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- PDB-7q8b: Leishmania major actin filament in ADP-Pi state -

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Basic information

Entry
Database: PDB / ID: 7q8b
TitleLeishmania major actin filament in ADP-Pi state
ComponentsActin
KeywordsSTRUCTURAL PROTEIN / Actin / Filament / Parasite / ADP-Pi
Function / homology
Function and homology information


kinetoplast / actin cytoskeleton / endonuclease activity / chromatin remodeling
Similarity search - Function
ATPase, substrate binding domain, subdomain 4 / 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 ...ATPase, substrate binding domain, subdomain 4 / 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 / ATPase, nucleotide binding domain / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / PHOSPHATE ION / Actin
Similarity search - Component
Biological speciesLeishmania major (eukaryote)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsKotila, T. / Muniyandi, S. / Lappalainen, P. / Huiskonen, J.T.
Funding support Finland, 2items
OrganizationGrant numberCountry
Academy of Finland320161 Finland
Jane and Aatos Erkko Foundation4708679 Finland
CitationJournal: Nat Commun / Year: 2022
Title: Structural basis of rapid actin dynamics in the evolutionarily divergent Leishmania parasite.
Authors: Tommi Kotila / Hugo Wioland / Muniyandi Selvaraj / Konstantin Kogan / Lina Antenucci / Antoine Jégou / Juha T Huiskonen / Guillaume Romet-Lemonne / Pekka Lappalainen /
Abstract: Actin polymerization generates forces for cellular processes throughout the eukaryotic kingdom, but our understanding of the 'ancient' actin turnover machineries is limited. We show that, ...Actin polymerization generates forces for cellular processes throughout the eukaryotic kingdom, but our understanding of the 'ancient' actin turnover machineries is limited. We show that, despite > 1 billion years of evolution, pathogenic Leishmania major parasite and mammalian actins share the same overall fold and co-polymerize with each other. Interestingly, Leishmania harbors a simple actin-regulatory machinery that lacks cofilin 'cofactors', which accelerate filament disassembly in higher eukaryotes. By applying single-filament biochemistry we discovered that, compared to mammalian proteins, Leishmania actin filaments depolymerize more rapidly from both ends, and are severed > 100-fold more efficiently by cofilin. Our high-resolution cryo-EM structures of Leishmania ADP-, ADP-Pi- and cofilin-actin filaments identify specific features at actin subunit interfaces and cofilin-actin interactions that explain the unusually rapid dynamics of parasite actin filaments. Our findings reveal how divergent parasites achieve rapid actin dynamics using a remarkably simple set of actin-binding proteins, and elucidate evolution of the actin cytoskeleton.
History
DepositionNov 11, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 18, 2022Provider: repository / Type: Initial release
Revision 1.0May 18, 2022Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
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Revision 1.1Jun 29, 2022Group: Database references / Category: citation / citation_author
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Revision 1.2Oct 1, 2025Group: Advisory / Data collection ...Advisory / Data collection / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / em_admin / pdbx_entry_details / pdbx_validate_close_contact / struct_conn / struct_conn_type
Item: _em_admin.last_update / _pdbx_entry_details.has_protein_modification
Revision 1.1Oct 1, 2025Data content type: EM metadata / Data content type: EM metadata / Group: Experimental summary / Data content type: EM metadata / Category: em_admin / Data content type: EM metadata / Item: _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
B: Actin
C: Actin
D: Actin
E: Actin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)213,05220
Polymers210,3195
Non-polymers2,73215
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: microscopy
TypeNameSymmetry operationNumber
identity operation1_5551
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1chain "B"
d_2ens_1chain "A"
d_3ens_1chain "C"
d_4ens_1chain "D"
d_5ens_1chain "E"

