Actin, alpha skeletal muscle
B: Actin, alpha skeletal muscle
D: Actin, alpha skeletal muscle
hetero molecules


Theoretical massNumber of molelcules
Total (without water)198,58110
Polymers197,2274
Non-polymers1,3556
Water00
1


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

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Components

#1: Protein Plastin-3 / T-plastin


Mass: 70896.867 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PLS3 / Production host: Escherichia coli (E. coli) / References: UniProt: P13797
#2: Protein Actin, alpha skeletal muscle / Alpha-actin-1


Mass: 42109.973 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / References: UniProt: P68139
#3: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
Has ligand of interestN

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Experimental details

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Experiment

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

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Sample preparation

ComponentName: T-Plastin-F-actin complex, pre-bundling intermediate state
Type: COMPLEX
Details: The pre-bundling intermediate state of full-length human T-Plastin (PLS3) bound to F-actin, in the absence of calcium
Entity ID: #1-#2 / Source: MULTIPLE SOURCES
Molecular weightValue: 27.5 kDa/nm / Experimental value: NO
Source (natural)Organism: Homo sapiens (human)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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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
Image recordingAverage exposure time: 10 sec. / Electron dose: 60 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of grids imaged: 1
Image scansMovie frames/image: 40 / Used frames/image: 1-40

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Processing

SoftwareName: PHENIX / Version: 1.18.2_3874: / Classification: refinement
EM software
IDNameVersionCategory
2SerialEMimage acquisition
4CTFFIND4CTF correction
7Cootmodel fitting
9PHENIXmodel refinement
10RELION3.1initial Euler assignment
11RELION3.1final Euler assignment
12RELION3.1classification
13RELION3.13D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 656414 / Details: helical auto-picking
3D reconstructionResolution: 6.87 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 31413 / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingPDB-ID: 7R94

7r94

Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00611507
ELECTRON MICROSCOPYf_angle_d0.81915610
ELECTRON MICROSCOPYf_dihedral_angle_d13.7114286
ELECTRON MICROSCOPYf_chiral_restr0.0461742
ELECTRON MICROSCOPYf_plane_restr0.0052001

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