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- EMDB-21155: Cryo-EM structure of F-actin/Plastin2-ABD2 complex -

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Basic information

Entry
Database: EMDB / ID: EMD-21155
TitleCryo-EM structure of F-actin/Plastin2-ABD2 complex
Map dataCryo-EM structure of F-actin/Plastin2-ABD2 complex
Sample
  • Complex: Complex of Plastin2-ABD2 with F-actin
    • Complex: F-actin
      • Protein or peptide: Actin, alpha skeletal muscle
    • Complex: Plastin2-ABD2
      • Protein or peptide: LCP1
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: MAGNESIUM ION
KeywordsF-actin / Plastin 2 / Helical reconstruction / PROTEIN FIBRIL
Function / homology
Function and homology information


actin filament network formation / actin crosslink formation / T cell activation involved in immune response / podosome / positive regulation of podosome assembly / cortical actin cytoskeleton organization / cytoskeletal motor activator activity / tropomyosin binding / mesenchyme migration / regulation of intracellular protein transport ...actin filament network formation / actin crosslink formation / T cell activation involved in immune response / podosome / positive regulation of podosome assembly / cortical actin cytoskeleton organization / cytoskeletal motor activator activity / tropomyosin binding / mesenchyme migration / regulation of intracellular protein transport / troponin I binding / myosin heavy chain binding / filamentous actin / actin filament bundle / glial cell projection / skeletal muscle thin filament assembly / phagocytic cup / striated muscle thin filament / actin filament bundle assembly / skeletal muscle myofibril / actin monomer binding / extracellular matrix disassembly / animal organ regeneration / skeletal muscle fiber development / stress fiber / titin binding / ruffle / protein kinase A signaling / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / actin filament polymerization / filopodium / actin filament / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / ruffle membrane / calcium-dependent protein binding / actin filament binding / cell migration / actin cytoskeleton / integrin binding / lamellipodium / GTPase binding / cell junction / actin binding / cell body / hydrolase activity / protein domain specific binding / focal adhesion / calcium ion binding / positive regulation of gene expression / perinuclear region of cytoplasm / magnesium ion binding / extracellular space / extracellular exosome / ATP binding / identical protein binding / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Plastin-2/3 / 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. ...Plastin-2/3 / 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-2 / Actin, alpha skeletal muscle / Epididymis secretory protein Li 37
Similarity search - Component
Biological speciesOryctolagus cuniculus (rabbit) / Homo sapiens (human)
Methodhelical reconstruction / cryo EM / Resolution: 3.9 Å
AuthorsZheng W / Kudryashov DS
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM122510 United States
CitationJournal: Bone Res / Year: 2020
Title: Osteogenesis imperfecta mutations in plastin 3 lead to impaired calcium regulation of actin bundling.
Authors: Christopher L Schwebach / Elena Kudryashova / Weili Zheng / Matthew Orchard / Harper Smith / Lucas A Runyan / Edward H Egelman / Dmitri S Kudryashov /
Abstract: Mutations in actin-bundling protein plastin 3 (PLS3) emerged as a cause of congenital osteoporosis, but neither the role of PLS3 in bone development nor the mechanisms underlying PLS3-dependent ...Mutations in actin-bundling protein plastin 3 (PLS3) emerged as a cause of congenital osteoporosis, but neither the role of PLS3 in bone development nor the mechanisms underlying PLS3-dependent osteoporosis are understood. Of the over 20 identified osteoporosis-linked PLS3 mutations, we investigated all five that are expected to produce full-length protein. One of the mutations distorted an actin-binding loop in the second actin-binding domain of PLS3 and abolished F-actin bundling as revealed by cryo-EM reconstruction and protein interaction assays. Surprisingly, the remaining four mutants fully retained F-actin bundling ability. However, they displayed defects in Ca sensitivity: two of the mutants lost the ability to be inhibited by Ca, while the other two became hypersensitive to Ca. Each group of the mutants with similar biochemical properties showed highly characteristic cellular behavior. Wild-type PLS3 was distributed between lamellipodia and focal adhesions. In striking contrast, the Ca-hyposensitive mutants were not found at the leading edge but localized exclusively at focal adhesions/stress fibers, which displayed reinforced morphology. Consistently, the Ca-hypersensitive PLS3 mutants were restricted to lamellipodia, while chelation of Ca caused their redistribution to focal adhesions. Finally, the bundling-deficient mutant failed to co-localize with any F-actin structures in cells despite a preserved F-actin binding through a non-mutation-bearing actin-binding domain. Our findings revealed that severe osteoporosis can be caused by a mutational disruption of the Ca-controlled PLS3's cycling between adhesion complexes and the leading edge. Integration of the structural, biochemical, and cell biology insights enabled us to propose a molecular mechanism of plastin activity regulation by Ca.
History
DepositionDec 31, 2019-
Header (metadata) releaseJan 15, 2020-
Map releaseDec 9, 2020-
UpdateMar 6, 2024-
Current statusMar 6, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0611
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.0611
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6vec
  • Surface level: 0.0611
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_21155.png

