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- EMDB-44020: INF2 in the Middle of F-Actin, Up state consensus refinement -

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Basic information

Entry
Database: EMDB / ID: EMD-44020
TitleINF2 in the Middle of F-Actin, Up state consensus refinement
Map data
Sample
  • Complex: INF2 in the Middle of Actin Filament
    • Complex: INF2
      • Protein or peptide: INF2
    • Complex: Actin FilamentMicrofilament
      • Protein or peptide: Actin
KeywordsActin / Formin / Filament / Severing / CYTOSOLIC PROTEIN
Function / homology
Function and homology information


cytoskeletal motor activator activity / regulation of mitochondrial fission / 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 ...cytoskeletal motor activator activity / regulation of mitochondrial fission / 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 / 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
Inverted formin-2 / 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 ...Inverted formin-2 / 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 / WH2 domain / WH2 domain profile. / 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
Actin, alpha skeletal muscle / Inverted formin-2
Similarity search - Component
Biological speciesHomo sapiens (human) / Oryctolagus cuniculus (rabbit)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.96 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: To Be Published
Title: Mechanisms of Actin Filament Severing and Elongation by Formins
Authors: Palmer NJ / Barrie KR / Dominguez R
History
DepositionMar 11, 2024-
Header (metadata) releaseMay 29, 2024-
Map releaseMay 29, 2024-
UpdateMay 29, 2024-
Current statusMay 29, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_44020.png

Downloads & links

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Map

FileDownload / File: emd_44020.map.gz / Format: CCP4 / Size: 91.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.08 Å
Density
Contour LevelBy AUTHOR: 0.128
Minimum - Maximum-0.5008837 - 0.9639283
Average (Standard dev.)0.0017304427 (±0.029109254)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions288288288
Spacing288288288
CellA=B=C: 311.04 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_44020_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_44020_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_44020_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : INF2 in the Middle of Actin Filament

EntireName: INF2 in the Middle of Actin Filament
Components
  • Complex: INF2 in the Middle of Actin Filament
    • Complex: INF2
      • Protein or peptide: INF2
    • Complex: Actin FilamentMicrofilament
      • Protein or peptide: Actin

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Supramolecule #1: INF2 in the Middle of Actin Filament

SupramoleculeName: INF2 in the Middle of Actin Filament / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all

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Supramolecule #2: INF2

SupramoleculeName: INF2 / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1
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: #2
Source (natural)Organism: Oryctolagus cuniculus (rabbit)

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Macromolecule #1: INF2

MacromoleculeName: INF2 / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: 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

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Macromolecule #2: Actin

MacromoleculeName: Actin / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO
Source (natural)Organism: Oryctolagus cuniculus (rabbit)
SequenceString: 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

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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 mMEGTA
1.0 mMDTT
2.0 mMATPAdenosine triphosphate
2.0 mMMgCl2
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: 2.96 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.0) / Number images used: 413488
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
RefinementProtocol: RIGID BODY FIT

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