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- EMDB-44013: F-actin-Talin(R13-DD) complex -

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Basic information

Entry
Database: EMDB / ID: EMD-44013
TitleF-actin-Talin(R13-DD) complex
Map datamap from 3D refine used for model building
Sample
  • Complex: F-actin-Talin(R13-DD) complex
    • Complex: Talin(R13-DD)
      • Protein or peptide: Talin-1
    • Complex: F-actin
      • Protein or peptide: Actin, alpha skeletal muscle
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: MAGNESIUM ION
Keywordsactin / talin / focal adhesion / tension sensor / ABS3 / single particle / CELL ADHESION
Function / homology
Function and homology information


GRB2:SOS provides linkage to MAPK signaling for Integrins / Integrin signaling / p130Cas linkage to MAPK signaling for integrins / SEMA3A-Plexin repulsion signaling by inhibiting Integrin adhesion / MAP2K and MAPK activation / Smooth Muscle Contraction / LIM domain binding / Platelet degranulation / cortical microtubule organization / vinculin binding ...GRB2:SOS provides linkage to MAPK signaling for Integrins / Integrin signaling / p130Cas linkage to MAPK signaling for integrins / SEMA3A-Plexin repulsion signaling by inhibiting Integrin adhesion / MAP2K and MAPK activation / Smooth Muscle Contraction / LIM domain binding / Platelet degranulation / cortical microtubule organization / vinculin binding / integrin activation / cell-substrate junction assembly / cortical actin cytoskeleton organization / cytoskeletal motor activator activity / tropomyosin binding / phosphatidylserine binding / myosin heavy chain binding / troponin I binding / mesenchyme migration / filamentous actin / actin filament bundle / striated muscle thin filament / actin filament bundle assembly / skeletal muscle thin filament assembly / skeletal muscle myofibril / actin monomer binding / stress fiber / skeletal muscle fiber development / titin binding / ruffle / actin filament polymerization / phosphatidylinositol binding / filopodium / adherens junction / integrin-mediated signaling pathway / actin filament / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / structural constituent of cytoskeleton / ruffle membrane / calcium-dependent protein binding / actin filament binding / integrin binding / lamellipodium / cell body / cytoskeleton / cell adhesion / hydrolase activity / protein domain specific binding / focal adhesion / calcium ion binding / positive regulation of gene expression / cell surface / magnesium ion binding / ATP binding / identical protein binding / cytoplasm
Similarity search - Function
Vinculin-binding site-containing domain / Talin, central / Talin, central domain superfamily / Talin-1/2, rod-segment / : / : / : / Vinculin Binding Site / Talin, middle domain / Talin, R4 domain ...Vinculin-binding site-containing domain / Talin, central / Talin, central domain superfamily / Talin-1/2, rod-segment / : / : / : / Vinculin Binding Site / Talin, middle domain / Talin, R4 domain / Talin 1-like, rod segment domain / Talin IBS2B domain / Talin, N-terminal F0 domain / N-terminal or F0 domain of Talin-head FERM / I/LWEQ domain / I/LWEQ domain superfamily / I/LWEQ domain / I/LWEQ domain profile. / I/LWEQ domain / Phosphotyrosine-binding domain / IRS-type PTB domain / PTB domain (IRS-1 type) / Alpha-catenin/vinculin-like superfamily / FERM domain signature 1. / FERM conserved site / FERM domain signature 2. / FERM central domain / FERM/acyl-CoA-binding protein superfamily / FERM central domain / FERM superfamily, second domain / FERM domain / FERM domain profile. / Band 4.1 domain / Band 4.1 homologues / 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 / PH-like domain superfamily / Ubiquitin-like domain superfamily
Similarity search - Domain/homology
Talin-1 / Actin, alpha skeletal muscle
Similarity search - Component
Biological speciesMus musculus (house mouse) / Oryctolagus cuniculus (rabbit)
Methodhelical reconstruction / cryo EM / Resolution: 2.98 Å
AuthorsBiertumpfel C / Yamada Y / Mizuno N
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI) United States
National Institutes of Health/National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIH/NIAMS) United States
CitationJournal: Proc Natl Acad Sci U S A / Year: 2025
Title: Biochemical and structural bases for talin ABSs-F-actin interactions.
Authors: Christian Biertümpfel / Yurika Yamada / Victor Vasquez-Montes / Thien Van Truong / A King Cada / Naoko Mizuno /
Abstract: Focal adhesions (FAs) are large intracellular macromolecular assemblies that play a critical role in cell polarization and migration. Talin serves as a direct connection between integrin receptor and ...Focal adhesions (FAs) are large intracellular macromolecular assemblies that play a critical role in cell polarization and migration. Talin serves as a direct connection between integrin receptor and actomyosin cytoskeleton within FAs. Talin contains three actin-binding sites (ABS1-3) that engage discreetly during the development of FAs, thus acting as a critical player in FA initiation and maturation. However, the molecular basis of the ABS-F-actin interactions remains unknown. Here, we explore interactions of ABSs with F-actin to understand the multivalent behavior of talin. Particularly, the cryo-EM structure of the F-actin-ABS3 complex at 2.9 Å shows ABS3 spanning through two actin monomers along the filament axis, each occupied by the R13 rod subdomain and the DD domain. The dimerization of ABS3 occurs through the DD domain where both protomers interact on the actin surface, and the dimerization of talin to the actin surface is necessary for the engagement to F-actin. The R13 helical bundle is distorted upon binding to F-actin and releases the H1 helix from the rest of the bundle. This phenomenon has also been observed with other tension-sensing proteins like vinculin and α-catenin, highlighting that unfolding is relevant for its force sensing activity. On the contrary, ABS2 (R4R8 subdomains), which is thought to be critical for the maintenance of mature FAs, had multiple F-actin-binding regions within ABS2 and the binding likely occurred by these subdomains running through the surface of F-actin, thus strengthening the interactions upon the maturation of FAs.
History
DepositionMar 10, 2024-
Header (metadata) releaseFeb 12, 2025-
Map releaseFeb 12, 2025-
UpdateFeb 12, 2025-
Current statusFeb 12, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_44013.png

