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- EMDB-22145: 10S myosin II (smooth muscle) -

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Basic information

Entry
Database: EMDB / ID: EMD-22145
Title10S myosin II (smooth muscle)
Map data10S myosin II (smooth muscle)
Sample
  • Complex: Smooth muscle myosin II
    • Protein or peptide: Myosin II heavy chain (smooth muscle)
    • Protein or peptide: Myosin light chain smooth muscle isoform
    • Protein or peptide: Myosin light chain 9
Keywordsmotor protein / auto-inhibited form / 10 S conformation / CONTRACTILE PROTEIN
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)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.3 Å
AuthorsYang S / Craig R
Funding support United States, 3 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIH/NIAMS)R01AR072036 United States
National Institutes of Health/National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIH/NIAMS)R01AR067279 United States
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)R01HL139883 United States
CitationJournal: Nature / Year: 2020
Title: Cryo-EM structure of the inhibited (10S) form of myosin II.
Authors: Shixin Yang / Prince Tiwari / Kyoung Hwan Lee / Osamu Sato / Mitsuo Ikebe / Raúl Padrón / Roger Craig /
Abstract: Myosin II is the motor protein that enables muscle cells to contract and nonmuscle cells to move and change shape. The molecule has two identical heads attached to an elongated tail, and can exist in ...Myosin II is the motor protein that enables muscle cells to contract and nonmuscle cells to move and change shape. The molecule has two identical heads attached to an elongated tail, and can exist in two conformations: 10S and 6S, named for their sedimentation coefficients. The 6S conformation has an extended tail and assembles into polymeric filaments, which pull on actin filaments to generate force and motion. In 10S myosin, the tail is folded into three segments and the heads bend back and interact with each other and the tail, creating a compact conformation in which ATPase activity, actin activation and filament assembly are all highly inhibited. This switched-off structure appears to function as a key energy-conserving storage molecule in muscle and nonmuscle cells, which can be activated to form functional filaments as needed-but the mechanism of its inhibition is not understood. Here we have solved the structure of smooth muscle 10S myosin by cryo-electron microscopy with sufficient resolution to enable improved understanding of the function of the head and tail regions of the molecule and of the key intramolecular contacts that cause inhibition. Our results suggest an atomic model for the off state of myosin II, for its activation and unfolding by phosphorylation, and for understanding the clustering of disease-causing mutations near sites of intramolecular interaction.
History
DepositionJun 12, 2020-
Header (metadata) releaseDec 2, 2020-
Map releaseDec 2, 2020-
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: 0.0125
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.0125
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6xe9
  • Surface level: 0.0125
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_22145.png

Downloads & links

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Map

FileDownload / File: emd_22145.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation10S myosin II (smooth muscle)
Voxel sizeX=Y=Z: 1.328 Å
Density
Contour LevelBy AUTHOR: 0.0125 / Movie #1: 0.0125
Minimum - Maximum-0.028260319 - 0.065150745
Average (Standard dev.)0.0001402507 (±0.001608689)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 398.4 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.3281.3281.328
M x/y/z300300300
origin x/y/z0.0000.0000.000
length x/y/z398.400398.400398.400
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ320320320
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS300300300
D min/max/mean-0.0280.0650.000

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Supplemental data

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Half map: 10S myosin II (smooth muscle) half map

Fileemd_22145_half_map_1.map
Annotation10S myosin II (smooth muscle) half map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: 10S myosin II (smooth muscle) half map

Fileemd_22145_half_map_2.map
Annotation10S myosin II (smooth muscle) half 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 : Smooth muscle myosin II

EntireName: Smooth muscle myosin II
Components
  • Complex: Smooth muscle myosin II
    • Protein or peptide: Myosin II heavy chain (smooth muscle)
    • Protein or peptide: Myosin light chain smooth muscle isoform
    • Protein or peptide: Myosin light chain 9

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Supramolecule #1: Smooth muscle myosin II

SupramoleculeName: Smooth muscle myosin II / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all / Details: Whole myosin II isolated from turkey gizzard
Source (natural)Organism: Meleagris gallopavo (turkey) / Organ: gizzard / Tissue: smooth muscle
Molecular weightTheoretical: 530 KDa

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Macromolecule #1: Myosin II heavy chain (smooth muscle)

MacromoleculeName: Myosin II heavy chain (smooth muscle) / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO / EC number: myosin ATPase
Source (natural)Organism: Meleagris gallopavo (turkey)
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: Meleagris gallopavo (turkey)
Molecular weightTheoretical: 16.989145 KDa
SequenceString:
MCDFSEEQTA EFKEAFQLFD RTGDGKILYS QCGDVMRALG QNPTNAEVMK VLGNPKSDEM NLKTLNFEQF LPMMQTIAKN KDQGCFEDY VEGLRVFDKE GNGTVMGAEI RHVLVTLGEK MTEEEVEQLV AGHEDSNGCI NYEELVRMVL SG

UniProtKB: Myosin light chain smooth muscle isoform

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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: Meleagris gallopavo (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

UniProtKB: EF-hand domain-containing protein

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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

Concentration0.1 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormulaName
0.15 MCH3COONasodium acetate
1.0 mMC14H24N2O10EGTA
2.5 mMMgCl2magnesium chloride
0.5 mMC10H16N5O13P3adenosine triphosphate
10.0 mMC7H15NO4SMOPS
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Support film - Film thickness: 2 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 283.15 K / Instrument: FEI VITROBOT MARK IV
DetailsThe specimen was cross-linked in presence of 0.1% glutaraldehyde for 60 seconds.

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 3.5 µm / Nominal defocus min: 1.5 µm / Nominal magnification: 105000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Digitization - Dimensions - Width: 5760 pixel / Digitization - Dimensions - Height: 4092 pixel / Number grids imaged: 2 / Number real images: 10951 / Average electron dose: 43.3 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 1765220
Startup modelType of model: OTHER / Details: 3D reconstruction from negative staining
Initial angle assignmentType: RANDOM ASSIGNMENT / Software - Name: RELION (ver. 3.0)
Final 3D classificationNumber classes: 6 / Software - Name: RELION (ver. 3.0)
Final angle assignmentType: PROJECTION MATCHING / Software - Name: RELION (ver. 3.0)
Final reconstructionNumber classes used: 3 / Applied symmetry - Point group: C1 (asymmetric) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 4.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0) / Number images used: 168613
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial model
PDB IDChain

1i84

source_name: PDB, initial_model_type: experimental model

2fxm

source_name: PDB, initial_model_type: experimental model
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-6xe9:
10S myosin II (smooth muscle)

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