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- EMDB-44018: INF2 at the Barbed End of F-Actin with Incoming Profilin-Actin -

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Basic information

Entry
Database: EMDB / ID: EMD-44018
TitleINF2 at the Barbed End of F-Actin with Incoming Profilin-Actin
Map data
Sample
  • Complex: Actin
    • Complex: INF2 Dimer
      • Protein or peptide: Inverted formin-2
    • Complex: Actin FilamentMicrofilament
      • Protein or peptide: Actin, alpha skeletal muscle
    • Protein or peptide: Profilin-1
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: MAGNESIUM ION
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
KeywordsActin / Filament / Elongation / Ends / CYTOSOLIC PROTEIN
Function / homology
Function and homology information


synapse maturation / modification of postsynaptic actin cytoskeleton / negative regulation of actin filament bundle assembly / adenyl-nucleotide exchange factor activity / positive regulation of actin filament bundle assembly / negative regulation of actin filament polymerization / Signaling by ROBO receptors / regulation of actin filament polymerization / positive regulation of ATP-dependent activity / PCP/CE pathway ...synapse maturation / modification of postsynaptic actin cytoskeleton / negative regulation of actin filament bundle assembly / adenyl-nucleotide exchange factor activity / positive regulation of actin filament bundle assembly / negative regulation of actin filament polymerization / Signaling by ROBO receptors / regulation of actin filament polymerization / positive regulation of ATP-dependent activity / PCP/CE pathway / proline-rich region binding / positive regulation of ruffle assembly / negative regulation of stress fiber assembly / cytoskeletal motor activator activity / regulation of mitochondrial fission / positive regulation of actin filament polymerization / positive regulation of epithelial cell migration / tropomyosin binding / mesenchyme migration / myosin heavy chain binding / troponin I binding / filamentous actin / actin filament bundle / skeletal muscle thin filament assembly / striated muscle thin filament / actin filament bundle assembly / skeletal muscle myofibril / actin monomer binding / skeletal muscle fiber development / stress fiber / titin binding / phosphatidylinositol-4,5-bisphosphate binding / actin filament polymerization / phosphotyrosine residue binding / filopodium / neural tube closure / RHO GTPases Activate Formins / actin filament / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / modulation of chemical synaptic transmission / small GTPase binding / calcium-dependent protein binding / Platelet degranulation / lamellipodium / actin binding / cell cortex / cell body / actin cytoskeleton organization / blood microparticle / cytoskeleton / protein stabilization / hydrolase activity / cadherin binding / protein domain specific binding / focal adhesion / glutamatergic synapse / calcium ion binding / positive regulation of gene expression / regulation of transcription by RNA polymerase II / perinuclear region of cytoplasm / magnesium ion binding / RNA binding / extracellular exosome / ATP binding / membrane / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Inverted formin-2 / Profilin1/2/3, vertebrate / 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. ...Inverted formin-2 / Profilin1/2/3, vertebrate / 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 / WH2 motif / Profilin conserved site / Profilin signature. / Profilin / WH2 domain / Profilin / WH2 domain profile. / Profilin / Profilin superfamily / 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
Profilin-1 / Actin, alpha skeletal muscle / Inverted formin-2
Similarity search - Component
Biological speciesHomo sapiens (human) / Oryctolagus cuniculus (rabbit)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.79 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 fifteen formins, playing crucial roles in actin-based processes, such as cytokinesis, cell motility, and mechanotransduction . However, the lack of structures bound to the actin ...Humans express fifteen formins, playing crucial roles in actin-based processes, such as 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. While 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), exemplify this diversity. INF2 displays potent severing activity but elongates weakly , whereas Dia1 has potent elongation activity but does not sever . Using cryo-electron microscopy (cryo-EM), we reveal 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 FH2 and WH2 domains of INF2 are positioned to sever F-actin, whereas Dia1 appears unsuited for severing. 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 11, 2024-
Header (metadata) releaseMay 29, 2024-
Map releaseMay 29, 2024-
UpdateJun 19, 2024-
Current statusJun 19, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_44018.png

Downloads & links

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Map

FileDownload / File: emd_44018.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
1.08 Å/pix.
x 288 pix.
= 311.04 Å		1.08 Å/pix.
x 288 pix.
= 311.04 Å		1.08 Å/pix.
x 288 pix.
= 311.04 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.08 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.164
Minimum - Maximum-0.20292602 - 0.61393875
Average (Standard dev.)0.000037463575 (±0.020122942)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 414.72003 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_44018_msk_1.map
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Half map: #2

Fileemd_44018_half_map_1.map
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Half map: #1

Fileemd_44018_half_map_2.map
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Sample components

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Entire : Actin

EntireName: Actin
Components
  • Complex: Actin
    • Complex: INF2 Dimer
      • Protein or peptide: Inverted formin-2
    • Complex: Actin FilamentMicrofilament
      • Protein or peptide: Actin, alpha skeletal muscle
    • Protein or peptide: Profilin-1
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: MAGNESIUM ION
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE

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Supramolecule #1: Actin

SupramoleculeName: Actin / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 264 KDa

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Supramolecule #2: INF2 Dimer

SupramoleculeName: INF2 Dimer / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #2
Source (natural)Organism: Homo sapiens (human)

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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: 7 / 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
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: Inverted formin-2

