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- EMDB-8165: Cryo-EM structure of a human cytoplasmic actomyosin complex at ne... -

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Basic information

Entry
Database: EMDB / ID: EMD-8165
TitleCryo-EM structure of a human cytoplasmic actomyosin complex at near-atomic resolution
Map dataNone
Sample
  • Complex: F-actin-myosin-tropomyosin complex
    • Complex: F-actin
      • Protein or peptide: Actin, cytoplasmic 2
    • Complex: Myosin
      • Protein or peptide: NON MUSCLE MYOSIN 2C, ALPHA-ACTININ
    • Complex: tropomyosin
      • Protein or peptide: Tropomyosin alpha-3 chain
Function / homology
Function and homology information


RHOBTB2 GTPase cycle / : / : / contractile vacuole / COPI-mediated anterograde transport / Platelet degranulation / basal body patch / myosin II filament / sorocarp development / Neutrophil degranulation ...RHOBTB2 GTPase cycle / : / : / contractile vacuole / COPI-mediated anterograde transport / Platelet degranulation / basal body patch / myosin II filament / sorocarp development / Neutrophil degranulation / tight junction assembly / macropinocytic cup / actin crosslink formation / profilin binding / actin filament-based movement / vocalization behavior / protein localization to bicellular tight junction / regulation of transepithelial transport / morphogenesis of a polarized epithelium / actomyosin / structural constituent of postsynaptic actin cytoskeleton / Formation of annular gap junctions / Formation of the dystrophin-glycoprotein complex (DGC) / Gap junction degradation / Cell-extracellular matrix interactions / myosin filament / dense body / regulation of stress fiber assembly / RHO GTPases Activate ROCKs / RHO GTPases activate CIT / actomyosin structure organization / Sema4D induced cell migration and growth-cone collapse / Adherens junctions interactions / myosin II complex / hyperosmotic response / Sensory processing of sound by inner hair cells of the cochlea / Sensory processing of sound by outer hair cells of the cochlea / Interaction between L1 and Ankyrins / sarcomere organization / regulation of focal adhesion assembly / EPHA-mediated growth cone collapse / apical junction complex / positive regulation of wound healing / microfilament motor activity / cortical actin cytoskeleton / maintenance of blood-brain barrier / filamentous actin / myofibril / NuA4 histone acetyltransferase complex / pseudopodium / cell leading edge / Recycling pathway of L1 / RHO GTPases activate PAKs / brush border / mitotic cytokinesis / actin filament bundle assembly / EPH-ephrin mediated repulsion of cells / RHO GTPases Activate WASPs and WAVEs / regulation of synaptic vesicle endocytosis / skeletal muscle contraction / phagocytosis / RHOBTB2 GTPase cycle / RHO GTPases activate IQGAPs / neuronal action potential / skeletal muscle tissue development / RHO GTPases activate PKNs / stress fiber / phagocytic vesicle / EPHB-mediated forward signaling / extracellular matrix / axonogenesis / calyx of Held / cellular response to starvation / cell projection / actin filament / FCGR3A-mediated phagocytosis / Translocation of SLC2A4 (GLUT4) to the plasma membrane / mitochondrion organization / cell motility / sensory perception of sound / RHO GTPases Activate Formins / Signaling by high-kinase activity BRAF mutants / MAP2K and MAPK activation / Regulation of actin dynamics for phagocytic cup formation / structural constituent of cytoskeleton / cellular response to type II interferon / VEGFA-VEGFR2 Pathway / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / platelet aggregation / Schaffer collateral - CA1 synapse / Signaling by RAF1 mutants / Signaling by moderate kinase activity BRAF mutants / Paradoxical activation of RAF signaling by kinase inactive BRAF / Signaling downstream of RAS mutants / cell-cell junction / actin filament binding / Signaling by BRAF and RAF1 fusions / regulation of cell shape / actin cytoskeleton / Clathrin-mediated endocytosis
Similarity search - Function
EF-hand, Ca insensitive / Ca2+ insensitive EF hand / Ca2+ insensitive EF hand / Spectrin repeat / Spectrin repeat / Myosin tail / Myosin tail / Myosin N-terminal SH3-like domain / Spectrin/alpha-actinin / Spectrin repeats ...EF-hand, Ca insensitive / Ca2+ insensitive EF hand / Ca2+ insensitive EF hand / Spectrin repeat / Spectrin repeat / Myosin tail / Myosin tail / Myosin N-terminal SH3-like domain / Spectrin/alpha-actinin / Spectrin repeats / Actinin-type actin-binding domain signature 1. / Actinin-type actin-binding domain signature 2. / Actinin-type actin-binding domain, conserved site / Myosin S1 fragment, N-terminal / Calponin homology domain / Myosin, N-terminal, SH3-like / Myosin N-terminal SH3-like domain profile. / Calponin homology (CH) domain / Calponin homology domain / CH domain superfamily / Calponin homology (CH) domain profile. / Short calmodulin-binding motif containing conserved Ile and Gln residues. / IQ motif, EF-hand binding site / Myosin motor domain profile. / Myosin head, motor domain / Myosin head (motor domain) / Myosin. Large ATPases. / IQ motif profile. / Kinesin motor domain 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 / EF-hand domain pair / EF-hand, calcium binding motif / ATPase, nucleotide binding domain / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Alpha-actinin A / Actin, cytoplasmic 2 / Myosin-14
Similarity search - Component
Biological speciesHomo sapiens (human) / Dictyostelium discoideum (eukaryote)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.9 Å
Authorsvon der Ecken J / Heissler SM / Pathan-Chhatbar S / Manstein DJ / Raunser S
CitationJournal: Nature / Year: 2016
Title: Cryo-EM structure of a human cytoplasmic actomyosin complex at near-atomic resolution.
Abstract: The interaction of myosin with actin filaments is the central feature of muscle contraction and cargo movement along actin filaments of the cytoskeleton. The energy for these movements is generated ...The interaction of myosin with actin filaments is the central feature of muscle contraction and cargo movement along actin filaments of the cytoskeleton. The energy for these movements is generated during a complex mechanochemical reaction cycle. Crystal structures of myosin in different states have provided important structural insights into the myosin motor cycle when myosin is detached from F-actin. The difficulty of obtaining diffracting crystals, however, has prevented structure determination by crystallography of actomyosin complexes. Thus, although structural models exist of F-actin in complex with various myosins, a high-resolution structure of the F-actin–myosin complex is missing. Here, using electron cryomicroscopy, we present the structure of a human rigor actomyosin complex at an average resolution of 3.9 Å. The structure reveals details of the actomyosin interface, which is mainly stabilized by hydrophobic interactions. The negatively charged amino (N) terminus of actin interacts with a conserved basic motif in loop 2 of myosin, promoting cleft closure in myosin. Surprisingly, the overall structure of myosin is similar to rigor-like myosin structures in the absence of F-actin, indicating that F-actin binding induces only minimal conformational changes in myosin. A comparison with pre-powerstroke and intermediate (Pi-release) states of myosin allows us to discuss the general mechanism of myosin binding to F-actin. Our results serve as a strong foundation for the molecular understanding of cytoskeletal diseases, such as autosomal dominant hearing loss and diseases affecting skeletal and cardiac muscles, in particular nemaline myopathy and hypertrophic cardiomyopathy.
History
DepositionApr 27, 2016-
Header (metadata) releaseMay 25, 2016-
Map releaseJun 15, 2016-
UpdateNov 28, 2018-
Current statusNov 28, 2018Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.04
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  • Surface view colored by cylindrical radius
  • Surface level: 0.04
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  • Surface view with fitted model
  • Atomic models: PDB-5jlh
  • Surface level: 0.04
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-5jlh
  • Surface level: 0.04
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-5jlh
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_8165.png

