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- EMDB-44010: INF2 at the Barbed End of F-Actin, Leading WH2 focus refinement -
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Open data
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Basic information
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Title | INF2 at the Barbed End of F-Actin, Leading WH2 focus refinement | |||||||||
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![]() | Actin / Filament / Elongation / Ends / CYTOSOLIC PROTEIN | |||||||||
Function / homology | ![]() cytoskeletal motor activator activity / regulation of mitochondrial fission / tropomyosin binding / mesenchyme migration / troponin I binding / myosin heavy chain binding / filamentous actin / actin filament bundle / skeletal muscle thin filament assembly / striated muscle thin filament ...cytoskeletal motor activator activity / regulation of mitochondrial fission / tropomyosin binding / mesenchyme migration / troponin I binding / myosin heavy chain 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 / actin filament polymerization / filopodium / actin filament / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / small GTPase binding / calcium-dependent protein binding / lamellipodium / actin binding / cell body / hydrolase activity / protein domain specific binding / calcium ion binding / positive regulation of gene expression / perinuclear region of cytoplasm / magnesium ion binding / ATP binding / identical protein binding / cytoplasm Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.17 Å | |||||||||
![]() | Palmer NJ / Barrie KR / Dominguez R | |||||||||
Funding support | ![]()
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![]() | ![]() 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 |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 107.9 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 18.9 KB 18.9 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 12.7 KB | Display | ![]() |
Images | ![]() | 31.4 KB | ||
Masks | ![]() | 216 MB | ![]() | |
Filedesc metadata | ![]() | 6.1 KB | ||
Others | ![]() ![]() | 200.2 MB 200.2 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
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Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 21.5 KB | Display | |
Data in CIF | ![]() | 28 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 9az4C ![]() 9azpC ![]() 9azqC ![]() 9b03C ![]() 9b0kC ![]() 9b27C ![]() 9b3dC C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Voxel size | X=Y=Z: 1.08 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
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Density Histograms |
-Half map: #1
File | emd_44010_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
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Projections & Slices |
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Density Histograms |
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Sample components
-Entire : Actin
Entire | Name: Actin |
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Components |
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-Supramolecule #1: Actin
Supramolecule | Name: Actin / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 264 KDa |
-Supramolecule #2: INF2 Dimer
Supramolecule | Name: INF2 Dimer / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #2 |
