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- EMDB-23810: Structure of the autoinhibited state of smooth muscle myosin-2 -

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Basic information

Entry
Database: EMDB / ID: EMD-23810
TitleStructure of the autoinhibited state of smooth muscle myosin-2
Map data
Sample
  • Complex: Smooth muscle myosin-2 10S complex
    • Protein or peptide: Myosin-11
    • Protein or peptide: Myosin light polypeptide 6
    • Protein or peptide: Myosin regulatory light chain 2, smooth muscle major isoform
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: PHOSPHATE ION
  • Ligand: MAGNESIUM ION
KeywordsMuscle contraction / ATPase / autoinhibition / 10S / CONTRACTILE PROTEIN
Function / homology
Function and homology information


RHO GTPases activate PAKs / myosin II filament / Smooth Muscle Contraction / myofibril assembly / elastic fiber assembly / myosin light chain binding / skeletal muscle myosin thick filament assembly / myosin II binding / muscle myosin complex / actomyosin ...RHO GTPases activate PAKs / myosin II filament / Smooth Muscle Contraction / myofibril assembly / elastic fiber assembly / myosin light chain binding / skeletal muscle myosin thick filament assembly / myosin II binding / muscle myosin complex / actomyosin / myosin filament / actomyosin structure organization / myosin II complex / cardiac muscle cell development / structural constituent of muscle / microfilament motor activity / myofibril / myosin heavy chain binding / smooth muscle contraction / stress fiber / ADP binding / actin filament binding / actin binding / calmodulin binding / calcium ion binding / magnesium ion binding / ATP binding / cytosol / 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. ...: / 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 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
Myosin light polypeptide 6 / Myosin regulatory light chain 2, smooth muscle major isoform / Myosin-11
Similarity search - Component
Biological speciesGallus gallus (chicken)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsHeissler SM / Arora AS
CitationJournal: Sci Adv / Year: 2021
Title: Cryo-EM structure of the autoinhibited state of myosin-2.
Authors: Sarah M Heissler / Amandeep S Arora / Neil Billington / James R Sellers / Krishna Chinthalapudi /
Abstract: We solved the near-atomic resolution structure of smooth muscle myosin-2 in the autoinhibited state (10) using single-particle cryo–electron microscopy. The 3.4-Å structure reveals the precise ...We solved the near-atomic resolution structure of smooth muscle myosin-2 in the autoinhibited state (10) using single-particle cryo–electron microscopy. The 3.4-Å structure reveals the precise molecular architecture of 10 and the structural basis for myosin-2 regulation. We reveal the position of the phosphorylation sites that control myosin autoinhibition and activation by phosphorylation of the regulatory light chain. Further, we present a previously unidentified conformational state in myosin-2 that traps ADP and P produced by the hydrolysis of ATP in the active site. This noncanonical state represents a branch of the myosin enzyme cycle and explains the autoinhibition of the enzyme function of 10 along with its reduced affinity for actin. Together, our structure defines the molecular mechanisms that drive 10 formation, stabilization, and relief by phosphorylation of the regulatory light chain.
History
DepositionApr 8, 2021-
Header (metadata) releaseJan 5, 2022-
Map releaseJan 5, 2022-
UpdateMay 29, 2024-
Current statusMay 29, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.12
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.12
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7mf3
  • Surface level: 0.12
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_23810.png

Downloads & links

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Map

FileDownload / File: emd_23810.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.9 Å/pix.
x 512 pix.
= 460.288 Å		0.9 Å/pix.
x 512 pix.
= 460.288 Å		0.9 Å/pix.
x 512 pix.
= 460.288 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.899 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.12 / Movie #1: 0.12
Minimum - Maximum-0.26195696 - 0.45025653
Average (Standard dev.)0.00066997716 (±0.009175238)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 460.288 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.8990.8990.899
M x/y/z512512512
origin x/y/z0.0000.0000.000
length x/y/z460.288460.288460.288
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS512512512
D min/max/mean-0.2620.4500.001

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Supplemental data

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Sample components

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Entire : Smooth muscle myosin-2 10S complex

EntireName: Smooth muscle myosin-2 10S complex
Components
  • Complex: Smooth muscle myosin-2 10S complex
    • Protein or peptide: Myosin-11
    • Protein or peptide: Myosin light polypeptide 6
    • Protein or peptide: Myosin regulatory light chain 2, smooth muscle major isoform
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: PHOSPHATE ION
  • Ligand: MAGNESIUM ION

