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- EMDB-44099: Dia1 at the Barbed End of F-Actin -

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Basic information

Entry
Database: EMDB / ID: EMD-44099
TitleDia1 at the Barbed End of F-Actin
Map data
Sample
  • Complex: Structure of mDia1 dimer bound at the barbed end of actin filaments.
    • Complex: mDia1 dimer
      • Protein or peptide: Protein diaphanous homolog 1
    • Complex: Actin filament
      • Protein or peptide: Actin, alpha skeletal muscle
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: MAGNESIUM ION
KeywordsActin / Filament / Elongation / Ends / CYTOSOLIC PROTEIN
Function / homology
Function and homology information


negative regulation of neuron projection regeneration / multicellular organismal locomotion / ERBB2 Regulates Cell Motility / RHOF GTPase cycle / RHOC GTPase cycle / RHOD GTPase cycle / actin nucleation / neuron projection retraction / RHOB GTPase cycle / RHO GTPases Activate Formins ...negative regulation of neuron projection regeneration / multicellular organismal locomotion / ERBB2 Regulates Cell Motility / RHOF GTPase cycle / RHOC GTPase cycle / RHOD GTPase cycle / actin nucleation / neuron projection retraction / RHOB GTPase cycle / RHO GTPases Activate Formins / RHOA GTPase cycle / profilin binding / regulation of microtubule-based process / axon midline choice point recognition / cytoskeletal motor activator activity / myosin heavy chain binding / tropomyosin binding / troponin I binding / filamentous actin / mesenchyme migration / actin filament bundle / brush border / actin filament bundle assembly / skeletal muscle myofibril / synaptic vesicle endocytosis / striated muscle thin filament / skeletal muscle thin filament assembly / actin monomer binding / ephrin receptor signaling pathway / stress fiber / skeletal muscle fiber development / titin binding / actin filament polymerization / cytoskeleton organization / Neutrophil degranulation / filopodium / actin filament / sensory perception of sound / brain development / small GTPase binding / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / spindle / ruffle membrane / neuron projection development / calcium-dependent protein binding / intracellular protein localization / lamellipodium / regulation of cell shape / presynapse / actin binding / cell body / actin cytoskeleton organization / gene expression / transmembrane transporter binding / hydrolase activity / neuron projection / protein domain specific binding / centrosome / calcium ion binding / positive regulation of gene expression / magnesium ion binding / ATP binding / identical protein binding / nucleus / cytoplasm
Similarity search - Function
Formin Homology Region 1 / Diaphanous, GTPase-binding domain superfamily / : / Diaphanous autoregulatory (DAD) domain / Diaphanous autoregulatory domain (DAD) profile. / Formin, FH3 domain / Formin, GTPase-binding domain / Diaphanous FH3 Domain / Diaphanous GTPase-binding Domain / Diaphanous FH3 Domain ...Formin Homology Region 1 / Diaphanous, GTPase-binding domain superfamily / : / Diaphanous autoregulatory (DAD) domain / Diaphanous autoregulatory domain (DAD) profile. / Formin, FH3 domain / Formin, GTPase-binding domain / Diaphanous FH3 Domain / Diaphanous GTPase-binding Domain / Diaphanous FH3 Domain / Diaphanous GTPase-binding Domain / Rho GTPase-binding/formin homology 3 (GBD/FH3) domain / Rho GTPase-binding/formin homology 3 (GBD/FH3) domain profile. / Formin, FH2 domain / Formin, FH2 domain superfamily / Formin Homology 2 Domain / Formin homology-2 (FH2) domain profile. / Formin Homology 2 Domain / 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 / Armadillo-like helical / Armadillo-type fold
Similarity search - Domain/homology
Protein diaphanous homolog 1 / Actin, alpha skeletal muscle
Similarity search - Component
Biological speciesOryctolagus cuniculus (rabbit) / Mus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.51 Å
AuthorsPalmer NJ / Barrie KR / Dominguez R
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
CitationJournal: Nature / Year: 2024
Title: Mechanisms of actin filament severing and elongation by formins.
Authors: Nicholas J Palmer / Kyle R Barrie / Roberto Dominguez /
Abstract: Humans express 15 formins that play crucial roles in actin-based processes, including cytokinesis, cell motility and mechanotransduction. However, the lack of structures bound to the actin filament ...Humans express 15 formins that play crucial roles in actin-based processes, including cytokinesis, cell motility and mechanotransduction. However, the lack of structures bound to the actin filament (F-actin) has been a major impediment to understanding formin function. Whereas formins are known for their ability to nucleate and elongate F-actin, some formins can additionally depolymerize, sever or bundle F-actin. Two mammalian formins, inverted formin 2 (INF2) and diaphanous 1 (DIA1, encoded by DIAPH1), exemplify this diversity. INF2 shows potent severing activity but elongates weakly whereas DIA1 has potent elongation activity but does not sever. Using cryo-electron microscopy (cryo-EM) we show five structural states of INF2 and two of DIA1 bound to the middle and barbed end of F-actin. INF2 and DIA1 bind differently to these sites, consistent with their distinct activities. The formin-homology 2 and Wiskott-Aldrich syndrome protein-homology 2 (FH2 and WH2, respectively) domains of INF2 are positioned to sever F-actin, whereas DIA1 appears unsuited for severing. These structures also show how profilin-actin is delivered to the fast-growing barbed end, and how this is followed by a transition of the incoming monomer into the F-actin conformation and the release of profilin. Combined, the seven structures presented here provide step-by-step visualization of the mechanisms of F-actin severing and elongation by formins.
History
DepositionMar 14, 2024-
Header (metadata) releaseMay 29, 2024-
Map releaseMay 29, 2024-
UpdateAug 21, 2024-
Current statusAug 21, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_44099.png

