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- EMDB-11069: Smooth muscle myosin shutdown state heads region -

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Basic information

Entry
Database: EMDB / ID: EMD-11069
TitleSmooth muscle myosin shutdown state heads region
Map dataSmooth muscle myosin shutdown heads region map
Sample
  • Complex: Smooth muscle myosin in the shutdown state
    • Protein or peptide: Myosin heavy chain 11Myosin
    • Protein or peptide: Myosin light chain smooth muscle isoform
    • Protein or peptide: Myosin light chain 9
  • Ligand: MAGNESIUM ION
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: PHOSPHATE IONPhosphate
Function / homology
Function and homology information


myosin complex / cytoskeletal motor activity / actin filament binding / calcium ion binding / ATP binding / cytosol
Similarity search - Function
DNA repair protein XRCC4-like, C-terminal / Myosin tail / Myosin tail / Myosin N-terminal SH3-like domain / Myosin S1 fragment, N-terminal / Myosin, N-terminal, SH3-like / Myosin N-terminal SH3-like domain profile. / Short calmodulin-binding motif containing conserved Ile and Gln residues. / Myosin head, motor domain / Myosin head (motor domain) ...DNA repair protein XRCC4-like, C-terminal / Myosin tail / Myosin tail / Myosin N-terminal SH3-like domain / Myosin S1 fragment, N-terminal / Myosin, N-terminal, SH3-like / Myosin N-terminal SH3-like domain profile. / 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 / Kinesin motor domain superfamily / EF-hand domain pair / EF-hand, calcium binding motif / 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
MYH11 protein / EF-hand domain-containing protein / Myosin light chain smooth muscle isoform
Similarity search - Component
Biological speciesMeleagris gallopavo (turkey) / turkey (turkey)
Methodsingle particle reconstruction / cryo EM / Resolution: 6.3 Å
AuthorsScarff CA / Carrington G / Casas Mao D / Chalovich JM / Knight PJ / Ranson NA / Peckham M
Funding support United Kingdom, 3 items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom)MR/R009406/1 United Kingdom
Wellcome Trust108466/Z/15/Z United Kingdom
Medical Research Council (MRC, United Kingdom)MR/S023593/1 United Kingdom
CitationJournal: Nature / Year: 2020
Title: Structure of the shutdown state of myosin-2.
Authors: Charlotte A Scarff / Glenn Carrington / David Casas-Mao / Joseph M Chalovich / Peter J Knight / Neil A Ranson / Michelle Peckham /
Abstract: Myosin-2 is essential for processes as diverse as cell division and muscle contraction. Dephosphorylation of its regulatory light chain promotes an inactive, 'shutdown' state with the filament- ...Myosin-2 is essential for processes as diverse as cell division and muscle contraction. Dephosphorylation of its regulatory light chain promotes an inactive, 'shutdown' state with the filament-forming tail folded onto the two heads, which prevents filament formation and inactivates the motors. The mechanism by which this happens is unclear. Here we report a cryo-electron microscopy structure of shutdown smooth muscle myosin with a resolution of 6 Å in the head region. A pseudo-atomic model, obtained by flexible fitting of crystal structures into the density and molecular dynamics simulations, describes interaction interfaces at the atomic level. The N-terminal extension of one regulatory light chain interacts with the tail, and the other with the partner head, revealing how the regulatory light chains stabilize the shutdown state in different ways and how their phosphorylation would allow myosin activation. Additional interactions between the three segments of the coiled coil, the motor domains and the light chains stabilize the shutdown molecule. The structure of the lever in each head is competent to generate force upon activation. This shutdown structure is relevant to all isoforms of myosin-2 and provides a framework for understanding their disease-causing mutations.
History
DepositionMay 22, 2020-
Header (metadata) releaseDec 9, 2020-
Map releaseDec 9, 2020-
UpdateDec 30, 2020-
Current statusDec 30, 2020Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.25
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.25
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6z47
  • Surface level: 0.25
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_11069.png

Downloads & links

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Map

FileDownload / File: emd_11069.map.gz / Format: CCP4 / Size: 166.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSmooth muscle myosin shutdown heads region map
Voxel sizeX=Y=Z: 1.07 Å
Density
Contour LevelBy AUTHOR: 0.28 / Movie #1: 0.25
Minimum - Maximum-0.53737754 - 1.671487
Average (Standard dev.)0.005624783 (±0.049308784)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions352352352
Spacing352352352
CellA=B=C: 376.64 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.071.071.07
M x/y/z352352352
origin x/y/z0.0000.0000.000
length x/y/z376.640376.640376.640
α/β/γ90.00090.00090.000
start NX/NY/NZ-31-35-52
NX/NY/NZ11798209
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS352352352
D min/max/mean-0.5371.6710.006

