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- EMDB-34121: Cryo-EM structure of full-length Myosin Va in the autoinhibited state -

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Basic information

Entry
Database: EMDB / ID: EMD-34121
TitleCryo-EM structure of full-length Myosin Va in the autoinhibited state
Map dataoverall_map
Sample
  • Complex: Myosin Va and Calmodulin complex
    • Protein or peptide: Unconventional myosin-Va
    • Protein or peptide: Calmodulin-1
Function / homology
Function and homology information


CaMK IV-mediated phosphorylation of CREB / Cam-PDE 1 activation / CREB1 phosphorylation through the activation of CaMKII/CaMKK/CaMKIV cascasde / Glycogen breakdown (glycogenolysis) / Activation of RAC1 downstream of NMDARs / Reduction of cytosolic Ca++ levels / Sodium/Calcium exchangers / Activation of Ca-permeable Kainate Receptor / CLEC7A (Dectin-1) induces NFAT activation / Synthesis of IP3 and IP4 in the cytosol ...CaMK IV-mediated phosphorylation of CREB / Cam-PDE 1 activation / CREB1 phosphorylation through the activation of CaMKII/CaMKK/CaMKIV cascasde / Glycogen breakdown (glycogenolysis) / Activation of RAC1 downstream of NMDARs / Reduction of cytosolic Ca++ levels / Sodium/Calcium exchangers / Activation of Ca-permeable Kainate Receptor / CLEC7A (Dectin-1) induces NFAT activation / Synthesis of IP3 and IP4 in the cytosol / RHO GTPases activate PAKs / Calmodulin induced events / Inactivation, recovery and regulation of the phototransduction cascade / Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / Calcineurin activates NFAT / eNOS activation / Ion transport by P-type ATPases / Unblocking of NMDA receptors, glutamate binding and activation / Protein methylation / RAF activation / VEGFR2 mediated vascular permeability / RAS processing / Smooth Muscle Contraction / Ca2+ pathway / FCERI mediated Ca+2 mobilization / RAF/MAP kinase cascade / RHO GTPases activate IQGAPs / Extra-nuclear estrogen signaling / PKA activation / Platelet degranulation / Stimuli-sensing channels / Ion homeostasis / type 3 metabotropic glutamate receptor binding / myosin complex / organelle localization by membrane tethering / regulation of cardiac muscle cell action potential / mitochondrion-endoplasmic reticulum membrane tethering / autophagosome membrane docking / nitric-oxide synthase binding / protein phosphatase activator activity / cytoskeletal motor activity / adenylate cyclase binding / catalytic complex / detection of calcium ion / negative regulation of ryanodine-sensitive calcium-release channel activity / regulation of cardiac muscle contraction / calcium channel inhibitor activity / cellular response to interferon-beta / voltage-gated potassium channel complex / phosphatidylinositol 3-kinase binding / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / positive regulation of protein dephosphorylation / titin binding / regulation of ryanodine-sensitive calcium-release channel activity / sperm midpiece / calcium channel complex / adenylate cyclase activator activity / regulation of heart rate / nitric-oxide synthase regulator activity / protein serine/threonine kinase activator activity / sarcomere / regulation of cytokinesis / spindle microtubule / positive regulation of receptor signaling pathway via JAK-STAT / spindle pole / cellular response to type II interferon / response to calcium ion / calcium-dependent protein binding / G2/M transition of mitotic cell cycle / myelin sheath / actin binding / growth cone / transmembrane transporter binding / protein domain specific binding / centrosome / calcium ion binding / protein kinase binding / protein-containing complex / nucleoplasm / ATP binding / cytosol / cytoplasm
Similarity search - Function
Myosin 5a, cargo-binding domain / Class V myosin, motor domain / Dilute domain / DIL domain / Dilute domain profile. / DIL / IQ calmodulin-binding motif / Myosin, N-terminal, SH3-like / Myosin N-terminal SH3-like domain profile. / Short calmodulin-binding motif containing conserved Ile and Gln residues. ...Myosin 5a, cargo-binding domain / Class V myosin, motor domain / Dilute domain / DIL domain / Dilute domain profile. / DIL / IQ calmodulin-binding motif / 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
Unconventional myosin-Va / Calmodulin-1
Similarity search - Component
Biological speciesMus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.78 Å
AuthorsNiu F / Wei Z
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31971131, 31870757, 32170697, 31800643 China
CitationJournal: Sci Adv / Year: 2022
Title: Autoinhibition and activation mechanisms revealed by the triangular-shaped structure of myosin Va.
Authors: Fengfeng Niu / Yong Liu / Kang Sun / Shun Xu / Jiayuan Dong / Cong Yu / Kaige Yan / Zhiyi Wei /
Abstract: As the prototype of unconventional myosin motor family, myosin Va (MyoVa) transport cellular cargos along actin filaments in diverse cellular processes. The off-duty MyoVa adopts a closed and ...As the prototype of unconventional myosin motor family, myosin Va (MyoVa) transport cellular cargos along actin filaments in diverse cellular processes. The off-duty MyoVa adopts a closed and autoinhibited state, which can be relieved by cargo binding. The molecular mechanisms governing the autoinhibition and activation of MyoVa remain unclear. Here, we report the cryo-electron microscopy structure of the two full-length, closed MyoVa heavy chains in complex with 12 calmodulin light chains at 4.78-Å resolution. The MyoVa adopts a triangular structure with multiple intra- and interpolypeptide chain interactions in establishing the closed state with cargo binding and adenosine triphosphatase activity inhibited. Structural, biochemical, and cellular analyses uncover an asymmetric autoinhibition mechanism, in which the cargo-binding sites in the two MyoVa heavy chains are differently protected. Thus, specific and efficient MyoVa activation requires coincident binding of multiple cargo adaptors, revealing an intricate and elegant activity regulation of the motor in response to cargos.
History
DepositionAug 19, 2022-
Header (metadata) releaseDec 21, 2022-
Map releaseDec 21, 2022-
UpdateDec 21, 2022-
Current statusDec 21, 2022Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_34121.png