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Supramolecule #1: Smooth muscle myosin-2 10S complex

SupramoleculeName: Smooth muscle myosin-2 10S complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Gallus gallus (chicken) / Organ: Gizzard
Molecular weightTheoretical: 531.256 KDa

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Macromolecule #1: Myosin-11

MacromoleculeName: Myosin-11 / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Gallus gallus (chicken) / Organ: gizzard
Molecular weightTheoretical: 229.018953 KDa
SequenceString: SQKPLSDDEK FLFVDKNFVN NPLAQADWSA KKLVWVPSEK HGFEAASIKE EKGDEVTVEL QENGKKVTLS KDDIQKMNPP KFSKVEDMA ELTCLNEASV LHNLRERYFS GLIYTYSGLF CVVINPYKQL PIYSEKIIDM YKGKKRHEMP PHIYAIADTA Y RSMLQDRE ...String:
SQKPLSDDEK FLFVDKNFVN NPLAQADWSA KKLVWVPSEK HGFEAASIKE EKGDEVTVEL QENGKKVTLS KDDIQKMNPP KFSKVEDMA ELTCLNEASV LHNLRERYFS GLIYTYSGLF CVVINPYKQL PIYSEKIIDM YKGKKRHEMP PHIYAIADTA Y RSMLQDRE DQSILCTGES GAGKTENTKK VIQYLAVVAS SHKGKKDTSI TQGPSFSYGE LEKQLLQANP ILEAFGNAKT VK NDNSSRF GKFIRINFDV TGYIVGANIE TYLLEKSRAI RQAKDERTFH IFYYLIAGAS EQMRNDLLLE GFNNYTFLSN GHV PIPAQQ DDEMFQETLE AMTIMGFTEE EQTSILRVVS SVLQLGNIVF KKERNTDQAS MPDNTAAQKV CHLMGINVTD FTRS ILTPR IKVGRDVVQK AQTKEQADFA IEALAKAKFE RLFRWILTRV NKALDKTKRQ GASFLGILDI AGFEIFEINS FEQLC INYT NEKLQQLFNH TMFILEQEEY QREGIEWNFI DFGLDLQPCI ELIERPTNPP GVLALLDEEC WFPKATDTSF VEKLIQ EQG NHAKFQKSKQ LKDKTEFCIL HYAGKVTYNA SAWLTKNMDP LNDNVTSLLN QSSDKFVADL WKDVDRIVGL DQMAKMT ES SLPSASKTKK GMFRTVGQLY KEQLTKLMTT LRNTNPNFVR CIIPNHEKRA GKLDAHLVLE QLRCNGVLEG IRICRQGF P NRIVFQEFRQ RYEILAANAI PKGFMDGKQA CILMIKALEL DPNLYRIGQS KIFFRTGVLA HLEEERDLKI TDVIIAFQA QCRGYLARKA FAKRQQQLTA MKVIQRNCAA YLKLRNWQWW RLFTKVKPLL QVTRQEEEMQ AKDEELQRTK ERQQKAEAEL KELEQKHTQ LCEEKNLLQE KLQAETELYA EAEEMRVRLA AKKQELEEIL HEMEARIEEE EERSQQLQAE KKKMQQQMLD L EEQLEEEE AARQKLQLEK VTADGKIKKM EDDILIMEDQ NNKLTKERKL LEERVSDLTT NLAEEEEKAK NLTKLKNKHE SM ISELEVR LKKEEKSRQE LEKIKRKLEG ESSDLHEQIA ELQAQIAELK AQLAKKEEEL QAALARLEDE TSQKNNALKK IRE LESHIS DLQEDLESEK AARNKAEKQK RDLSEELEAL KTELEDTLDT TATQQELRAK REQEVTVLKR ALEEETRTHE AQVQ EMRQK HTQAVEELTE QLEQFKRAKA NLDKTKQTLE KDNADLANEI RSLSQAKQDV EHKKKKLEVQ LQDLQSKYSD GERVR TELN EKVHKLQIEV ENVTSLLNEA ESKNIKLTKD VATLGSQLQD TQELLQEETR QKLNVTTKLR QLEDDKNSLQ EQLDEE VEA KQNLERHIST LTIQLSDSKK KLQEFTATVE TMEEGKKKLQ REIESLTQQF EEKAASYDKL EKTKNRLQQE LDDLVVD LD NQRQLVSNLE KKQKKFDQML AEEKNISSKY ADERDRAEAE AREKETKALS LARALEEALE AKEELERTNK MLKAEMED L VSSKDDVGKN VHELEKSKRT LEQQVEEMKT QLEELEDELQ AAEDAKLRLE VNMQAMKSQF ERDLQARDEQ NEEKRRQLL KQLHEHETEL EDERKQRALA AAAKKKLEVD VKDLESQVDS ANKAREEAIK QLRKLQAQMK DYQRDLDDAR AAREEIFATA RENEKKAKN LEAELIQLQE DLAAAERARK QADLEKEEMA EELASANSGR TSLQDEKRRL EARIAQLEEE LDEEHSNIET M SDRMRKAV QQAEQLNNEL ATERATAQKN ENARQQLERQ NKELRSKLQE MEGAVKSKFK STIAALEAKI ASLEEQLEQE AR EKQAAAK TLRQKDKKLK DALLQVEDER KQAEQYKDQA EKGNLRLKQL KRQLEEAEEE SQRINANRRK LQRELDEATE SND ALGREV AALKSKLRRG NEPVSFAPPR RSGGRRVIEN ATDGGEEEID GRDGDFNGKA SE