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1SERPHEE1 - 370
d_12ens_1MGMGF
d_13ens_1ADPADPG
d_14ens_1PO4PO4H
d_21ens_1SERPHEA1 - 370
d_22ens_1MGMGB
d_23ens_1ADPADPC
d_24ens_1PO4PO4D
d_31ens_1SERPHEI1 - 370
d_32ens_1MGMGJ
d_33ens_1ADPADPK
d_34ens_1PO4PO4L
d_41ens_1SERPHEM1 - 370
d_42ens_1MGMGN
d_43ens_1ADPADPO
d_44ens_1PO4PO4P
d_51ens_1SERPHEQ1 - 370
d_52ens_1MGMGR
d_53ens_1ADPADPS
d_54ens_1PO4PO4T

NCS oper:
IDCodeMatrixVector
1given(0.89274339702, 0.4505654526, 1.79722766986E-7), (-0.4505654526, 0.89274339702, -2.41917947943E-7), (-2.69446183228E-7, 1.34993780798E-7, 1)-42.5840628488, 69.1922905831, -55.5399809706
2given(-0.972816408102, -0.231577710774, -5.93284644791E-7), (0.231577710774, -0.972816408102, -3.34861669799E-7), (-4.9961053821E-7, -4.63150426703E-7, 1)273.433130641, 215.983293967, -27.7698829998
3given(-0.972815986721, 0.231579480913, 8.57415848445E-7), (-0.231579480914, -0.972815986721, -4.66122573937E-7), (7.2616342092E-7, -6.52011408808E-7, 1)215.982909776, 273.433267529, 27.7699780507
4given(0.89274291362, -0.450566410401, 2.79385680808E-7), (0.450566410401, 0.89274291362, -2.91219653556E-7), (-1.18205792767E-7, 3.85866085338E-7, 1)69.1923696832, -42.5840714288, 55.5399728521

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Components

#1: Protein
Actin


Mass: 42063.867 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Leishmania major (eukaryote) / Gene: ACT, LMJF_04_1230 / Cell line (production host): ExpiSF / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q9U1E8
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM
#4: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: PO4 / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationN

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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

ComponentName: Polymerized actin / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Leishmania major (eukaryote)
Source (recombinant)Organism: Spodoptera frugiperda (fall armyworm)
Buffer solutionpH: 7.2
Details: Phosphate buffered saline supplemented with 0.2 mM ATP, 1 mM MgCl2, 0.4 mM EGTA and 1 mM DTT.
SpecimenConc.: 0.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 95 % / Chamber temperature: 279.15 K

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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 / Cs: 2.7 mm
Image recordingElectron dose: 45 e/Å2 / Film or detector model: FEI FALCON II (4k x 4k) / Num. of real images: 45

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Processing

Software
NameVersionClassification
phenix.real_space_refine1.19.2_4158refinement
PHENIX1.19.2_4158refinement
EM software
IDNameVersionCategory
1RELION3.1particle selection
4CTFFIND4.1CTF correction
7UCSF Chimera1.14model fitting
9RELION3.1initial Euler assignment
10RELION3.1final Euler assignment
11RELION3.1classification
12RELION3.13D reconstruction
13PHENIX1.19.2-4158-000model refinement
14ISOLDE1.1.1model refinement
15UCSF ChimeraX1.1.1model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: -166.61 ° / Axial rise/subunit: 27.77 Å / Axial symmetry: C1
3D reconstructionResolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 89543 / Algorithm: FOURIER SPACE / Symmetry type: HELICAL
Atomic model buildingSpace: REAL
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 16.46 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.002814955
ELECTRON MICROSCOPYf_angle_d0.496220280
ELECTRON MICROSCOPYf_chiral_restr0.04582235
ELECTRON MICROSCOPYf_plane_restr0.00352605
ELECTRON MICROSCOPYf_dihedral_angle_d8.8325610
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2EELECTRON MICROSCOPYNCS constraints0.000582812218343
ens_1d_3EELECTRON MICROSCOPYNCS constraints0.000583557041319
ens_1d_4EELECTRON MICROSCOPYNCS constraints0.000581180770052
ens_1d_5EELECTRON MICROSCOPYNCS constraints0.000581370212635

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