Downloads & links

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Map

FileDownload / File: emd_8165.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationNone
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.1 Å/pix.
x 256 pix.
= 281.6 Å		1.1 Å/pix.
x 256 pix.
= 281.6 Å		1.1 Å/pix.
x 256 pix.
= 281.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.1 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.049 / Movie #1: 0.04
Minimum - Maximum-0.08232533 - 0.18568054
Average (Standard dev.)0.00005229109 (±0.011984889)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-129-128-123
Dimensions256256256
Spacing256256256
CellA=B=C: 281.6 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.11.11.1
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z281.600281.600281.600
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS-128-129-123
NC/NR/NS256256256
D min/max/mean-0.0820.1860.000

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Supplemental data

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Sample components

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Entire : F-actin-myosin-tropomyosin complex

EntireName: F-actin-myosin-tropomyosin complex
Components
  • Complex: F-actin-myosin-tropomyosin complex
    • Complex: F-actin
      • Protein or peptide: Actin, cytoplasmic 2
    • Complex: Myosin
      • Protein or peptide: NON MUSCLE MYOSIN 2C, ALPHA-ACTININ
    • Complex: tropomyosin
      • Protein or peptide: Tropomyosin alpha-3 chain

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Supramolecule #1: F-actin-myosin-tropomyosin complex

SupramoleculeName: F-actin-myosin-tropomyosin complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all / Details: Filament
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #2: F-actin