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Source (natural) | Organism: ![]() |
-Supramolecule #3: Actin Filament
Supramolecule | Name: Actin Filament / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #1 |
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-Macromolecule #1: Actin, alpha skeletal muscle
Macromolecule | Name: Actin, alpha skeletal muscle / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Sequence | String: MCDEDETTAL VCDNGSGLVK AGFAGDDAPR AVFPSIVGRP RHQGVMVGMG QKDSYVGDEA QSKRGILTLK YPIEHGIITN WDDMEKIWHH TFYNELRVAP EEHPTLLTEA PLNPKANREK MTQIMFETFN VPAMYVAIQA VLSLYASGRT TGIVLDSGDG VTHNVPIYEG ...String: MCDEDETTAL VCDNGSGLVK AGFAGDDAPR AVFPSIVGRP RHQGVMVGMG QKDSYVGDEA QSKRGILTLK YPIEHGIITN WDDMEKIWHH TFYNELRVAP EEHPTLLTEA PLNPKANREK MTQIMFETFN VPAMYVAIQA VLSLYASGRT TGIVLDSGDG VTHNVPIYEG YALPHAIMRL DLAGRDLTDY LMKILTERGY SFVTTAEREI VRDIKEKLCY VALDFENEMA TAASSSSLEK SYELPDGQVI TIGNERFRCP ETLFQPSFIG MESAGIHETT YNSIMKCDID IRKDLYANNV MSGGTTMYPG IADRMQKEIT ALAPSTMKIK IIAPPERKYS VWIGGSILAS LSTFQQMWIT KQEYDEAGPS IVHRKCF UniProtKB: Actin, alpha skeletal muscle |
-Macromolecule #2: INF2
Macromolecule | Name: INF2 / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: MSVKEGAQRK WAALKEKLGP QDSDPTEANL ESADPELCIR LLQMPSVVNY SGLRKRLEGS DGGWMVQFLE QSGLDLLLEA LARLSGRGVA RISDALLQLT CVSCVRAVMN SRQGIEYILS NQGYVRQLSQ ALDTSNVMVK KQVFELLAAL CIYSPEGHVL TLDALDHYKT ...String: MSVKEGAQRK WAALKEKLGP QDSDPTEANL ESADPELCIR LLQMPSVVNY SGLRKRLEGS DGGWMVQFLE QSGLDLLLEA LARLSGRGVA RISDALLQLT CVSCVRAVMN SRQGIEYILS NQGYVRQLSQ ALDTSNVMVK KQVFELLAAL CIYSPEGHVL TLDALDHYKT VCSQQYRFSI VMNELSGSDN VPYVVTLLSV INAVILGPED LRARTQLRNE FIGLQLLDVL ARLRDLEDAD LLIQLEAFEE AKAEDEEELL RVSGGVDMSS HQEVFASLFH KVSCSPVSAQ LLSVLQGLLH LEPTLRSSQL LWEALESLVN RAVLLASDAQ ECTLEEVVER LLSVKGRPRP SPLVKAHKSV QANLDQSQRG SSPQNTTTPK PSVEGQQPAA AAACEPVDHA QSESILKVSQ PRALEQQAST PPPPPPPPLL PGSSAEPPPP PPPPPLPSVG AKALPTAPPP PPLPGLGAMA PPAPPLPPPL PGSCEFLPPP PPPLPGLGCP PPPPPLLPGM GWGPPPPPPP LLPCTCSPPV AGGMEEVIVA QVDHGLGSAW VPSHRRVNPP TLRMKKLNWQ KLPSNVAREH NSMWASLSSP DAEAVEPDFS SIERLFSFPA AKPKEPTMVA PRARKEPKEI TFLDAKKSLN LNIFLKQFKC SNEEVAAMIR AGDTTKFDVE VLKQLLKLLP EKHEIENLRA FTEERAKLAS ADHFYLLLLA IPCYQLRIEC MLLCEGAAAV LDMVRPKAQL VLAACESLLT SRQLPIFCQL ILRIGNFLNY GSHTGDADGF KISTLLKLTE TKSQQNRVTL LHHVLEEAEK SHPDLLQLPR DLEQPSQAAG INLEIIRSEA SSNLKKLLET ERKVSASVAE VQEQYTERLQ ASISAFRALD ELFEAIEQKQ RELADYLCED AQQLSLEDTF STMKAFRDLF LRALKENKDR KEQAAKAERR KQQLAEEEAR RPRGEDGKPV RKGPGKQEEV CVIDALLADI RKGFQLRKTA RGRGDTDGGS KAASMDPPRA TEPVATSNPA GDPVGSTRCP ASEPGLDATT ASESRGWDLV DAVTPGPQPT LEQLEEGGPR PLERRSSWYV DASDVLTTED PQCPQPLEGA WPVTLGDAQA LKPLKFSSNQ PPAAGSSRQD AKDPTSLLGV LQAEADSTSE GLEDAVHSRG ARPPAAGPGG DEDEDEEDTA PESALDTSLD KSFSEDAVTD SSGSGTLPRA RGRASKGTGK RRKKRPSRSQ EEVPPDSDDN KTKKLCVIQ UniProtKB: Inverted formin-2 |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 1.45 mg/mL | ||||||||||||
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Buffer | pH: 8 Component:
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Grid | Model: 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. | ||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Number real images: 41926 / Average electron dose: 44.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.5 µm |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |