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- PDB-9zzk: One Lmod2 and incoming actin at the pointed end of F-actin -

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Basic information

Entry
Database: PDB / ID: 9zzk
TitleOne Lmod2 and incoming actin at the pointed end of F-actin
Components
  • Actin, alpha skeletal muscle
  • Leiomodin-2
KeywordsSTRUCTURAL PROTEIN / actin / Lmod2 / leiomodin
Function / homology
Function and homology information


pointed-end actin filament capping / actin nucleation / myofibril assembly / positive regulation of actin filament polymerization / sarcomere organization / M band / cytoskeletal motor activator activity / myosin heavy chain binding / tropomyosin binding / actin filament bundle ...pointed-end actin filament capping / actin nucleation / myofibril assembly / positive regulation of actin filament polymerization / sarcomere organization / M band / cytoskeletal motor activator activity / myosin heavy chain binding / tropomyosin binding / actin filament bundle / troponin I binding / filamentous actin / mesenchyme migration / myofibril / skeletal muscle myofibril / striated muscle thin filament / actin filament bundle assembly / skeletal muscle thin filament assembly / actin monomer binding / skeletal muscle fiber development / stress fiber / actin filament polymerization / titin binding / muscle contraction / actin filament organization / sarcomere / filopodium / actin filament / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / calcium-dependent protein binding / lamellipodium / actin binding / cell body / cytoskeleton / protein domain specific binding / hydrolase activity / positive regulation of gene expression / calcium ion binding / magnesium ion binding / ATP binding / identical protein binding / cytoplasm
Similarity search - Function
Tropomodulin / Tropomodulin / TMOD/LMOD Leucine-rich domain / WH2 domain / WH2 domain profile. / Actins signature 1. / Actin, conserved site / Actins signature 2. / Actin/actin-like conserved site / Actins and actin-related proteins signature. ...Tropomodulin / Tropomodulin / TMOD/LMOD Leucine-rich domain / WH2 domain / WH2 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 / Leucine-rich repeat domain superfamily / ATPase, nucleotide binding domain
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / ADENOSINE-5'-TRIPHOSPHATE / Actin, alpha skeletal muscle / Leiomodin-2
Similarity search - Component
Biological speciesHomo sapiens (human)
Oryctolagus cuniculus (rabbit)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.06 Å
AuthorsBrotzman, S.B. / Palmer, N.J. / Dominguez, R.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)5R01GM152412 United States
National Institutes of Health/National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIH/NIAMS)5R01GM073791 United States
National Institutes of Health/National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIH/NIAMS)5T32AR053461-20 United States
CitationJournal: Nat Commun / Year: 2026
Title: Leiomodin 2 is a processive pointed-end elongator of actin filaments.
Authors: Sudipta Biswas / Tania M Larrinaga / Sandeep Choubey / Carol C Gregorio / Shashank Shekhar /
Abstract: The actin cytoskeleton drives essential processes like cell migration and muscle contraction. While barbed-end polymerization is well-established, pointed-end elongation was long considered ...The actin cytoskeleton drives essential processes like cell migration and muscle contraction. While barbed-end polymerization is well-established, pointed-end elongation was long considered impossible in vivo. Here, we demonstrate that Leiomodin 2 (Lmod2), which localizes to thin-filament pointed ends in striated muscle cells, functions as an actin polymerase for pointed-end elongation. Single-molecule and single-filament imaging reveal that Lmod2 remains processively bound to pointed ends in vitro, enabling elongation even in the presence of high profilin concentrations found in the cytoplasm that otherwise would cause depolymerization of free pointed ends. Kinetic analysis indicates that Lmod2-mediated elongation proceeds through a linked two-step mechanism, in which monomer addition is followed by a first-order transition at the Lmod2-bound pointed end that limits elongation at high actin concentrations. Lmod2's activity also persists in the presence of tropomyosin, underscoring its physiological relevance. Both processivity and elongation rate of Lmod2 are dependent on its WH2 domain. Remarkably, human dilated cardiomyopathy-associated mutations in Lmod2 greatly reduce Lmod2's pointed-end elongation activity, providing a potential mechanism for disease progression and supporting a role for Lmod2-mediated polymerization in the formation and maintenance of muscle sarcomeres.
History
DepositionJan 7, 2026Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 24, 2026Provider: repository / Type: Initial release
Revision 1.0Jun 24, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jun 24, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Jun 24, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jun 24, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jun 24, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jun 24, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1Aug 5, 2026Group: Data collection / Database references / Category: citation / citation_author / em_admin
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Revision 1.1Aug 5, 2026Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Database references / Experimental summary / Data content type: EM metadata / EM metadata / EM metadata / Category: citation / citation_author / em_admin
Data content type: EM metadata / EM metadata ...EM metadata / EM metadata / EM metadata / EM metadata / EM metadata / EM metadata / EM metadata / EM metadata / EM metadata / EM metadata
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _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, alpha skeletal muscle
B: Actin, alpha skeletal muscle
C: Actin, alpha skeletal muscle
D: Actin, alpha skeletal muscle
E: Actin, alpha skeletal muscle
M: Leiomodin-2
O: Actin, alpha skeletal muscle
hetero molecules


