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- EMDB-24400: Cryo-EM structure of the rigor state Jordan myosin-15-F-actin complex -

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Basic information

Entry
Database: EMDB / ID: EMD-24400
TitleCryo-EM structure of the rigor state Jordan myosin-15-F-actin complex
Map datathe rigor state Jordan myosin-15-F-actin complex
Sample
  • Complex: the rigor state Jordan myosin-15-F-actin complex
    • Complex: Actin
      • Protein or peptide: Actin, alpha skeletal muscle, intermediate form
    • Complex: Isoform 3 of Unconventional myosin-XV
      • Protein or peptide: Isoform 3 of Unconventional myosin-XV
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: MAGNESIUM ION
Function / homology
Function and homology information


actin-based cell projection / Striated Muscle Contraction / stereocilium bundle / stereocilium / vesicle transport along actin filament / myosin complex / microfilament motor activity / inner ear morphogenesis / skeletal muscle thin filament assembly / striated muscle thin filament ...actin-based cell projection / Striated Muscle Contraction / stereocilium bundle / stereocilium / vesicle transport along actin filament / myosin complex / microfilament motor activity / inner ear morphogenesis / skeletal muscle thin filament assembly / striated muscle thin filament / response to light stimulus / skeletal muscle fiber development / stress fiber / locomotory behavior / actin filament organization / actin filament / sensory perception of sound / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / actin filament binding / actin cytoskeleton / vesicle / hydrolase activity / ATP binding / cytosol / cytoplasm
Similarity search - Function
Class XV myosin, motor domain / Myosin-XV, FERM domain C-lobe / MyTH4 domain / MyTH4 domain superfamily / MyTH4 domain / MyTH4 domain profile. / Domain in Myosin and Kinesin Tails / IQ calmodulin-binding motif / Variant SH3 domain / FERM central domain ...Class XV myosin, motor domain / Myosin-XV, FERM domain C-lobe / MyTH4 domain / MyTH4 domain superfamily / MyTH4 domain / MyTH4 domain profile. / Domain in Myosin and Kinesin Tails / IQ calmodulin-binding motif / Variant SH3 domain / FERM central domain / 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 / FERM central domain / FERM superfamily, second domain / FERM domain / FERM domain profile. / Actins signature 1. / Actin, conserved site / Actins signature 2. / Kinesin motor domain superfamily / Actin/actin-like conserved site / Actins and actin-related proteins signature. / Actin / Actin family / Actin / ATPase, nucleotide binding domain / Src homology 3 domains / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / PH-like domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Actin, alpha skeletal muscle / Unconventional myosin-XV
Similarity search - Component
Biological speciesGallus gallus (chicken) / Mus musculus (house mouse) / Chicken (chicken)
Methodhelical reconstruction / cryo EM / Resolution: 3.76 Å
AuthorsGong R / Reynolds MJ / Gurel P / Alushin GM
Funding support United States, 3 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Dental and Craniofacial Research (NIH/NIDCR)DP5OD017885 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM141044 United States
National Institutes of Health/National Institute on Deafness and Other Communication Disorders (NIH/NIDCD)R01DC018827 United States
Citation
Journal: Sci Adv / Year: 2022
Title: Structural basis for tunable control of actin dynamics by myosin-15 in mechanosensory stereocilia.
Authors: Rui Gong / Fangfang Jiang / Zane G Moreland / Matthew J Reynolds / Santiago Espinosa de Los Reyes / Pinar Gurel / Arik Shams / James B Heidings / Michael R Bowl / Jonathan E Bird / Gregory M Alushin /
Abstract: The motor protein myosin-15 is necessary for the development and maintenance of mechanosensory stereocilia, and mutations in myosin-15 cause hereditary deafness. In addition to transporting actin ...The motor protein myosin-15 is necessary for the development and maintenance of mechanosensory stereocilia, and mutations in myosin-15 cause hereditary deafness. In addition to transporting actin regulatory machinery to stereocilia tips, myosin-15 directly nucleates actin filament ("F-actin") assembly, which is disrupted by a progressive hearing loss mutation (p.D1647G, ""). Here, we present cryo-electron microscopy structures of myosin-15 bound to F-actin, providing a framework for interpreting the impacts of deafness mutations on motor activity and actin nucleation. Rigor myosin-15 evokes conformational changes in F-actin yet maintains flexibility in actin's D-loop, which mediates inter-subunit contacts, while the mutant locks the D-loop in a single conformation. Adenosine diphosphate-bound myosin-15 also locks the D-loop, which correspondingly blunts actin-polymerization stimulation. We propose myosin-15 enhances polymerization by bridging actin protomers, regulating nucleation efficiency by modulating actin's structural plasticity in a myosin nucleotide state-dependent manner. This tunable regulation of actin polymerization could be harnessed to precisely control stereocilium height.
#1: Journal: Biorxiv / Year: 2021
Title: Structural basis for tunable control of actin dynamics by myosin-15 in mechanosensory stereocilia
Authors: Gong R / Jiang F / Moreland ZG / Reynolds MJ / Gurel PS / Shams A / Bowl MR / Bird JE / Alushin GM
History
DepositionJul 5, 2021-
Header (metadata) releaseJul 28, 2021-
Map releaseJul 28, 2021-
UpdateAug 3, 2022-
Current statusAug 3, 2022Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.015
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.015
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  • Surface view with fitted model
  • Atomic models: PDB-7rb9
  • Surface level: 0.015
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-7rb9
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_24400.png