UniProtKB: Myosin-11

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Macromolecule #2: Myosin light polypeptide 6

MacromoleculeName: Myosin light polypeptide 6 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Gallus gallus (chicken) / Organ: Gizzard
Molecular weightTheoretical: 16.873025 KDa
SequenceString:
CDFSEEQTAE FKEAFQLFDR TGDGKILYSQ CGDVMRALGQ NPTNAEVMKV LGNPKSDEMN LKTLKFEQFL PMMQTIAKNK DQGCFEDYV EGLRVFDKEG NGTVMGAEIR HVLVTLGEKM TEEEVEQLVA GHEDSNGCIN YEELVRMVLS G

UniProtKB: Myosin light polypeptide 6

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Macromolecule #3: Myosin regulatory light chain 2, smooth muscle major isoform

MacromoleculeName: Myosin regulatory light chain 2, smooth muscle major isoform
type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Gallus gallus (chicken) / Organ: Gizzard
Molecular weightTheoretical: 19.741047 KDa
SequenceString:
SSKRAKAKTT KKRPQRATSN VFAMFDQSQI QEFKEAFNMI DQNRDGFIDK EDLHDMLASM GKNPTDEYLE GMMSEAPGPI NFTMFLTMF GEKLNGTDPE DVIRNAFACF DEEASGFIHE DHLRELLTTM GDRFTDEEVD EMYREAPIDK KGNFNYVEFT R ILKHGAKD KDD

UniProtKB: Myosin regulatory light chain 2, smooth muscle major isoform

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Macromolecule #4: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 4 / Number of copies: 2 / Formula: ADP
Molecular weightTheoretical: 427.201 Da
Chemical component information

ChemComp-ADP:
ADENOSINE-5'-DIPHOSPHATE / ADP, energy-carrying molecule*YM

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Macromolecule #5: PHOSPHATE ION

MacromoleculeName: PHOSPHATE ION / type: ligand / ID: 5 / Number of copies: 2 / Formula: PO4
Molecular weightTheoretical: 94.971 Da
Chemical component information

ChemComp-PO4:
PHOSPHATE ION

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Macromolecule #6: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 6 / Number of copies: 4 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation statetissue

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Sample preparation

BufferpH: 7.3 / Component - Concentration: 150.0 mM / Component - Formula: NaCl / Component - Name: sodium chloride / Details: 150 mM NaCl, 1mM EGTA, 2mM MgCl2
GridModel: C-flat-1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 45 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 292 K / Instrument: LEICA EM GP
Details1 mg/ml

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number grids imaged: 1 / Average electron dose: 65.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD / Cs: 0.01 mm / Nominal magnification: 81000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

1br2

Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 234464
Initial angle assignmentType: OTHER / Software - Name: cryoSPARC
Final angle assignmentType: OTHER / Software - Name: cryoSPARC

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Atomic model buiding 1

Initial modelPDB ID:

5i4e


Chain - Chain ID: A / Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-7mf3:
Structure of the autoinhibited state of smooth muscle myosin-2

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