Downloads & links

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Map

FileDownload / File: emd_44099.map.gz / Format: CCP4 / Size: 266.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.08 Å/pix.
x 412 pix.
= 444.96 Å		1.08 Å/pix.
x 412 pix.
= 444.96 Å		1.08 Å/pix.
x 412 pix.
= 444.96 Å

Surface

Projections

Slices (1/3)

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.08 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.183
Minimum - Maximum-0.26519215 - 0.7369327
Average (Standard dev.)-0.00008809933 (±0.020031326)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions412412412
Spacing412412412
CellA=B=C: 444.96002 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_44099_msk_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_44099_half_map_1.map
Projections & Slices
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Histogram

Histogram (log scale)

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Half map: #1

Fileemd_44099_half_map_2.map
Projections & Slices
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Histogram (log scale)

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Sample components

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Entire : Structure of mDia1 dimer bound at the barbed end of actin filaments.

EntireName: Structure of mDia1 dimer bound at the barbed end of actin filaments.
Components
  • Complex: Structure of mDia1 dimer bound at the barbed end of actin filaments.
    • Complex: mDia1 dimer
      • Protein or peptide: Protein diaphanous homolog 1
    • Complex: Actin filament
      • Protein or peptide: Actin, alpha skeletal muscle
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: MAGNESIUM ION

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Supramolecule #1: Structure of mDia1 dimer bound at the barbed end of actin filaments.

SupramoleculeName: Structure of mDia1 dimer bound at the barbed end of actin filaments.
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Oryctolagus cuniculus (rabbit)
Molecular weightTheoretical: 252 KDa

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Supramolecule #2: mDia1 dimer

SupramoleculeName: mDia1 dimer / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #2
Source (natural)Organism: Mus musculus (house mouse)

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Supramolecule #3: Actin filament