Theoretical massNumber of molelcules
Total (without water)316,90819
Polymers314,1197
Non-polymers2,78912
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein
Actin, alpha skeletal muscle / Alpha-actin-1


Mass: 41875.633 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / Tissue: skeletal muscle
References: UniProt: P68135, Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement
#2: Protein Leiomodin-2 / Cardiac leiomodin / C-LMOD / Leiomodin


Mass: 62865.445 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LMOD2
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q6P5Q4
#3: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 5 / 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.: 6 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
Has ligand of interestN
Has protein modificationY

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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

Component
IDNameTypeEntity IDParent-IDSource
1One Lmod2 and incoming actin at the pointed end of F-actinCOMPLEX#1-#20MULTIPLE SOURCES
2F-actinCOMPLEX#11NATURAL
Molecular weight
IDEntity assembly-IDValue (°)Experimental value
11NO
211.5 kDa/nmYES
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
21Homo sapiens (human)9606
32Oryctolagus cuniculus (rabbit)9986
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-ID
21Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)866768
32Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)866768
Buffer solutionpH: 7.5
Buffer component
IDConc.NameFormulaBuffer-ID
120 mMHEPESC8H18N2O4S1
250 mMPotassium acetateKAc1
31 mMEGTAC14H24N2O101
41 mMmagnesium chlorideMgCl21
50.2 mMadenosine triphosphateATP1
61 mMDTTC4H10O2S21
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 81000 X / Nominal defocus max: 2500 nm / Nominal defocus min: 500 nm
Image recordingElectron dose: 49 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software
IDNameVersionCategoryImage processing-ID
1cryoSPARCparticle selection1
2EPUimage acquisition
7Cootmodel fitting
12PHENIX3D reconstruction1
13cryoSPARCparticle selection2
18PHENIX3D reconstruction2
19PHENIX1.21.2_5419model refinement
Image processing
IDImage recording-ID
11
21
CTF correction
IDEM image processing-IDType
11NONE
22NONE
3D reconstruction
IDResolution (Å)Resolution methodNum. of particlesImage processing-IDEntry-IDSymmetry type
14.06FSC 0.143 CUT-OFF1295519ZZKPOINT
24.06FSC 0.143 CUT-OFF1295519ZZKPOINT
34.06FSC 0.143 CUT-OFF1295519ZZKPOINT
44.06FSC 0.143 CUT-OFF1295519ZZKPOINT
54.06FSC 0.143 CUT-OFF1295529ZZKPOINT
64.06FSC 0.143 CUT-OFF1295529ZZKPOINT
74.06FSC 0.143 CUT-OFF1295529ZZKPOINT
84.06FSC 0.143 CUT-OFF1295529ZZKPOINT
Atomic model buildingPDB-ID: 8F8S

8f8s


Accession code: 8F8S / Source name: PDB / Type: experimental model
RefinementHighest resolution: 4.06 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00619187
ELECTRON MICROSCOPYf_angle_d1.28826036
ELECTRON MICROSCOPYf_dihedral_angle_d8.5582684
ELECTRON MICROSCOPYf_chiral_restr0.0692912
ELECTRON MICROSCOPYf_plane_restr0.013327

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