SupramoleculeName: F-actin / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Dictyostelium discoideum (eukaryote)
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)

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Supramolecule #3: Myosin

SupramoleculeName: Myosin / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Escherichia coli (E. coli)

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Supramolecule #4: tropomyosin

SupramoleculeName: tropomyosin / type: complex / ID: 4 / Parent: 1 / Macromolecule list: #3

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Macromolecule #1: Actin, cytoplasmic 2

MacromoleculeName: Actin, cytoplasmic 2 / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Dictyostelium discoideum (eukaryote)
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: EEEIAALVID NGSGMCKAGF AGDDAPRAVF PSIVGRPRHQ GVMVGMGQKD SYVGDEAQSK RGILTLKYPI EHGIVTNWDD MEKIWHHTF YNELRVAPEE HPVLLTEAPL NPKANREKMT QIMFETFNTP AMYVAIQAVL SLYASGRTTG IVMDSGDGVT H TVPIYEGY ...String:
EEEIAALVID NGSGMCKAGF AGDDAPRAVF PSIVGRPRHQ GVMVGMGQKD SYVGDEAQSK RGILTLKYPI EHGIVTNWDD MEKIWHHTF YNELRVAPEE HPVLLTEAPL NPKANREKMT QIMFETFNTP AMYVAIQAVL SLYASGRTTG IVMDSGDGVT H TVPIYEGY ALPHAILRLD LAGRDLTDYL MKILTERGYS FTTTAEREIV RDIKEKLCYV ALDFEQEMAT AASSSSLEKS YE LPDGQVI TIGNERFRCP EALFQPSFLG MESCGIHETT FNSIMKCDVD IRKDLYANTV LSGGTTMYPG IADRMQKEIT ALA PSTMKI KIIAPPERKY SVWIGGSILA SLSTFQQMWI SKQEYDESGP SIVHRKCF

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Macromolecule #2: NON MUSCLE MYOSIN 2C, ALPHA-ACTININ

MacromoleculeName: NON MUSCLE MYOSIN 2C, ALPHA-ACTININ / type: protein_or_peptide / ID: 2
Details: NON MUSCLE MYOSIN 2C HEAVY CHAIN, MOTOR DOMAIN RESIDUES 1-799 LINKED TO ALPHA-ACTININ 3, REPEATS 1 AND 2 RESIDUES 800-1039 FRAGMENT: UNP Q7Z406-1 RESIDUES 1-799, UNP P05095 RESIDUES 265-502
Enantiomer: LEVO / EC number: ec: 3.6.4.1
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MAAVTMSVPG RKAPPRPGPV PEAAQPFLFT PRGPSAGGGP GSGTSPQVEW TARRLVWVPS ELHGFEAAAL RDEGEEEAEV ELAESGRRL RLPRDQIQRM NPPKFSKAED MAELTCLNEA SVLHNLRERY YSGLIYTYSG LFCVVINPYK QLPIYTEAIV E MYRGKKRH ...String:
MAAVTMSVPG RKAPPRPGPV PEAAQPFLFT PRGPSAGGGP GSGTSPQVEW TARRLVWVPS ELHGFEAAAL RDEGEEEAEV ELAESGRRL RLPRDQIQRM NPPKFSKAED MAELTCLNEA SVLHNLRERY YSGLIYTYSG LFCVVINPYK QLPIYTEAIV E MYRGKKRH EVPPHVYAVT EGAYRSMLQD REDQSILCTG ESGAGKTENT KKVIQYLAHV ASSPKGRKEP GVPGELERQL LQ ANPILEA FGNAKTVKND NSSRFGKFIR INFDVAGYIV GANIETYLLE KSRAIRQAKD ECSFHIFYQL LGGAGEQLKA DLL LEPCSH YRFLTNGPSS SPGQERELFQ ETLESLRVLG FSHEEIISML RMVSAVLQFG NIALKRERNT DQATMPDNTA AQKL CRLLG LGVTDFSRAL LTPRIKVGRD YVQKAQTKEQ ADFALEALAK ATYERLFRWL VLRLNRALDR SPRQGASFLG ILDIA GFEI FQLNSFEQLC INYTNEKLQQ LFNHTMFVLE QEEYQREGIP WTFLDFGLDL QPCIDLIERP ANPPGLLALL DEECWF PKA TDKSFVEKVA QEQGGHPKFQ RPRHLRDQAD FSVLHYAGKV DYKANEWLMK NMDPLNDNVA ALLHQSTDRL TAEIWKD VE GIVGLEQVSS LGDGPPGGRP RRGMFRTVGQ LYKESLSRLM ATLSNTNPSF VRCIVPNHEK RAGKLEPRLV LDQLRCNG V LEGIRICRQG FPNRILFQEF RQRYEILTPN AIPKGFMDGK QACEKMIQAL ELDPNLYRVG QSKIFFRAGV LAQLEEERA SEQTKSDYLK RANELVQWIN DKQASLESRD FGDSIESVQS FMNAHKEYKK TEKPPKGQEV SELEAIYNSL QTKLRLIKRE PFVAPAGLT PNEIDSTWSA LEKAEQEHAE ALRIELKRQK KIAVLLQKYN RILKKLENWA TTKSVYLGSN ETGDSITAVQ A KLKNLEAF DGECQSLEGQ SNSDLLSILA QLTELNYNGV PELTERKDTF FAQQWTGVKS SAETYKNTLL AELERLQKIE D