Downloads & links

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Map

FileDownload / File: emd_24400.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationthe rigor state Jordan myosin-15-F-actin complex
Voxel sizeX=Y=Z: 1.03 Å
Density
Contour LevelBy AUTHOR: 0.015 / Movie #1: 0.015
Minimum - Maximum-0.038739294 - 0.09062594
Average (Standard dev.)3.827548e-05 (±0.0021799388)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 527.36 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.031.031.03
M x/y/z512512512
origin x/y/z0.0000.0000.000
length x/y/z527.360527.360527.360
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ400400400
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS512512512
D min/max/mean-0.0390.0910.000

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Supplemental data

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Mask #1

Fileemd_24400_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half1

Fileemd_24400_half_map_1.map
Annotationhalf1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half2

Fileemd_24400_half_map_2.map
Annotationhalf2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : the rigor state Jordan myosin-15-F-actin complex

EntireName: the rigor state Jordan myosin-15-F-actin complex
Components
  • Complex: the rigor state Jordan myosin-15-F-actin complex
    • Complex: Actin
      • Protein or peptide: Actin, alpha skeletal muscle, intermediate form
    • Complex: Isoform 3 of Unconventional myosin-XV
      • Protein or peptide: Isoform 3 of Unconventional myosin-XV
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: MAGNESIUM ION

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Supramolecule #1: the rigor state Jordan myosin-15-F-actin complex

SupramoleculeName: the rigor state Jordan myosin-15-F-actin complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Molecular weightExperimental: 5.4 kDa/nm

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Supramolecule #2: Actin

SupramoleculeName: Actin / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Gallus gallus (chicken)

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Supramolecule #3: Isoform 3 of Unconventional myosin-XV

SupramoleculeName: Isoform 3 of Unconventional myosin-XV / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2
Source (natural)Organism: Mus musculus (house mouse)

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Macromolecule #1: Actin, alpha skeletal muscle, intermediate form

MacromoleculeName: Actin, alpha skeletal muscle, intermediate form / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Chicken (chicken)
Molecular weightTheoretical: 41.63143 KDa
SequenceString: DETTALVCDN GSGLVKAGFA GDDAPRAVFP SIVGRPRHQG VMVGMGQKDS YVGDEAQSKR GILTLKYPIE (HIC)GIITN WDD MEKIWHHTFY NELRVAPEEH PTLLTEAPLN PKANREKMTQ IMFETFNVPA MYVAIQAVLS LYASGRTTGI VLDSGDG VT HNVPIYEGYA ...String:
DETTALVCDN GSGLVKAGFA GDDAPRAVFP SIVGRPRHQG VMVGMGQKDS YVGDEAQSKR GILTLKYPIE (HIC)GIITN WDD MEKIWHHTFY NELRVAPEEH PTLLTEAPLN PKANREKMTQ IMFETFNVPA MYVAIQAVLS LYASGRTTGI VLDSGDG VT HNVPIYEGYA LPHAIMRLDL AGRDLTDYLM KILTERGYSF VTTAEREIVR DIKEKLCYVA LDFENEMATA ASSSSLEK S YELPDGQVIT IGNERFRCPE TLFQPSFIGM ESAGIHETTY NSIMKCDIDI RKDLYANNVM SGGTTMYPGI ADRMQKEIT ALAPSTMKIK IIAPPERKYS VWIGGSILAS LSTFQQMWIT KQEYDEAGPS IVHRKCF