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Supplemental data

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Half map: Smooth muscle myosin shutdown heads region half map A

Fileemd_11069_half_map_1.map
AnnotationSmooth muscle myosin shutdown heads region half map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Smooth muscle myosin shutdown heads region half map B

Fileemd_11069_half_map_2.map
AnnotationSmooth muscle myosin shutdown heads region half map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Smooth muscle myosin in the shutdown state

EntireName: Smooth muscle myosin in the shutdown state
Components
  • Complex: Smooth muscle myosin in the shutdown state
    • Protein or peptide: Myosin heavy chain 11Myosin
    • Protein or peptide: Myosin light chain smooth muscle isoform
    • Protein or peptide: Myosin light chain 9
  • Ligand: MAGNESIUM ION
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: PHOSPHATE IONPhosphate

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Supramolecule #1: Smooth muscle myosin in the shutdown state

SupramoleculeName: Smooth muscle myosin in the shutdown state / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Meleagris gallopavo (turkey)

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Macromolecule #1: Myosin heavy chain 11

MacromoleculeName: Myosin heavy chain 11 / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: turkey (turkey) / Tissue: Gizzard
Molecular weightTheoretical: 229.14825 KDa
SequenceString: MSQKPLSDDE KFLFVDKNFV NNPLAQADWS AKKLVWVPSE KHGFEAASIK EEKGDEVTVE LQENGKKVTL SKDDIQKMNP PKFSKVEDM AELTCLNEAS VLHNLRERYF SGLIYTYSGL FCVVVNPYKQ LPIYSEKIID MYKGKKRHEM PPHIYAIADT A YRSMLQDR ...String:
MSQKPLSDDE KFLFVDKNFV NNPLAQADWS AKKLVWVPSE KHGFEAASIK EEKGDEVTVE LQENGKKVTL SKDDIQKMNP PKFSKVEDM AELTCLNEAS VLHNLRERYF SGLIYTYSGL FCVVVNPYKQ LPIYSEKIID MYKGKKRHEM PPHIYAIADT A YRSMLQDR EDQSILCTGE SGAGKTENTK KVIQYLAVVA SSHKGKKDTS ITQGPSFSYG ELEKQLLQAN PILEAFGNAK TV KNDNSSR FGKFIRINFD VTGYIVGANI ETYLLEKSRA IRQAKDERTF HIFYYLIAGA SEQMRNDLLL EGFNNYTFLS NGH VPIPAQ QDDEMFQETL EAMRIMGFTE EEQTSILRVV SSVLQLGNIV FKKERNTDQA SMPDNTAAQK VCHLMGINVT DFTR SILTP RIKVGRDVVQ KAQTKEQADF AIEALAKAKF ERLFRWILTR VNKALDKTKR QGASFLGILD IAGFEIFEIN SFEQL CINY TNEKLQQLFN HTMFILEQEE YQREGIEWNF IDFGLDLQPC IELIERPTNP PGVLALLDEE CWFPKATDTS FVEKLI QEQ GNHPKFQKSK QLKDKTEFCI LHYAGKVSYN ASAWLTKNMD PLNDNVTSLL NQSSDKFVAD LWKDVDRIVG LDQMAKM TE SSLPSSSKTK KGMFRTVGQL YKEQLTKLMT TLRNTNPNFV RCIIPNHEKR AGKLDAHLVL EQLRCNGVLE GIRICRQG F PNRIVFQEFR QRYEILAANA IPKGFMDGKQ ACILMIKALE LDPNLYRIGQ SKIFFRTGVL AHLEEERDLK ITDVIIAFQ AQCRGYLARK AFAKRQQQLT AMKVIQRNCA AYLKLRNWQW WRLFTKVKPL LQVTRQEEEM QAKDEELQRT KERQQKAEAE LKELEQKHT QLCEEKNLLQ EKLQAETELY AEAEEMRVRL AAKKQELEEI LHEMEARIEE EEERSQQLQA EKKKMQQQML D LEEQLEEE EAARQKLQLE KVTADGKIKK MEDDILIMED QNNKLTKERK LLEERVSDLT TNLAEEEEKA KNLTKLKNKH ES MISELEV RLKKEEKTRQ ELEKTKRKLE GESSDLHEQI AELQAQIAEL KAQLAKKEEE LQAALARLED ETSQKNNALK KIR ELESHI SDLQEDLESE KAARNKAEKQ KRDLGEELEA LKTELEDTLD TTATQQELRA KREQEVTVLK RALEEETRTH EAQV QEMRQ KHTQAVEELT EQLEQFKRAK ANLDKTKQTL EKDNADLANE VRSLSQAKQD VEHKKKKLEV QLQDLQSKYT DGERV RTEL NEKVHKLQIE VENVTSLLNE AESKNIKLTK DVATLGSQLQ DTQELLQEET RQKLNVTTKL RQLEDDKNSL QEQLDE EVE AKQNLERHIS TLTIQLSDSK KKLQEFTATI ETMEEGKKKF QREIESLTQQ FEEKAASYDK LEKTKNRLQQ ELDDLVV DL DNQRQLVSNL EKKQKKFDQM LAEEKNISSK YADERDRAEA EAREKETKAL SLARALEEAL EAKEELERTN KMLKAEME D LVSSKDDVGK NVHELEKSKR TLEQQVEEMK TQLEELEDEL QAAEDAKLRL EVNMQAMKSQ FERDLQARDE QNEEKRRQL LKQLHEHETE LEDERKQRAL AAAAKKKLEV DVKDLESQVD SVNKAREEAI KQLRKLQAQM KDYQRDLDDA RAAREEIFAT ARENEKKAK NLEAELIQLQ EDLAAAERAR KQADLEKEEM AEELASATSG RTSLQDDKRR LEARIAQLEE ELDEEHSNIE A MSDRMRKA VQQAEQLNNE LATERATAQK NENARQQLER QNKELRSKLQ EMEGAVKSKF KSTIAALEAK IASLEEQLEQ EA REKQAAA KTLRQKDKKL KDALLQVEDE KKQAEQYKDQ AEKGNLRLKQ LKRQLEEAEE ESQRINANRR KLQRELDEAT ESN DALGRE VAALKSKLRR GNEPVSFAPP RRSGGRRVIE NATDGGEQEI DGRDGDLNGK ASE

