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- EMDB-25494: T-Plastin-F-actin complex, parallel bundled state -

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Basic information

Entry
Database: EMDB / ID: EMD-25494
TitleT-Plastin-F-actin complex, parallel bundled state
Map datamain map, consensus
Sample
  • Complex: T-Plastin-F-actin complex, parallel bundled state
    • Protein or peptide: Actin, alpha skeletal muscle
    • Protein or peptide: Plastin-3
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: MAGNESIUM ION
Function / homology
Function and homology information


actin filament network formation / Striated Muscle Contraction / actin filament bundle / skeletal muscle thin filament assembly / actin filament bundle assembly / striated muscle thin filament / skeletal muscle fiber development / stress fiber / actin filament / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement ...actin filament network formation / Striated Muscle Contraction / actin filament bundle / skeletal muscle thin filament assembly / actin filament bundle assembly / striated muscle thin filament / skeletal muscle fiber development / stress fiber / actin filament / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / bone development / actin filament binding / hydrolase activity / calcium ion binding / ATP binding / plasma membrane / cytosol / cytoplasm
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 / ATPase, nucleotide binding domain / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair
Similarity search - Domain/homology
Plastin-3 / Actin, alpha skeletal muscle
Similarity search - Component
Biological speciesHomo sapiens (human) / Chicken (chicken)
Methodsingle particle reconstruction / cryo EM / Resolution: 9.0 Å
AuthorsMei L / Reynolds MJ / Alushin GM
Funding support United States, 2 items
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, 2021-
Header (metadata) releaseAug 31, 2022-
Map releaseAug 31, 2022-
UpdateSep 21, 2022-
Current statusSep 21, 2022Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_25494.png

Downloads & links

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Map

FileDownload / File: emd_25494.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationmain map, consensus
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.06 Å/pix.
x 256 pix.
= 527.36 Å		2.06 Å/pix.
x 256 pix.
= 527.36 Å		2.06 Å/pix.
x 256 pix.
= 527.36 Å

Surface

Projections

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Images are generated by Spider.

Voxel sizeX=Y=Z: 2.06 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.003
Minimum - Maximum-0.019256346 - 0.061132133
Average (Standard dev.)-4.043134e-05 (±0.0036947273)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 527.36 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_25494_msk_1.map
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Mask #2

Fileemd_25494_msk_2.map
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Mask #3

Fileemd_25494_msk_3.map
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Additional map: main map, body 1

Fileemd_25494_additional_1.map
Annotationmain map, body 1
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Additional map: main map, body 2

Fileemd_25494_additional_2.map
Annotationmain map, body 2
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Additional map: half-map 1, body002

Fileemd_25494_additional_3.map
Annotationhalf-map 1, body002
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Additional map: half-map 1, body001

Fileemd_25494_additional_4.map
Annotationhalf-map 1, body001
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Additional map: half-map 2, body001

Fileemd_25494_additional_5.map
Annotationhalf-map 2, body001
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Additional map: half-map 2, body002

Fileemd_25494_additional_6.map
Annotationhalf-map 2, body002
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Half map: half-map 2, consensus

Fileemd_25494_half_map_1.map
Annotationhalf-map 2, consensus
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Half map: half-map 1, consensus

Fileemd_25494_half_map_2.map
Annotationhalf-map 1, consensus
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Sample components

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Entire : T-Plastin-F-actin complex, parallel bundled state

EntireName: T-Plastin-F-actin complex, parallel bundled state
Components
  • Complex: T-Plastin-F-actin complex, parallel bundled state
    • Protein or peptide: Actin, alpha skeletal muscle
    • Protein or peptide: Plastin-3
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: MAGNESIUM ION

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Supramolecule #1: T-Plastin-F-actin complex, parallel bundled state

SupramoleculeName: T-Plastin-F-actin complex, parallel bundled state / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Details: Parallel actin bundles formed by actin-crosslinking T-plastin
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 27.5 kDa/nm

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Macromolecule #1: Actin, alpha skeletal muscle