Downloads & links

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Map

FileDownload / File: emd_34121.map.gz / Format: CCP4 / Size: 824 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationoverall_map
Voxel sizeX=Y=Z: 1.072 Å
Density
Contour LevelBy AUTHOR: 0.35
Minimum - Maximum-0.4055887 - 1.2358571
Average (Standard dev.)-1.6887396e-05 (±0.026625745)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions600600600
Spacing600600600
CellA=B=C: 643.2 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: local map1

Fileemd_34121_additional_1.map
Annotationlocal_map1
Projections & Slices
AxesZYX

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Additional map: local map2

Fileemd_34121_additional_2.map
Annotationlocal_map2
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Additional map: local map3

Fileemd_34121_additional_3.map
Annotationlocal_map3
Projections & Slices
AxesZYX

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Half map: half A map

Fileemd_34121_half_map_1.map
Annotationhalf_A_map
Projections & Slices
AxesZYX

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Half map: half B map

Fileemd_34121_half_map_2.map
Annotationhalf_B_map
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Sample components

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Entire : Myosin Va and Calmodulin complex

EntireName: Myosin Va and Calmodulin complex
Components
  • Complex: Myosin Va and Calmodulin complex
    • Protein or peptide: Unconventional myosin-Va
    • Protein or peptide: Calmodulin-1

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Supramolecule #1: Myosin Va and Calmodulin complex

SupramoleculeName: Myosin Va and Calmodulin complex / type: complex / Chimera: Yes / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 630 KDa

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Macromolecule #1: Unconventional myosin-Va