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Macromolecule #2: Myosin light chain smooth muscle isoform

MacromoleculeName: Myosin light chain smooth muscle isoform / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: turkey (turkey)
Molecular weightTheoretical: 16.989145 KDa
SequenceString:
MCDFSEEQTA EFKEAFQLFD RTGDGKILYS QCGDVMRALG QNPTNAEVMK VLGNPKSDEM NLKTLNFEQF LPMMQTIAKN KDQGCFEDY VEGLRVFDKE GNGTVMGAEI RHVLVTLGEK MTEEEVEQLV AGHEDSNGCI NYEELVRMVL SG

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Macromolecule #3: Myosin light chain 9

MacromoleculeName: Myosin light chain 9 / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: turkey (turkey)
Molecular weightTheoretical: 19.872244 KDa
SequenceString:
MSSKRAKAKT TKKRPQRATS NVFAMFDQSQ IQEFKEAFNM IDQNRDGFID KEDLHDMLAS MGKNPTDEYL EGMMSEAPGP INFTMFLTM FGEKLNGTDP EDVIRNAFAC FDEEASGFIH EDHLRELLTT MGDRFTDEEV DEMYREAPID KKGNFNYVEF T RILKHGAK DKDD

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Macromolecule #4: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 4 / Number of copies: 4 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #5: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 5 / Number of copies: 2 / 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 #6: PHOSPHATE ION

MacromoleculeName: PHOSPHATE ION / type: ligand / ID: 6 / Number of copies: 2 / Formula: PO4
Molecular weightTheoretical: 94.971 Da
Chemical component information

ChemComp-PO4:
PHOSPHATE ION / Phosphate

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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

Concentration0.45 mg/mL
BufferpH: 7.2
Component:
ConcentrationFormula
150.0 mMKCl
10.0 mMMOPS
0.1 mMEGTA
2.0 mMMgCl2
1.0 mMATPAdenosine triphosphate
GridModel: Quantifoil R2/1 / Material: COPPER / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AMYLAMINE / Details: GloCube
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 281 K / Instrument: FEI VITROBOT MARK IV / Details: Blot force 6, blot time 3 seconds.
DetailsSmooth muscle myosin from turkey gizzard, stored under liquid nitrogen, was thawed quickly. MgATP was added before dilution into the final buffer conditions stated below

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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
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingFilm or detector model: GATAN K2 QUANTUM (4k x 4k) / Detector mode: COUNTING / Average electron dose: 60.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 6.3 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 96351
FSC plot (resolution estimation)

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