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- EMDB-28080: Human cardiac myosin II and associated essential light chain in t... -

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Basic information

Entry
Database: EMDB / ID: EMD-28080
TitleHuman cardiac myosin II and associated essential light chain in the rigor conformation
Map dataPrimary map for human beta-cardiac myosin II in the rigor form and the associated essential light chain.
Sample
  • Complex: Complex of the human beta cardiac myosin II in the rigor form with the associated essential light chain.
    • Complex: Human beta-cardiac myosin II
      • Protein or peptide: Beta-cardiac myosin II
    • Complex: Mouse skeletal essential light chain
      • Protein or peptide: Myosin light chain 1/3, skeletal muscle isoform
Keywordsactin / tropomyosin / myosin / cardiac / CONTRACTILE PROTEIN
Function / homology
Function and homology information


regulation of slow-twitch skeletal muscle fiber contraction / regulation of the force of skeletal muscle contraction / Striated Muscle Contraction / muscle myosin complex / regulation of the force of heart contraction / transition between fast and slow fiber / myosin filament / adult heart development / cardiac muscle hypertrophy in response to stress / muscle filament sliding ...regulation of slow-twitch skeletal muscle fiber contraction / regulation of the force of skeletal muscle contraction / Striated Muscle Contraction / muscle myosin complex / regulation of the force of heart contraction / transition between fast and slow fiber / myosin filament / adult heart development / cardiac muscle hypertrophy in response to stress / muscle filament sliding / myosin complex / myosin II complex / structural constituent of muscle / ventricular cardiac muscle tissue morphogenesis / microfilament motor activity / myofibril / skeletal muscle contraction / striated muscle contraction / ATP metabolic process / cardiac muscle contraction / stress fiber / muscle contraction / regulation of heart rate / sarcomere / Z disc / actin filament binding / calmodulin binding / calcium ion binding / ATP binding / cytoplasm
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. / IQ motif, EF-hand binding site / 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. / IQ motif, EF-hand binding site / Myosin head, motor domain / Myosin head (motor domain) / Myosin motor domain profile. / Myosin. Large ATPases. / IQ motif profile. / Kinesin motor domain superfamily / : / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Myosin light chain 1/3, skeletal muscle isoform / Myosin-7
Similarity search - Component
Biological speciesHomo sapiens (human) / Mus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.8 Å
AuthorsDoran MH / Lehman W / Rynkiewicz MJ
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)R01HL036153 United States
CitationJournal: J Gen Physiol / Year: 2023
Title: Conformational changes linked to ADP release from human cardiac myosin bound to actin-tropomyosin.
Authors: Matthew H Doran / Michael J Rynkiewicz / David Rasicci / Skylar M L Bodt / Meaghan E Barry / Esther Bullitt / Christopher M Yengo / Jeffrey R Moore / William Lehman /
Abstract: Following binding to the thin filament, β-cardiac myosin couples ATP-hydrolysis to conformational rearrangements in the myosin motor that drive myofilament sliding and cardiac ventricular ...Following binding to the thin filament, β-cardiac myosin couples ATP-hydrolysis to conformational rearrangements in the myosin motor that drive myofilament sliding and cardiac ventricular contraction. However, key features of the cardiac-specific actin-myosin interaction remain uncertain, including the structural effect of ADP release from myosin, which is rate-limiting during force generation. In fact, ADP release slows under experimental load or in the intact heart due to the afterload, thereby adjusting cardiac muscle power output to meet physiological demands. To further elucidate the structural basis of this fundamental process, we used a combination of cryo-EM reconstruction methodologies to determine structures of the human cardiac actin-myosin-tropomyosin filament complex at better than 3.4 Å-resolution in the presence and in the absence of Mg2+·ADP. Focused refinements of the myosin motor head and its essential light chains in these reconstructions reveal that small changes in the nucleotide-binding site are coupled to significant rigid body movements of the myosin converter domain and a 16-degree lever arm swing. Our structures provide a mechanistic framework to understand the effect of ADP binding and release on human cardiac β-myosin, and offer insights into the force-sensing mechanism displayed by the cardiac myosin motor.
History
DepositionSep 8, 2022-
Header (metadata) releaseJan 11, 2023-
Map releaseJan 11, 2023-
UpdateJun 19, 2024-
Current statusJun 19, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_28080.png

Downloads & links

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Map

FileDownload / File: emd_28080.map.gz / Format: CCP4 / Size: 325 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationPrimary map for human beta-cardiac myosin II in the rigor form and the associated essential light chain.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.08 Å/pix.
x 440 pix.
= 474.32 Å		1.08 Å/pix.
x 440 pix.
= 474.32 Å		1.08 Å/pix.
x 440 pix.
= 474.32 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.078 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0117
Minimum - Maximum-0.015528124 - 0.04534486
Average (Standard dev.)0.000023983008 (±0.0005957385)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions440440440
Spacing440440440
CellA=B=C: 474.31998 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_28080_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Unmasked and relion filtered version of the primary map.

Fileemd_28080_additional_1.map
AnnotationUnmasked and relion filtered version of the primary map.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map 2.

Fileemd_28080_half_map_1.map
AnnotationHalf map 2.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map 2.

Fileemd_28080_half_map_2.map
AnnotationHalf map 2.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Complex of the human beta cardiac myosin II in the rigor form wit...