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Macromolecule #2: Isoform 3 of Unconventional myosin-XV

MacromoleculeName: Isoform 3 of Unconventional myosin-XV / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 78.124672 KDa
Recombinant expressionOrganism: Spodoptera aff. frugiperda 2 RZ-2014 (butterflies/moths)
SequenceString: EDGVEDMTQL EDLQETTVLA NLKTRFERNL IYTYIGSILV SVNPYRMFAI YGPEQVQQYS GRALGENPPH LFAIANLAFA KMLDAKQNQ CVIISGESGS GKTEATKLIL RCLAAMNQRR DVMQQIKILE ATPLLEAFGN AKTVRNDNSS RFGKFVEIFL E GGVICGAI ...String:
EDGVEDMTQL EDLQETTVLA NLKTRFERNL IYTYIGSILV SVNPYRMFAI YGPEQVQQYS GRALGENPPH LFAIANLAFA KMLDAKQNQ CVIISGESGS GKTEATKLIL RCLAAMNQRR DVMQQIKILE ATPLLEAFGN AKTVRNDNSS RFGKFVEIFL E GGVICGAI TSQYLLEKSR IVFQAKNERN YHIFYELLAG LPAQLRQAFS LQEAETYYYL NQGGNCEIAG KSDADDFRRL LA AMEVLGF TSEDQDSIFR ILASILHLGN VYFEKHETDA QEVASVVSAR EIQAVAELLQ VSPEGLQKAI TFKVTETIRE KIF TPLTVE SAVDARDAIA KVLYALLFGW LITRVNALVS PKQDTLSIAI LDIYGFEDLS FNSFEQLCIN YANENLQYLF NKIV FQEEQ EEYIREQMDW REIAFADNQP CINLISLKPY GILRILDGQC CFPQATDHTF LQKCHYHHGA NPLYSKPKMP LPEFT IKHY AGKVTYQVHK FLDKNHDQVR QDVLDLFVHS RTRVVAHLFS SHAAQTAPPR LGKSSSITRL YKAHTVAAKF QQSLLD LVE KMERCNPLFV RCLKPNHKKE PGLFEPDVMM AQLRYSGVLE TVRIRKEGFP VRLPFQVFID RYRCLVALKL NVPADGD MC VSLLSRLCTV TPDMYRVGIS KLFLKEHLHQ LLESMRERVQ NRA

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Macromolecule #3: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 3 / Number of copies: 3 / 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 #4: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 4 / Number of copies: 3 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statefilament

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Sample preparation

BufferpH: 7
Details: 10 mM imidazole pH 7.0, 50 mM KCl, 1 mM MgCl2, 1 mM EGTA, 0.5 mM DTT, 0.01% NaN3
GridModel: C-flat-1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: OTHER
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 293 K / Instrument: LEICA EM GP

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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 / Nominal defocus max: 3.5 µm / Nominal defocus min: 1.5 µm / Nominal magnification: 29000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Digitization - Frames/image: 1-40 / Number grids imaged: 1 / Average exposure time: 10.0 sec. / Average electron dose: 60.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Segment selectionNumber selected: 113662 / Software - Name: RELION (ver. 3.0)
CTF correctionSoftware - Name: CTFFIND (ver. 4.1)
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

6bno

Final angle assignmentType: NOT APPLICABLE / Software - Name: RELION (ver. 3.0)
Final reconstructionApplied symmetry - Helical parameters - Δz: 27.08 Å
Applied symmetry - Helical parameters - Δ&Phi: -166.66 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 3.76 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0) / Number images used: 91340
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

6bno

RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-7rb9:
Cryo-EM structure of the rigor state Jordan myosin-15-F-actin complex

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