SupramoleculeName: Actin filament / 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 / Number of copies: 6 / Enantiomer: LEVO
EC number: Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement
Source (natural)Organism: Oryctolagus cuniculus (rabbit)
Molecular weightTheoretical: 41.387227 KDa
Recombinant expressionOrganism: Oryctolagus cuniculus (rabbit)
SequenceString: TTALVCDNGS GLVKAGFAGD DAPRAVFPSI VGRPRHQGVM VGMGQKDSYV GDEAQSKRGI LTLKYPIE(HIC)G IITNWD DME KIWHHTFYNE LRVAPEEHPT LLTEAPLNPK ANREKMTQIM FETFNVPAMY VAIQAVLSLY ASGRTTGIVL DSGDGVT HN VPIYEGYALP ...String:
TTALVCDNGS GLVKAGFAGD DAPRAVFPSI VGRPRHQGVM VGMGQKDSYV GDEAQSKRGI LTLKYPIE(HIC)G IITNWD DME KIWHHTFYNE LRVAPEEHPT LLTEAPLNPK ANREKMTQIM FETFNVPAMY VAIQAVLSLY ASGRTTGIVL DSGDGVT HN VPIYEGYALP HAIMRLDLAG RDLTDYLMKI LTERGYSFVT TAEREIVRDI KEKLCYVALD FENEMATAAS SSSLEKSY E LPDGQVITIG NERFRCPETL FQPSFIGMES AGIHETTYNS IMKCDIDIRK DLYANNVMSG GTTMYPGIAD RMQKEITAL APSTMKIKII APPERKYSVW IGGSILASLS TFQQMWITKQ EYDEAGPSIV HRKCF

UniProtKB: Actin, alpha skeletal muscle

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Macromolecule #2: Protein diaphanous homolog 1

MacromoleculeName: Protein diaphanous homolog 1 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 49.189508 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: VLPFGLTPKK VYKPEVQLRR PNWSKFVAED LSQDCFWTKV KEDRFENNEL FAKLTLAFSA QTKTSKAKKD QEGGEEKKSV QKKKVKELK VLDSKTAQNL SIFLGSFRMP YQEIKNVILE VNEAVLTESM IQNLIKQMPE PEQLKMLSEL KEEYDDLAES E QFGVVMGT ...String:
VLPFGLTPKK VYKPEVQLRR PNWSKFVAED LSQDCFWTKV KEDRFENNEL FAKLTLAFSA QTKTSKAKKD QEGGEEKKSV QKKKVKELK VLDSKTAQNL SIFLGSFRMP YQEIKNVILE VNEAVLTESM IQNLIKQMPE PEQLKMLSEL KEEYDDLAES E QFGVVMGT VPRLRPRLNA ILFKLQFSEQ VENIKPEIVS VTAACEELRK SENFSSLLEL TLLVGNYMNA GSRNAGAFGF NI SFLCKLR DTKSADQKMT LLHFLAELCE NDHPEVLKFP DELAHVEKAS RVSAENLQKS LDQMKKQIAD VERDVQNFPA ATD EKDKFV EKMTSFVKDA QEQYNKLRMM HSNMETLYKE LGDYFVFDPK KLSVEEFFMD LHNFRNMFLQ AVKENQKRRE TEEK MRRAK LAKEKAEKER LEKQQKR

UniProtKB: Protein diaphanous homolog 1

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Macromolecule #3: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 3 / Number of copies: 6 / 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: 6 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration1.48 mg/mL
BufferpH: 8
Component:
ConcentrationName
20.0 mMHEPES
50.0 mMNaCl
1.0 mMEDTA
1.0 mMDTT
0.05 %Thesit
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Support film - Film thickness: 100 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 120 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 42.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 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: 112565
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

8f8p


Details: Actin filament from 8F8P, mDia1 from alphafold model
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.51 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 36931
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: RANDOM ASSIGNMENT
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial model
PDB IDChainDetails

8f8p

source_name: PDB, initial_model_type: experimental model
source_name: AlphaFold, initial_model_type: in silico modelMultimer
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-9b27:
Dia1 at the Barbed End of F-Actin

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