Downloads & links

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Map

FileDownload / File: emd_21155.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-EM structure of F-actin/Plastin2-ABD2 complex
Voxel sizeX=Y=Z: 1.4 Å
Density
Contour LevelBy AUTHOR: 0.0611 / Movie #1: 0.0611
Minimum - Maximum-0.08551913 - 0.26118404
Average (Standard dev.)0.0000426111 (±0.011353404)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 358.4 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.41.41.4
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z358.400358.400358.400
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS256256256
D min/max/mean-0.0860.2610.000

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Supplemental data

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Sample components

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Entire : Complex of Plastin2-ABD2 with F-actin

EntireName: Complex of Plastin2-ABD2 with F-actin
Components
  • Complex: Complex of Plastin2-ABD2 with F-actin
    • Complex: F-actin
      • Protein or peptide: Actin, alpha skeletal muscle
    • Complex: Plastin2-ABD2
      • Protein or peptide: LCP1
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: MAGNESIUM ION

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Supramolecule #1: Complex of Plastin2-ABD2 with F-actin

SupramoleculeName: Complex of Plastin2-ABD2 with F-actin / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2

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Supramolecule #2: F-actin

SupramoleculeName: F-actin / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Oryctolagus cuniculus (rabbit)

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Supramolecule #3: Plastin2-ABD2

SupramoleculeName: Plastin2-ABD2 / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Actin, alpha skeletal muscle

MacromoleculeName: Actin, alpha skeletal muscle / type: protein_or_peptide / ID: 1 / Number of copies: 11 / Enantiomer: LEVO
Source (natural)Organism: Oryctolagus cuniculus (rabbit)
Molecular weightTheoretical: 42.096953 KDa
SequenceString: MCDEDETTAL VCDNGSGLVK AGFAGDDAPR AVFPSIVGRP RHQGVMVGMG QKDSYVGDEA QSKRGILTLK YPIEHGIITN WDDMEKIWH HTFYNELRVA PEEHPTLLTE APLNPKANRE KMTQIMFETF NVPAMYVAIQ AVLSLYASGR TTGIVLDSGD G VTHNVPIY ...String:
MCDEDETTAL VCDNGSGLVK AGFAGDDAPR AVFPSIVGRP RHQGVMVGMG QKDSYVGDEA QSKRGILTLK YPIEHGIITN WDDMEKIWH HTFYNELRVA PEEHPTLLTE APLNPKANRE KMTQIMFETF NVPAMYVAIQ AVLSLYASGR TTGIVLDSGD G VTHNVPIY EGYALPHAIM RLDLAGRDLT DYLMKILTER GYSFVTTAER EIVRDIKEKL CYVALDFENE MATAASSSSL EK SYELPDG QVITIGNERF RCPETLFQPS FIGMESAGIH ETTYNSIMKC DIDIRKDLYA NNVMSGGTTM YPGIADRMQK EIT ALAPST MKIKIIAPPE RKYSVWIGGS ILASLSTFQQ MWITKQEYDE AGPSIVHRKC F

UniProtKB: Actin, alpha skeletal muscle

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Macromolecule #2: LCP1

MacromoleculeName: LCP1 / type: protein_or_peptide / ID: 2 / Number of copies: 11 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 47.983633 KDa
Recombinant expressionOrganism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
SequenceString: MNHKVHHHHH HIEGRHMELG TLEENLYFQG ELADIELSRN EALIALLREG ESLEDLMKLS PEELLLRWAN YHLENAGCNK IGNFSTDIK DSKAYYHLLE QVAPKGDEEG VPAVVIDMSG LREKDDIQRA ECMLQQAERL GCRQFVTATD VVRGNPKLNL A FIANLFNR ...String:
MNHKVHHHHH HIEGRHMELG TLEENLYFQG ELADIELSRN EALIALLREG ESLEDLMKLS PEELLLRWAN YHLENAGCNK IGNFSTDIK DSKAYYHLLE QVAPKGDEEG VPAVVIDMSG LREKDDIQRA ECMLQQAERL GCRQFVTATD VVRGNPKLNL A FIANLFNR YPALHKPENQ DIDWGALEGE TREERTFRNW MNSLGVNPRV NHLYSDLSDA LVIFQLYEKI KVPVDWNRVN KP PYPKLGG NMKKLENCNY AVELGKNQAK FSLVGIGGQD LNEGNRTLTL ALIWQLMRRY TLNILEEIGG GQKVNDDIIV NWV NETLRE AEKSSSISSF KDPKISTSLP VLDLIDAIQP GSINYDLLKT ENLNDDEKLN NAKYAISMAR KIGARVYALP EDLV EVNPK MVMTVFACLM GKGMKRV

UniProtKB: Epididymis secretory protein Li 37

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Macromolecule #3: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 3 / Number of copies: 11 / 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: 11 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statefilament

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Sample preparation

BufferpH: 7.5
GridPretreatment - Type: PLASMA CLEANING / Details: unspecified
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Detector mode: INTEGRATING / Average electron dose: 20.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 28.0 Å
Applied symmetry - Helical parameters - Δ&Phi: -166.5 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 124092
Segment selectionNumber selected: 248184 / Software - Name: EMAN2
Startup modelType of model: OTHER
Final angle assignmentType: NOT APPLICABLE

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Atomic model buiding 1

Initial modelPDB ID:

5onv


Chain - Source name: PDB / Chain - Initial model type: experimental model
Output model

PDB-6vec:
Cryo-EM structure of F-actin/Plastin2-ABD2 complex

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