EntireName: Complex of the human beta cardiac myosin II in the rigor form with the associated essential light chain.
Components
  • Complex: Complex of the human beta cardiac myosin II in the rigor form with the associated essential light chain.
    • Complex: Human beta-cardiac myosin II
      • Protein or peptide: Beta-cardiac myosin II
    • Complex: Mouse skeletal essential light chain
      • Protein or peptide: Myosin light chain 1/3, skeletal muscle isoform

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Supramolecule #1: Complex of the human beta cardiac myosin II in the rigor form wit...

SupramoleculeName: Complex of the human beta cardiac myosin II in the rigor form with the associated essential light chain.
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all

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Supramolecule #2: Human beta-cardiac myosin II

SupramoleculeName: Human beta-cardiac myosin II / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #3: Mouse skeletal essential light chain

SupramoleculeName: Mouse skeletal essential light chain / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2
Source (natural)Organism: Mus musculus (house mouse) / Cell: C2C12

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Macromolecule #1: Beta-cardiac myosin II

MacromoleculeName: Beta-cardiac myosin II / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 99.157695 KDa
Recombinant expressionOrganism: Mus musculus (house mouse)
SequenceString: MGDSEMAVFG AAAPYLRKSE KERLEAQTRP FDLKKDVFVP DDKQEFVKAK IVSREGGKVT AETEYGKTVT VKEDQVMQQN PPKFDKIED MAMLTFLHEP AVLYNLKDRY GSWMIYTYSG LFCVTVNPYK WLPVYTPEVV AAYRGKKRSE APPHIFSISD N AYQYMLTD ...String:
MGDSEMAVFG AAAPYLRKSE KERLEAQTRP FDLKKDVFVP DDKQEFVKAK IVSREGGKVT AETEYGKTVT VKEDQVMQQN PPKFDKIED MAMLTFLHEP AVLYNLKDRY GSWMIYTYSG LFCVTVNPYK WLPVYTPEVV AAYRGKKRSE APPHIFSISD N AYQYMLTD RENQSILITG ESGAGKTVNT KRVIQYFAVI AAIGDRSKKD QSPGKGTLED QIIQANPALE AFGNAKTVRN DN SSRFGKF IRIHFGATGK LASADIETYL LEKSRVIFQL KAERDYHIFY QILSNKKPEL LDMLLITNNP YDYAFISQGE TTV ASIDDA EELMATDNAF DVLGFTSEEK NSMYKLTGAI MHFGNMKFKL KQREEQAEPD GTEEADKSAY LMGLNSADLL KGLC HPRVK VGNEYVTKGQ NVQQVIYATG ALAKAVYERM FNWMVTRINA TLETKQPRQY FIGVLDIAGF EIFDFNSFEQ LCINF TNEK LQQFFNHHMF VLEQEEYKKE GIEWTFIDFG MDLQACIDLI EKPMGIMSIL EEECMFPKAT DMTFKAKLFD NHLGKS ANF QKPRNIKGKP EAHFSLIHYA GIVDYNIIGW LQKNKDPLNE TVVGLYQKSS LKLLSTLFAN YAGADAPIEK GKGKAKK GS SFQTVSALHR ENLNKLMTNL RSTHPHFVRC IIPNETKSPG VMDNPLVMHQ LRCNGVLEGI RICRKGFPNR ILYGDFRQ R YRILNPAAIP EGQFIDSRKG AEKLLSSLDI DHNQYKFGHT KVFFKAGLLG LLEEMRDERL SRIITRIQAQ SRGVLARME YKKLLERRDS LLVIQWNIRA FMGVKNWPWM KLYFKIKPLL KSGLNDIFEA QKIEWHEDYK DDDDK

UniProtKB: Myosin-7

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Macromolecule #2: Myosin light chain 1/3, skeletal muscle isoform

MacromoleculeName: Myosin light chain 1/3, skeletal muscle isoform / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 20.62049 KDa
SequenceString:
MAPKKDVKKP AAAPAPAPAP APAPAKPKEE KIDLSAIKIE FSKEQQEDFK EAFLLFDRTG ECKITLSQVG DVLRALGTNP TNAEVKKVL GNPSNEEMNA KKIEFEQFLP MMQAISNNKD QGGYEDFVEG LRVFDKEGNG TVMGAELRHV LATLGEKMKE E EVEALLAG QEDSNGCINY EAFVKHIMSV

UniProtKB: Myosin light chain 1/3, skeletal muscle isoform

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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

Concentration0.13 mg/mL
BufferpH: 7
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 400 / Support film - Material: GOLD / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec.
Details: 15 mA was used in the Pelco Easiglow glow discharge machine
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 283 K / Instrument: FEI VITROBOT MARK III
DetailsThis complex was part of a larger filament containing actin-tropomyosin. The map was a result of a focused single particle approach.

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsEnergy filter - Name: In-column Omega Filter / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Detector mode: COUNTING / Digitization - Frames/image: 1-35 / Number grids imaged: 4 / Number real images: 3961 / Average exposure time: 3.12 sec. / Average electron dose: 53.7 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 80000 / Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 0.7000000000000001 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 176178
Startup modelType of model: OTHER / Details: Featureless Cylinder
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1.1) / Number images used: 88048
Initial angle assignmentType: NOT APPLICABLE / Software - Name: RELION (ver. 3.1.1)
Final angle assignmentType: NOT APPLICABLE / Software - Name: RELION (ver. 3.1.1)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

6x5z


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL / Protocol: OTHER
Output model

PDB-8efd:
Human cardiac myosin II and associated essential light chain in the rigor conformation

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