Downloads & links

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Map

FileDownload / File: emd_44013.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationmap from 3D refine used for model building
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 320 pix.
= 265.6 Å		0.83 Å/pix.
x 320 pix.
= 265.6 Å		0.83 Å/pix.
x 320 pix.
= 265.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.83 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.009
Minimum - Maximum-0.0141057335 - 0.052054316
Average (Standard dev.)0.00009730189 (±0.002350831)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 265.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: postprocessed map (low resolution parts are not well resolved)

Fileemd_44013_additional_1.map
Annotationpostprocessed map (low resolution parts are not well resolved)
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map2 from 3D refine

Fileemd_44013_half_map_1.map
Annotationhalf map2 from 3D refine
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map1 from 3D refine

Fileemd_44013_half_map_2.map
Annotationhalf map1 from 3D refine
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : F-actin-Talin(R13-DD) complex

EntireName: F-actin-Talin(R13-DD) complex
Components
  • Complex: F-actin-Talin(R13-DD) complex
    • Complex: Talin(R13-DD)
      • Protein or peptide: Talin-1
    • Complex: F-actin
      • Protein or peptide: Actin, alpha skeletal muscle
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: MAGNESIUM ION

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Supramolecule #1: F-actin-Talin(R13-DD) complex

SupramoleculeName: F-actin-Talin(R13-DD) complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2 / Details: Talin(R13-DD) mixed with polymerized F-actin

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Supramolecule #2: Talin(R13-DD)

SupramoleculeName: Talin(R13-DD) / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #2
Source (natural)Organism: Mus musculus (house mouse)

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Supramolecule #3: F-actin

SupramoleculeName: F-actin / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Oryctolagus cuniculus (rabbit)

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Macromolecule #1: Actin, alpha skeletal muscle