MacromoleculeName: Inverted formin-2 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 135.778828 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MSVKEGAQRK WAALKEKLGP QDSDPTEANL ESADPELCIR LLQMPSVVNY SGLRKRLEGS DGGWMVQFLE QSGLDLLLEA LARLSGRGV ARISDALLQL TCVSCVRAVM NSRQGIEYIL SNQGYVRQLS QALDTSNVMV KKQVFELLAA LCIYSPEGHV L TLDALDHY ...String:
MSVKEGAQRK WAALKEKLGP QDSDPTEANL ESADPELCIR LLQMPSVVNY SGLRKRLEGS DGGWMVQFLE QSGLDLLLEA LARLSGRGV ARISDALLQL TCVSCVRAVM NSRQGIEYIL SNQGYVRQLS QALDTSNVMV KKQVFELLAA LCIYSPEGHV L TLDALDHY KTVCSQQYRF SIVMNELSGS DNVPYVVTLL SVINAVILGP EDLRARTQLR NEFIGLQLLD VLARLRDLED AD LLIQLEA FEEAKAEDEE ELLRVSGGVD MSSHQEVFAS LFHKVSCSPV SAQLLSVLQG LLHLEPTLRS SQLLWEALES LVN RAVLLA SDAQECTLEE VVERLLSVKG RPRPSPLVKA HKSVQANLDQ SQRGSSPQNT TTPKPSVEGQ QPAAAAACEP VDHA QSESI LKVSQPRALE QQASTPPPPP PPPLLPGSSA EPPPPPPPPP LPSVGAKALP TAPPPPPLPG LGAMAPPAPP LPPPL PGSC EFLPPPPPPL PGLGCPPPPP PLLPGMGWGP PPPPPPLLPC TCSPPVAGGM EEVIVAQVDH GLGSAWVPSH RRVNPP TLR MKKLNWQKLP SNVAREHNSM WASLSSPDAE AVEPDFSSIE RLFSFPAAKP KEPTMVAPRA RKEPKEITFL DAKKSLN LN IFLKQFKCSN EEVAAMIRAG DTTKFDVEVL KQLLKLLPEK HEIENLRAFT EERAKLASAD HFYLLLLAIP CYQLRIEC M LLCEGAAAVL DMVRPKAQLV LAACESLLTS RQLPIFCQLI LRIGNFLNYG SHTGDADGFK ISTLLKLTET KSQQNRVTL LHHVLEEAEK SHPDLLQLPR DLEQPSQAAG INLEIIRSEA SSNLKKLLET ERKVSASVAE VQEQYTERLQ ASISAFRALD ELFEAIEQK QRELADYLCE DAQQLSLEDT FSTMKAFRDL FLRALKENKD RKEQAAKAER RKQQLAEEEA RRPRGEDGKP V RKGPGKQE EVCVIDALLA DIRKGFQLRK TARGRGDTDG GSKAASMDPP RATEPVATSN PAGDPVGSTR CPASEPGLDA TT ASESRGW DLVDAVTPGP QPTLEQLEEG GPRPLERRSS WYVDASDVLT TEDPQCPQPL EGAWPVTLGD AQALKPLKFS SNQ PPAAGS SRQDAKDPTS LLGVLQAEAD STSEGLEDAV HSRGARPPAA GPGGDEDEDE EDTAPESALD TSLDKSFSED AVTD SSGSG TLPRARGRAS KGTGKRRKKR PSRSQEEVPP DSDDNKTKKL CVIQ

UniProtKB: Inverted formin-2

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Macromolecule #3: Profilin-1

MacromoleculeName: Profilin-1 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 14.940021 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
AGWNAYIDNL MADGTCQDAA IVGYKDSPSV WAAVPGKTFV NITPAEVGVL VGKDRSSFYV NGLTLGGQKC SVIRDSLLQD GEFSMDLRT KSTGGAPTFN VTVTKTDKTL VLLMGKEGVH GGLINKKCYE MASHLRRSQY

UniProtKB: Profilin-1

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Macromolecule #4: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 4 / Number of copies: 6 / Formula: ADP
Molecular weightTheoretical: 427.201 Da
Chemical component information

ChemComp-ADP:
ADENOSINE-5'-DIPHOSPHATE / ADP, energy-carrying molecule*YM / Adenosine diphosphate

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Macromolecule #5: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 5 / Number of copies: 7 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #6: ADENOSINE-5'-TRIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 6 / Number of copies: 1 / Formula: ATP
Molecular weightTheoretical: 507.181 Da
Chemical component information

ChemComp-ATP:
ADENOSINE-5'-TRIPHOSPHATE / ATP, energy-carrying molecule*YM / Adenosine triphosphate

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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

Concentration1.45 mg/mL
BufferpH: 8
Component:
ConcentrationName
20.0 mMHEPES
50.0 mMNaClSodium chloride
1.0 mMEDTAEthylenediaminetetraacetic acid
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
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELDBright-field microscopy / 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
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number real images: 41926 / Average electron dose: 44.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Initial angle assignmentType: RANDOM ASSIGNMENT / Software - Name: cryoSPARC (ver. 4.0)
Final angle assignmentType: RANDOM ASSIGNMENT / Software - Name: cryoSPARC (ver. 4.0)
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.79 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.0) / Number images used: 20093
FSC plot (resolution estimation)

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