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- EMDB-77973: pointed end of actin filament with one Lmod2 molecule bound -

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Basic information

Entry
Database: EMDB / ID: EMD-77973
Titlepointed end of actin filament with one Lmod2 molecule bound
Map datapointed end of actin filament with one Lmod2 molecule bound
Sample
  • Complex: Actin, alpha skeletal muscle
    • Complex: Leiomodin-2
Keywordscryo-EM / actin / Lmod2 / actin filament / pointed end / motor protein
Biological speciesOryctolagus cuniculus (rabbit) / Mus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 8.5 Å
AuthorsRisi CM / Galkin VE
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM120137 United States
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)R01 HL160966 United States
CitationJournal: J Mol Cell Cardiol / Year: 2026
Title: Structure of the actively growing actin filament pointed end facilitated by Leiomodin-2.
Authors: Cristina M Risi / Tania M Larrinaga / Alla S Kostyukova / Carol C Gregorio / Vitold E Galkin /
Abstract: Cardiac contraction depends on synchronized interactions between myosin-based thick filaments and actin-based thin filaments (TFs). Precise regulation of TF length is vital for cardiac function, as ...Cardiac contraction depends on synchronized interactions between myosin-based thick filaments and actin-based thin filaments (TFs). Precise regulation of TF length is vital for cardiac function, as any alteration in length leads to severe myopathies. Actin filaments form the backbone of the TF and have two unequal ends - fast-growing barbed and slow-growing pointed. In muscle, the barbed end is capped at the Z-line, so the thin filament can elongate only from the pointed end. Leiomodin-2 (Lmod2) promotes actin nucleation and possesses a unique C-terminal extension (CTE) that is important for actin nucleation and binds to the sides of mature TFs. Single-molecule studies have shown that Lmod2 remains bound processively to the growing pointed end. We employed cryo-electron microscopy to visualize the structure of actively growing pointed ends in the presence of Lmod2 from G-actin complexed with profilin (profilactin). We show that Lmod2's leucine-rich repeat domain (LRR) stabilizes terminal actin subunits by binding across the helical groove of actin on one or both actin strands. LRR binding pushes the terminal actins outward from their ideal positions in the actin filament, introducing strain at the pointed end that squeezes Lmod2 from the filament's exterior, thereby maintaining the concentration of Lmod2 required for further elongation. Further, we suggest that the unique Lmod2 CTE may stabilize Lmod2 binding to the actively growing pointed end.
History
DepositionJul 7, 2026-
Header (metadata) releaseOct 21, 2026-
Map releaseOct 21, 2026-
UpdateOct 21, 2026-
Current statusOct 21, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_77973.png

Downloads & links

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Map

FileDownload / File: emd_77973.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationpointed end of actin filament with one Lmod2 molecule bound
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.36 Å/pix.
x 400 pix.
= 542.4 Å		1.36 Å/pix.
x 400 pix.
= 542.4 Å		1.36 Å/pix.
x 400 pix.
= 542.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.356 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.7
Minimum - Maximum-3.1549873 - 5.739662
Average (Standard dev.)0.00027118673 (±0.14717339)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 542.39996 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half Map A

Fileemd_77973_half_map_1.map
AnnotationHalf Map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half Map B

Fileemd_77973_half_map_2.map
AnnotationHalf Map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Actin, alpha skeletal muscle

EntireName: Actin, alpha skeletal muscle
Components
  • Complex: Actin, alpha skeletal muscle
    • Complex: Leiomodin-2

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Supramolecule #1: Actin, alpha skeletal muscle

SupramoleculeName: Actin, alpha skeletal muscle / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Oryctolagus cuniculus (rabbit)

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Supramolecule #2: Leiomodin-2

SupramoleculeName: Leiomodin-2 / type: complex / ID: 2 / Parent: 1
Source (natural)Organism: Mus musculus (house mouse)

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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
GridModel: EMS Lacey Carbon / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: LACEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 45 sec.
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 4 / Number real images: 11689 / Average electron dose: 34.0 e/Å2 / Details: 40 frames taken per image
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.5 µm / Nominal defocus min: 0.5 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 21712
CTF correctionSoftware - Name: CTFFIND (ver. 4) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

5jlh

Final reconstructionAlgorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 8.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 4.0) / Details: Map low-pass filtered to 9.5 Angstroms / Number images used: 1992
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 4)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 4)
Final 3D classificationNumber classes: 3 / Software - Name: RELION (ver. 4)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial model
PDB IDChain

8f8s

source_name: PDB, initial_model_type: experimental model

5wfn

source_name: PDB, initial_model_type: experimental model
RefinementSpace: REAL / Protocol: FLEXIBLE FIT

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