MacromoleculeName: Actin, alpha skeletal muscle / type: protein_or_peptide / ID: 1 / Details: post-translationally modified / Number of copies: 5 / Enantiomer: LEVO
Source (natural)Organism: Oryctolagus cuniculus (rabbit)
Molecular weightTheoretical: 41.875633 KDa
SequenceString: DEDETTALVC DNGSGLVKAG FAGDDAPRAV FPSIVGRPRH QGVMVGMGQK DSYVGDEAQS KRGILTLKYP IE(HIC)GII TNW DDMEKIWHHT FYNELRVAPE EHPTLLTEAP LNPKANREKM TQIMFETFNV PAMYVAIQAV LSLYASGRTT GIVLDSG DG VTHNVPIYEG ...String:
DEDETTALVC DNGSGLVKAG FAGDDAPRAV FPSIVGRPRH QGVMVGMGQK DSYVGDEAQS KRGILTLKYP IE(HIC)GII TNW DDMEKIWHHT FYNELRVAPE EHPTLLTEAP LNPKANREKM TQIMFETFNV PAMYVAIQAV LSLYASGRTT GIVLDSG DG VTHNVPIYEG YALPHAIMRL DLAGRDLTDY LMKILTERGY SFVTTAEREI VRDIKEKLCY VALDFENEMA TAASSSSL E KSYELPDGQV ITIGNERFRC PETLFQPSFI GMESAGIHET TYNSIMKCDI DIRKDLYANN VMSGGTTMYP GIADRMQKE ITALAPSTMK IKIIAPPERK YSVWIGGSIL ASLSTFQQMW ITKQEYDEAG PSIVHRKCF

UniProtKB: Actin, alpha skeletal muscle

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Macromolecule #2: Talin-1

MacromoleculeName: Talin-1 / type: protein_or_peptide / ID: 2 / Number of copies: 8 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 26.109645 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: GPDSMPTVIA ENELLGAAAA IEAAAKKLEQ LKPRAKPKEA DESLNFEEQI LEAAKSIAAA TSALVKAASA AQRELVAQGK VGAIPANAL DDGQWSQGLI SAARMVAAAT NNLCEAANAA VQGHASQEKL ISSAKQVAAS TAQLLVACKV KADQDSEAMK R LQAAGNAV ...String:
GPDSMPTVIA ENELLGAAAA IEAAAKKLEQ LKPRAKPKEA DESLNFEEQI LEAAKSIAAA TSALVKAASA AQRELVAQGK VGAIPANAL DDGQWSQGLI SAARMVAAAT NNLCEAANAA VQGHASQEKL ISSAKQVAAS TAQLLVACKV KADQDSEAMK R LQAAGNAV KRASDNLVKA AQKAAAFEDQ ENETVVVKEK MVGGIAQIIA AQEEMLRKER ELEEARKKLA QIRQQQYKFL PS ELRDEH

UniProtKB: Talin-1

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Macromolecule #3: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 3 / Number of copies: 5 / 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: 5 / 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

Concentration5 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormulaName
20.0 mMC8H18N2O4SHEPES
75.0 mMKClKCl
1.0 mMMgCl2MgCl2
1.0 mM[-CH2OCH2CH2N(CH2CO2H)2]2EGTA
1.0 mMHSCH2CH(OH)CH(OH)CH2SHDTT

Details: pH 7.5
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: PLASMA CLEANING / Pretreatment - Time: 45 sec. / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 35.0 kPa
VitrificationCryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV
Details: 3.0 ul sample, blotted for 5 s from both sides with filter paper Whatman No.1.
DetailsG-actin was polymerized for 60 min at RT. 90 uM talin fragments were then incubated with 10 uM F-actin for 30 min at RT and ultra-centrifuged at 100,000 x g for 20 minutes at RT

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum
Image recordingFilm or detector model: GATAN K3 BIOCONTINUUM (6k x 4k) / Number grids imaged: 1 / Number real images: 6767 / Average exposure time: 6.6 sec. / Average electron dose: 52.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.6 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 105000
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

Final reconstructionNumber classes used: 1
Applied symmetry - Helical parameters - Δz: 27.6 Å
Applied symmetry - Helical parameters - Δ&Phi: -166.66 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 2.98 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1.0) / Number images used: 206326
Segment selectionNumber selected: 2280210 / Software - Name: RELION (ver. 3.1.0)
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

5jlf

Final angle assignmentType: NOT APPLICABLE / Software - Name: RELION (ver. 3.1.0)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial model
PDB IDChain

8a2t

source_name: PDB, initial_model_type: experimental model

2jsw

source_name: PDB, initial_model_type: experimental model

2qdq

source_name: PDB, initial_model_type: experimental model
RefinementSpace: REAL / Protocol: BACKBONE TRACE
Output model

PDB-9az6:
F-actin-Talin(R13-DD) complex

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