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- EMDB-22808: Myosin XI-F-actin complex -

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Basic information

Entry
Database: EMDB / ID: EMD-22808
TitleMyosin XI-F-actin complex
Map data
Sample
  • Complex: Myosin XI-F-actin complex
    • Protein or peptide: Actin, alpha skeletal muscle
    • Protein or peptide: Unconventional myosin heavy chain
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: MAGNESIUM ION
Keywordsmyosin / actin / cytoskeleton / motor protein / CONTRACTILE PROTEIN
Function / homology
Function and homology information


Striated Muscle Contraction / myosin complex / skeletal muscle thin filament assembly / cytoskeletal motor activity / striated muscle thin filament / skeletal muscle fiber development / stress fiber / actin filament organization / actin filament / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement ...Striated Muscle Contraction / myosin complex / skeletal muscle thin filament assembly / cytoskeletal motor activity / striated muscle thin filament / skeletal muscle fiber development / stress fiber / actin filament organization / actin filament / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / actin filament binding / calmodulin binding / hydrolase activity / ATP binding
Similarity search - Function
Plant myosin, class XI, motor domain / Class XI myosin, cargo binding domain / Dilute domain / DIL domain / Dilute domain profile. / DIL / IQ calmodulin-binding motif / Myosin S1 fragment, N-terminal / Short calmodulin-binding motif containing conserved Ile and Gln residues. / Myosin head, motor domain ...Plant myosin, class XI, motor domain / Class XI myosin, cargo binding domain / Dilute domain / DIL domain / Dilute domain profile. / DIL / IQ calmodulin-binding motif / Myosin S1 fragment, N-terminal / Short calmodulin-binding motif containing conserved Ile and Gln residues. / Myosin head, motor domain / Myosin head (motor domain) / Myosin motor domain profile. / Myosin. Large ATPases. / IQ motif profile. / IQ motif, EF-hand binding site / Actins signature 1. / Actin, conserved site / Actins signature 2. / Kinesin motor domain superfamily / Actin/actin-like conserved site / Actins and actin-related proteins signature. / Actin / Actin family / Actin / ATPase, nucleotide binding domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Actin, alpha skeletal muscle / Unconventional myosin heavy chain
Similarity search - Component
Biological speciesGallus gallus (chicken) / Chara corallina (plant)
Methodhelical reconstruction / cryo EM / Resolution: 4.33 Å
AuthorsGong R / Alushin GM
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01-GM114627 United States
CitationJournal: Nat Chem Biol / Year: 2021
Title: Optical control of fast and processive engineered myosins in vitro and in living cells.
Authors: Paul V Ruijgrok / Rajarshi P Ghosh / Sasha Zemsky / Muneaki Nakamura / Rui Gong / Lin Ning / Robert Chen / Vipul T Vachharajani / Alexander E Chu / Namrata Anand / Raphael R Eguchi / Po-Ssu ...Authors: Paul V Ruijgrok / Rajarshi P Ghosh / Sasha Zemsky / Muneaki Nakamura / Rui Gong / Lin Ning / Robert Chen / Vipul T Vachharajani / Alexander E Chu / Namrata Anand / Raphael R Eguchi / Po-Ssu Huang / Michael Z Lin / Gregory M Alushin / Jan T Liphardt / Zev Bryant /
Abstract: Precision tools for spatiotemporal control of cytoskeletal motor function are needed to dissect fundamental biological processes ranging from intracellular transport to cell migration and division. ...Precision tools for spatiotemporal control of cytoskeletal motor function are needed to dissect fundamental biological processes ranging from intracellular transport to cell migration and division. Direct optical control of motor speed and direction is one promising approach, but it remains a challenge to engineer controllable motors with desirable properties such as the speed and processivity required for transport applications in living cells. Here, we develop engineered myosin motors that combine large optical modulation depths with high velocities, and create processive myosin motors with optically controllable directionality. We characterize the performance of the motors using in vitro motility assays, single-molecule tracking and live-cell imaging. Bidirectional processive motors move efficiently toward the tips of cellular protrusions in the presence of blue light, and can transport molecular cargo in cells. Robust gearshifting myosins will further enable programmable transport in contexts ranging from in vitro active matter reconstitutions to microfabricated systems that harness molecular propulsion.
History
DepositionOct 5, 2020-
Header (metadata) releaseJan 13, 2021-
Map releaseJan 13, 2021-
UpdateMar 6, 2024-
Current statusMar 6, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.019
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.019
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7kch
  • Surface level: 0.019
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-7kch
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_22808.png

Downloads & links

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Map

FileDownload / File: emd_22808.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.096 Å
Density
Contour LevelBy AUTHOR: 0.019 / Movie #1: 0.019
Minimum - Maximum-0.039146766 - 0.094151214
Average (Standard dev.)0.000031223404 (±0.002722491)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 561.152 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0961.0961.096
M x/y/z512512512
origin x/y/z0.0000.0000.000
length x/y/z561.152561.152561.152
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ300300300
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS512512512
D min/max/mean-0.0390.0940.000

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Supplemental data

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Mask #1

Fileemd_22808_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_22808_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_22808_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 : Myosin XI-F-actin complex

EntireName: Myosin XI-F-actin complex
Components
  • Complex: Myosin XI-F-actin complex
    • Protein or peptide: Actin, alpha skeletal muscle
    • Protein or peptide: Unconventional myosin heavy chain
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: MAGNESIUM ION

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Supramolecule #1: Myosin XI-F-actin complex

SupramoleculeName: Myosin XI-F-actin complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Gallus gallus (chicken)
Molecular weightTheoretical: 209 kDa/nm

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Macromolecule #1: Actin, alpha skeletal muscle