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Macromolecule #3: Tropomyosin alpha-3 chain

MacromoleculeName: Tropomyosin alpha-3 chain / type: protein_or_peptide / ID: 3
Details: Human TROPOMYSIN WAS USED (UNP P06753-2,TPM3_HUMAN, RESIDUES 62-196). DUE TO THE LIMITED RESOLUTION OF THE CRYO-EM DENSITY IN THE REGION OF TROPOMYOSIN, TROPOMYOSIN HAS BEEN REPRESENTED AS POLY(UNK).
Enantiomer: LEVO
SequenceString: (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) ...String:
(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation statefilament

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Sample preparation

BufferpH: 7.5
Component:
ConcentrationFormula
5.0 mMTris-HCl
1.0 mMDTT
100.0 mMKCl
2.0 mMMgCl2

Details: 5 mM Tris-HCl pH 7.5, 1 mM DTT, 100 mM KCl, and 2 mM MgCl2
Sugar embeddingMaterial: I
GridModel: C-flat-2/1 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 90 % / Instrument: GATAN CRYOPLUNGE 3
Details: Sample (2 uL of F-actin-tropomyosin solution) was applied to a glow-discharged holey carbon grid, incubated for 20 s and manually blotted from the backside for less than a second with filter ...Details: Sample (2 uL of F-actin-tropomyosin solution) was applied to a glow-discharged holey carbon grid, incubated for 20 s and manually blotted from the backside for less than a second with filter paper. Afterwards 1.5 uL of myosin solution (3 uM without nucleotide) were added directly on the grid, incubated for 10 s and then manually blotted for 5 s from the backside with filter paper..

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Electron microscopy

MicroscopeFEI TITAN KRIOS
DetailsCs corrected microscope
Image recordingFilm or detector model: FEI FALCON II (4k x 4k) / Detector mode: COUNTING / Digitization - Frames/image: 2-8 / Number real images: 6300 / Average exposure time: 0.475 sec. / Average electron dose: 16.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated defocus max: 2.8 µm / Calibrated defocus min: 0.7 µm / Illumination mode: OTHER / Imaging mode: BRIGHT FIELD / Nominal magnification: 59000
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 138000
CTF correctionSoftware: (Name: CTFFIND (ver. 4), RELION (ver. 1.3))
Startup modelType of model: EMDB MAP
EMDB ID:

6124

Final reconstructionApplied symmetry - Helical parameters - Δz: 27.5 Å
Applied symmetry - Helical parameters - Δ&Phi: 166.9 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 1.3)
Details: THE TROPOMYOSIN MAP FILTERED TO 7.0 ANGSTROM WAS MERGED WITH THE FINAL F-ACTIN-MYOSIN MAP (3.9 ANGSTROM) TO OBTAIN A MAP OF THE ENTIRE F-ACTIN-MYOSIN-TROPOMYOSIN COMPLEX.
Number images used: 118000
Initial angle assignmentType: NOT APPLICABLE / Software - Name: RELION (ver. 1.3)
Final angle assignmentType: NOT APPLICABLE / Software - Name: RELION (ver. 1.3)

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Atomic model buiding 1

Initial model
PDB IDChain

3j8a

chain_id: A, B, C, D, E

4pd3

chain_id: A
RefinementProtocol: BACKBONE TRACE / Overall B value: 180
Output model

PDB-5jlh:
Cryo-EM structure of a human cytoplasmic actomyosin complex at near-atomic resolution

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Atomic model buiding 2

Initial modelPDB ID:

4a7f


Chain - Chain ID - 0: B / Chain - Chain ID - 1: H
Detailstropomyosin fitting
RefinementProtocol: RIGID BODY FIT
Output model

PDB-5jlh:
Cryo-EM structure of a human cytoplasmic actomyosin complex at near-atomic resolution

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