MacromoleculeName: Unconventional myosin-Va / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 212.657359 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MAASELYTKF ARVWIPDPEE VWKSAELLKD YKPGDKVLLL HLEEGKDLEY RLDPKTGELP HLRNPDILVG ENDLTALSYL HEPAVLHNL RVRFIDSKLI YTYCGIVLVA INPYEQLPIY GEDIINAYSG QNMGDMDPHI FAVAEEAYKQ MARDERNQSI I VSGESGAG ...String:
MAASELYTKF ARVWIPDPEE VWKSAELLKD YKPGDKVLLL HLEEGKDLEY RLDPKTGELP HLRNPDILVG ENDLTALSYL HEPAVLHNL RVRFIDSKLI YTYCGIVLVA INPYEQLPIY GEDIINAYSG QNMGDMDPHI FAVAEEAYKQ MARDERNQSI I VSGESGAG KTVSAKYAMR YFATVSGSAS EANVEEKVLA SNPIMESIGN AKTTRNDNSS RFGKYIEIGF DKRYRIIGAN MR TYLLEKS RVVFQAEEER NYHIFYQLCA SAKLPEFKML RLGNADSFHY TKQGGSPMIE GVDDAKEMAH TRQACTLLGI SES YQMGIF RILAGILHLG NVGFASRDSD SCTIPPKHEP LTIFCDLMGV DYEEMCHWLC HRKLATATET YIKPISKLQA TNAR DALAK HIYAKLFNWI VDHVNQALHS AVKQHSFIGV LDIYGFETFE INSFEQFCIN YANEKLQQQF NMHVFKLEQE EYMKE QIPW TLIDFYDNQP CINLIESKLG ILDLLDEECK MPKGTDDTWA QKLYNTHLNK CALFEKPRMS NKAFIIKHFA DKVEYQ CEG FLEKNKDTVF EEQIKVLKSS KFKMLPELFQ DDEKAISPTS ATSSGRTPLT RVPVKPTKGR PGQTAKEHKK TVGHQFR NS LHLLMETLNA TTPHYVRCIK PNDFKFPFTF DEKRAVQQLR ACGVLETIRI SAAGFPSRWT YQEFFSRYRV LMKQKDVL G DRKQTCKNVL EKLILDKDKY QFGKTKIFFR AGQVAYLEKL RADKLRAACI RIQKTIRGWL LRKRYLCMQR AAITVQRYV RGYQARCYAK FLRRTKAATT IQKYWRMYVV RRRYKIRRAA TIVIQSYLRG YLTRNRYRKI LREYKAVIIQ KRVRGWLART HYKRTMKAI VYLQCCFRRM MAKRELKKLK IEARSVERYK KLHIGMENKI MQLQRKVDEQ NKDYKCLMEK LTNLEGVYNS E TEKLRNDV ERLQLSEEEA KVATGRVLSL QEEIAKLRKD LEQTRSEKKS IEERADKYKQ ETDQLVSNLK EENTLLKQEK ET LNHRIVE QAKEMTETME RKLVEETKQL ELDLNDERLR YQNLLNEFSR LEERYDDLKE EMTLMLNVPK PGHKRTDSTH SSN ESEYTF SSEFAETEDI APRTEEPIEK KVPLDMSLFL KLQKRVTELE QEKQLMQDEL DRKEEQVFRS KAKEEERPQI RGAE LEYES LKRQELESEN KKLKNELNEL RKALSEKSAP EVTAPGAPAY RVLMEQLTSV SEELDVRKEE VLILRSQLVS QKEAI QPKD DKNTMTDSTI LLEDVQKMKD KGEIAQAYIG LKETNRLLES QLQSQKRSHE NEAEALRGEI QSLKEENNRQ QQLLAQ NLQ LPPEARIEAS LQHEITRLTN ENLDLMEQLE KQDKTVRKLK KQLKVFAKKI GELEVGQMEN ISPGQIIDEP IRPVNIP RK EKDFQGMLEY KREDEQKLVK NLILELKPRG VAVNLIPGLP AYILFMCVRH ADYLNDDQKV RSLLTSTINS IKKVLKKR G DDFETVSFWL SNTCRFLHCL KQYSGEEGFM KHNTSRQNEH CLTNFDLAEY RQVLSDLAIQ IYQQLVRVLE NILQPMIVS GMLEHETIQG VSGVKPTGLR KRTSSIADEG TYTLDSILRQ LNSFHSVMCQ HGMDPELIKQ VVKQMFYIVG AITLNNLLLR KDMCSWSKG MQIRYNVSQL EEWLRDKNLM NSGAKETLEP LIQAAQLLQV KKKTDDDAEA ICSMCNALTT AQIVKVLNLY T PVNEFEER VSVSFIRTIQ MRLRDRKDSP QLLMDAKHIF PVTFPFNPSS LALETIQIPA SLGLGFIARV

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Macromolecule #2: Calmodulin-1

MacromoleculeName: Calmodulin-1 / type: protein_or_peptide / ID: 2 / Number of copies: 12 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 16.848605 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString:
MADQLTEEQI AEFKEAFSLF DKDGDGTITT KQLGTVMRSL GQNPTEAELQ DMINEVDADG NGTIDFPQFL TMMARKMKDT DSEEEIREA FRVFDKDGNG YISAAQLRHV MTNLGEKLTD EEVDEMIREA DIDGDGQVNY EQFVQMMTAK

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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

Concentration0.3 mg/mL
BufferpH: 7.4
Component:
ConcentrationFormulaName
50.0 mMC4H11NO3Tris
80.0 mMNaClSodium chloridesodium chloride
2.0 mMMgCl2magnesium chloride
1.0 mMC14H24N2O10EGTA
1.0 mMC4H10O2S2DTT
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 45 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.5 µm / Nominal magnification: 81000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average exposure time: 2.0 sec. / Average electron dose: 50.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 20747000
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. V3.1.0)
Final 3D classificationSoftware - Name: cryoSPARC (ver. V3.1.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. V3.1.0)
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 4.78 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. V3.1.0) / Number images used: 160273

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Atomic model buiding 1

Initial model(PDB ID:

1oe9

,

3wb8

,

2ix7

)
RefinementSpace: REAL / Protocol: OTHER / Overall B value: 167.3 / Target criteria: Correlation coefficient
Output model

PDB-7yv9:
Cryo-EM structure of full-length Myosin Va in the autoinhibited state

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