MacromoleculeName: Actin, alpha skeletal muscle / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Chicken (chicken)
Molecular weightTheoretical: 42.109973 KDa
SequenceString: MCDEDETTAL VCDNGSGLVK AGFAGDDAPR AVFPSIVGRP RHQGVMVGMG QKDSYVGDEA QSKRGILTLK YPIE(HIC)G IIT NWDDMEKIWH HTFYNELRVA PEEHPTLLTE APLNPKANRE KMTQIMFETF NVPAMYVAIQ AVLSLYASGR TTGIVLD SG DGVTHNVPIY ...String:
MCDEDETTAL VCDNGSGLVK AGFAGDDAPR AVFPSIVGRP RHQGVMVGMG QKDSYVGDEA QSKRGILTLK YPIE(HIC)G IIT NWDDMEKIWH HTFYNELRVA PEEHPTLLTE APLNPKANRE KMTQIMFETF NVPAMYVAIQ AVLSLYASGR TTGIVLD SG DGVTHNVPIY EGYALPHAIM RLDLAGRDLT DYLMKILTER GYSFVTTAER EIVRDIKEKL CYVALDFENE MATAASSS S LEKSYELPDG QVITIGNERF RCPETLFQPS FIGMESAGIH ETTYNSIMKC DIDIRKDLYA NNVMSGGTTM YPGIADRMQ KEITALAPST MKIKIIAPPE RKYSVWIGGS ILASLSTFQQ MWITKQEYDE AGPSIVHRKC F

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Macromolecule #2: Plastin-3

MacromoleculeName: Plastin-3 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 70.896867 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MDEMATTQIS KDELDELKEA FAKVDLNSNG FICDYELHEL FKEANMPLPG YKVREIIQKL MLDGDRNKDG KISFDEFVYI FQEVKSSDI AKTFRKAINR KEGICALGGT SELSSEGTQH SYSEEEKYAF VNWINKALEN DPDCRHVIPM NPNTDDLFKA V GDGIVLCK ...String:
MDEMATTQIS KDELDELKEA FAKVDLNSNG FICDYELHEL FKEANMPLPG YKVREIIQKL MLDGDRNKDG KISFDEFVYI FQEVKSSDI AKTFRKAINR KEGICALGGT SELSSEGTQH SYSEEEKYAF VNWINKALEN DPDCRHVIPM NPNTDDLFKA V GDGIVLCK MINLSVPDTI DERAINKKKL TPFIIQENLN LALNSASAIG CHVVNIGAED LRAGKPHLVL GLLWQIIKIG LF ADIELSR NEALAALLRD GETLEELMKL SPEELLLRWA NFHLENSGWQ KINNFSADIK DSKAYFHLLN QIAPKGQKEG EPR IDINMS GFNETDDLKR AESMLQQADK LGCRQFVTPA DVVSGNPKLN LAFVANLFNK YPALTKPENQ DIDWTLLEGE TREE RTFRN WMNSLGVNPH VNHLYADLQD ALVILQLYER IKVPVDWSKV NKPPYPKLGA NMKKLENCNY AVELGKHPAK FSLVG IGGQ DLNDGNQTLT LALVWQLMRR YTLNVLEDLG DGQKANDDII VNWVNRTLSE AGKSTSIQSF KDKTISSSLA VVDLID AIQ PGCINYDLVK SGNLTEDDKH NNAKYAVSMA RRIGARVYAL PEDLVEVKPK MVMTVFACLM GRGMKRV

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Macromolecule #3: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 3 / Number of copies: 6 / Formula: ADP
Molecular weightTheoretical: 427.201 Da
Chemical component information

ChemComp-ADP:
ADENOSINE-5'-DIPHOSPHATE / ADP, energy-carrying molecule*YM

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Macromolecule #4: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 4 / Number of copies: 6 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation statefilament

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Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Digitization - Frames/image: 1-40 / Number grids imaged: 1 / Average exposure time: 10.0 sec. / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 656414 / Details: custom machine learning picking procedure
CTF correctionSoftware - Name: CTFFIND (ver. 4.0)
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

7r94

Final reconstructionNumber classes used: 1 / Resolution.type: BY AUTHOR / Resolution: 9.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Number images used: 41701
Initial angle assignmentType: PROJECTION MATCHING / Software - Name: RELION (ver. 3.1)
Final angle assignmentType: PROJECTION MATCHING / Software - Name: RELION (ver. 3.1)
Final 3D classificationNumber classes: 1 / Software - Name: RELION (ver. 3.1)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

7r94

Output model

PDB-7sx8:
T-Plastin-F-actin complex, parallel bundled state

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