MacromoleculeName: Actin, alpha skeletal muscle / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Gallus gallus (chicken)
Molecular weightTheoretical: 42.096953 KDa
Recombinant expressionOrganism: Gallus gallus (chicken)
SequenceString: MCDEDETTAL VCDNGSGLVK AGFAGDDAPR AVFPSIVGRP RHQGVMVGMG QKDSYVGDEA QSKRGILTLK YPIEHGIITN WDDMEKIWH HTFYNELRVA PEEHPTLLTE APLNPKANRE KMTQIMFETF NVPAMYVAIQ AVLSLYASGR TTGIVLDSGD G VTHNVPIY ...String:
MCDEDETTAL VCDNGSGLVK AGFAGDDAPR AVFPSIVGRP RHQGVMVGMG QKDSYVGDEA QSKRGILTLK YPIEHGIITN WDDMEKIWH HTFYNELRVA PEEHPTLLTE APLNPKANRE KMTQIMFETF NVPAMYVAIQ AVLSLYASGR TTGIVLDSGD G VTHNVPIY EGYALPHAIM RLDLAGRDLT DYLMKILTER GYSFVTTAER EIVRDIKEKL CYVALDFENE MATAASSSSL EK SYELPDG QVITIGNERF RCPETLFQPS FIGMESAGIH ETTYNSIMKC DIDIRKDLYA NNVMSGGTTM YPGIADRMQK EIT ALAPST MKIKIIAPPE RKYSVWIGGS ILASLSTFQQ MWITKQEYDE AGPSIVHRKC F

UniProtKB: Actin, alpha skeletal muscle

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Macromolecule #2: Unconventional myosin heavy chain

MacromoleculeName: Unconventional myosin heavy chain / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Chara corallina (plant)
Molecular weightTheoretical: 83.01532 KDa
Recombinant expressionOrganism: Spodoptera aff. frugiperda 2 RZ-2014 (butterflies/moths)
SequenceString: GSPAWVEDVE TVWIEATVVK LDGDAITART VNGDLVETTM ANALPRDEDV TMRGVDDMTK LSYLHEPGVL HNLYTRFKHD EIYTFTGNI LIAVNPFTRL PHLFNTYMMK QYQDAQPGDL NPHVYSVADA AYKAMMEEMK SQAILVSGES GAGKTETTKQ I MQYLAFVG ...String:
GSPAWVEDVE TVWIEATVVK LDGDAITART VNGDLVETTM ANALPRDEDV TMRGVDDMTK LSYLHEPGVL HNLYTRFKHD EIYTFTGNI LIAVNPFTRL PHLFNTYMMK QYQDAQPGDL NPHVYSVADA AYKAMMEEMK SQAILVSGES GAGKTETTKQ I MQYLAFVG GRTVGDERSV EQQVLQSNPL LEAFGNAKTV RNNNSSRFGK FVEIQFNNGK ISGAAVRTYL LERSRVTQIS SP ERNYHCF YQLVAGASPE DAERLKLGPP DSFHYLNQSK CVEVGAIDDC KEYQLTREAM DIVGITTEEQ EAIFRTIAAV LHL GNIEFD SGESDASEVS TEKSKFHLKA AAEMLMCDEQ MLEKSLTTRI MKATRTESIT KILNKSQATD NRDSIAKTIY AKLF DWLVN KVNKSIGQDP HSTVLIGVLD IYGFESFEIN SFEQFCINLT NEKLQQHFNT HVFKMEQAEY RKEEINWDNI DFVDN IDVL DLIEKKPLGI IALLDEACML PRSTAESFAR KLGDTFNNHR RFSKHKFKRT AFTIDHYAGQ VEYRADLFLE KNKDFV VPE HQQLLHASRC AFVSGLFPAD EGGGKKGGTK APSKKKFMSI GSQFKLQLAA LMETLKLTAP HYIRCVKPNM QLKPQIF EN KNVLQQLRCS GVLEAVRISC AGFPTRRTFE EFLDRFGLLH PEVLIESAEE SADEKVACQN LLEKCNLKGY QIGKTKVF L RAGQMAILDT LRSN

UniProtKB: Unconventional myosin heavy chain

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Macromolecule #3: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 3 / Number of copies: 3 / 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 #4: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 4 / Number of copies: 3 / 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

BufferpH: 7
Component:
ConcentrationFormulaName
10.0 mMC3N2H4Imidazole
50.0 mMKClPotassium chloride
1.0 mMMgCl2Magnesium chloride
1.0 mMC14H24N2O10EGTA
0.5 mMC4H10O2S2DTT
0.01 weight/volumeNaN3sodium azide

Details: 10 mM imidazole pH 7.0,50 mM KCl,1mM MgCl2, 1mM EGTA, 0.5 mM DTT, 0.01% NaN3
GridModel: C-flat-1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Support film - Film thickness: 20 / Pretreatment - Type: PLASMA CLEANING / Pretreatment - Time: 10 sec. / Pretreatment - Atmosphere: OTHER
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 293 K / Instrument: LEICA EM GP

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 0.0 mm / Nominal defocus max: -4.0 µm / Nominal defocus min: -1.0 µm / Nominal magnification: 105000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 67.12 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Segment selectionNumber selected: 70000 / Software - Name: RELION (ver. 3.0)
Startup modelType of model: EMDB MAP
EMDB ID:

7116

Final angle assignmentType: NOT APPLICABLE / Software - Name: RELION (ver. 3.0)
Final reconstructionNumber classes used: 23
Applied symmetry - Helical parameters - Δz: 27.45 Å
Applied symmetry - Helical parameters - Δ&Phi: -167.11 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 4.33 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0) / Number images used: 45779
FSC plot (resolution estimation)

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