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- PDB-7ztc: Non-muscle F-actin decorated with non-muscle tropomyosin 1.6 -

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Basic information

Entry
Database: PDB / ID: 7ztc
TitleNon-muscle F-actin decorated with non-muscle tropomyosin 1.6
Components
  • Non-muscle tropomyosin 1.6
  • actin, cytoplasmic 1
KeywordsCYTOSOLIC PROTEIN / actin / tropomyosin / non-muscle / complex
Function / homology
Function and homology information


Actins signature 1. / Actin, conserved site / Actins signature 2. / Actin/actin-like conserved site / Actins and actin-related proteins signature. / Actin / Actin family / Actin / ATPase, nucleotide binding domain
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / Actin, cytoplasmic 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 3.9 Å
AuthorsSelvaraj, M. / Kokate, S. / Kogan, K. / Kotila, T. / Kremneva, E. / Lappalainen, P. / Huiskonen, J.T.
Funding support Finland, 2items
OrganizationGrant numberCountry
Academy of Finland302161 Finland
Sigrid Juselius Foundation4708344 Finland
CitationJournal: Cell Rep / Year: 2023
Title: Structural basis underlying specific biochemical activities of non-muscle tropomyosin isoforms.
Authors: Muniyandi Selvaraj / Shrikant B Kokate / Gabriella Reggiano / Konstantin Kogan / Tommi Kotila / Elena Kremneva / Frank DiMaio / Pekka Lappalainen / Juha T Huiskonen /
Abstract: The actin cytoskeleton is critical for cell migration, morphogenesis, endocytosis, organelle dynamics, and cytokinesis. To support diverse cellular processes, actin filaments form a variety of ...The actin cytoskeleton is critical for cell migration, morphogenesis, endocytosis, organelle dynamics, and cytokinesis. To support diverse cellular processes, actin filaments form a variety of structures with specific architectures and dynamic properties. Key proteins specifying actin filaments are tropomyosins. Non-muscle cells express several functionally non-redundant tropomyosin isoforms, which differentially control the interactions of other proteins, including myosins and ADF/cofilin, with actin filaments. However, the underlying molecular mechanisms have remained elusive. By determining the cryogenic electron microscopy structures of actin filaments decorated by two functionally distinct non-muscle tropomyosin isoforms, Tpm1.6 and Tpm3.2, we reveal that actin filament conformation remains unaffected upon binding. However, Tpm1.6 and Tpm3.2 follow different paths along the actin filament major groove, providing an explanation for their incapability to co-polymerize on actin filaments. We also elucidate the molecular basis underlying specific roles of Tpm1.6 and Tpm3.2 in myosin II activation and protecting actin filaments from ADF/cofilin-catalyzed severing.
History
DepositionMay 9, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 11, 2023Provider: repository / Type: Initial release
Revision 1.1Feb 15, 2023Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.year
Revision 1.2Jul 24, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / em_3d_fitting_list / em_admin
Item: _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id ..._em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type / _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
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
W: Non-muscle tropomyosin 1.6
X: Non-muscle tropomyosin 1.6
Y: Non-muscle tropomyosin 1.6
Z: Non-muscle tropomyosin 1.6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)383,70820
Polymers380,29012
Non-polymers3,4188
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: assay for oligomerization, co-sedimentation assay
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area31760 Å2
ΔGint-239 kcal/mol
Surface area147440 Å2
MethodPISA

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Components

#1: Protein
actin, cytoplasmic 1


Mass: 41782.660 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Tissue: Platelets / References: UniProt: A0A6I9HGD1
#2: Protein
Non-muscle tropomyosin 1.6


Mass: 11507.176 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli BL21(DE3) (bacteria)
#3: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM
Has ligand of interestY

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Experimental details

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Experiment

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

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Sample preparation

Component
IDNameTypeEntity IDParent-IDSource
1Non-muscle F-actin decorated with non-muscle tropomyosin 1.6COMPLEX#1-#20RECOMBINANT
2Beta actin (non-muscle)ORGANELLE OR CELLULAR COMPONENT#11NATURAL
3Non-muscle tropomyosin 1.6ORGANELLE OR CELLULAR COMPONENT#21RECOMBINANT
Molecular weight
IDEntity assembly-IDExperimental value
11NO
21NO
31NO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
21Homo sapiens (human)9606
32Homo sapiens (human)9606
43Homo sapiens (human)9606
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-IDStrain
21Escherichia coli (E. coli)562BL21-DE3
32Escherichia coli (E. coli)562BL21-DE3
43Escherichia coli (E. coli)562BL21-DE3
Buffer solutionpH: 7.4
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: Talos Arctica / Image courtesy: FEI Company
MicroscopyModel: FEI TALOS ARCTICA
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 3000 nm / Nominal defocus min: 1000 nm
Image recordingAverage exposure time: 45 sec. / Electron dose: 45 e/Å2 / Film or detector model: FEI FALCON III (4k x 4k) / Num. of real images: 1700

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Processing

SoftwareName: PHENIX / Version: 1.19rc6_4061: / Classification: refinement
EM software
IDNameCategory
7ISOLDEmodel fitting
12RELION3D reconstruction
13PHENIXmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: -166.5 ° / Axial rise/subunit: 27.8 Å / Axial symmetry: C1
3D reconstructionResolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 79298 / Symmetry type: HELICAL
Atomic model buildingProtocol: OTHER / Space: REAL
Atomic model building
IDPDB-ID 3D fitting-IDAccession codeInitial refinement model-IDSource nameType
15JLF

5jlf

15JLF1PDBexperimental model
23J8A

3j8a

13J8A2PDBexperimental model
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00426160
ELECTRON MICROSCOPYf_angle_d0.84335608
ELECTRON MICROSCOPYf_dihedral_angle_d13.2889256
ELECTRON MICROSCOPYf_chiral_restr0.054084
ELECTRON MICROSCOPYf_plane_restr0.014600

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