[English] 日本語
Yorodumi
- PDB-2dfs: 3-D structure of Myosin-V inhibited state -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2dfs
Title3-D structure of Myosin-V inhibited state
Components
  • Calmodulin
  • Myosin-5A
KeywordsCONTRACTILE PROTEIN/TRANSPORT PROTEIN / myosin-V / inhibited state / calmodulin / cryoelectron tomography / CONTRACTILE PROTEIN-TRANSPORT PROTEIN COMPLEX
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 / minus-end directed microfilament motor activity / Ca2+ pathway / negative regulation of calcium ion transmembrane transporter activity / FCERI mediated Ca+2 mobilization / RAF/MAP kinase cascade / RHO GTPases activate IQGAPs / Extra-nuclear estrogen signaling / insulin-responsive compartment / PKA activation / regulation of response to tumor cell / positive regulation of autophagic cell death / DAPK1-calmodulin complex / Platelet degranulation / : / establishment of protein localization to mitochondrial membrane / Stimuli-sensing channels / Ion homeostasis / type 3 metabotropic glutamate receptor binding / vesicle transport along actin filament / myosin complex / regulation of synaptic vesicle endocytosis / microfilament motor activity / negative regulation of high voltage-gated calcium channel activity / regulation of synaptic vesicle exocytosis / negative regulation of calcium ion export across plasma membrane / organelle localization by membrane tethering / regulation of cardiac muscle cell action potential / mitochondrion-endoplasmic reticulum membrane tethering / autophagosome membrane docking / response to corticosterone / positive regulation of ryanodine-sensitive calcium-release channel activity / nitric-oxide synthase binding / filamentous actin / protein phosphatase activator activity / positive regulation of cyclic-nucleotide phosphodiesterase activity / positive regulation of phosphoprotein phosphatase activity / adenylate cyclase binding / catalytic complex / detection of calcium ion / negative regulation of ryanodine-sensitive calcium-release channel activity / cellular response to interferon-beta / regulation of cardiac muscle contraction / calcium channel inhibitor activity / enzyme regulator activity / voltage-gated potassium channel complex / phosphatidylinositol 3-kinase binding / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / regulation of calcium-mediated signaling / positive regulation of protein dephosphorylation / titin binding / regulation of ryanodine-sensitive calcium-release channel activity / vesicle-mediated transport / potassium ion transmembrane transport / sperm midpiece / response to amphetamine / calcium channel complex / activation of adenylate cyclase activity / adenylate cyclase activator activity / regulation of heart rate / nitric-oxide synthase regulator activity / protein serine/threonine kinase activator activity / sarcomere / regulation of cytokinesis / actin filament organization / positive regulation of nitric-oxide synthase activity / protein localization to plasma membrane / calcium-mediated signaling / spindle microtubule / mitochondrial membrane / positive regulation of receptor signaling pathway via JAK-STAT / synaptic vesicle membrane / spindle pole / cellular response to type II interferon / response to calcium ion / cellular response to insulin stimulus / calcium-dependent protein binding / disordered domain specific binding
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
Calmodulin-1 / Calmodulin-2 / Unconventional myosin-Va
Similarity search - Component
Biological speciesGallus gallus (chicken)
Mus musculus (house mouse)
MethodELECTRON CRYSTALLOGRAPHY / electron tomography / Resolution: 24 Å
AuthorsLiu, J. / Taylor, D.W. / Krementsova, E.B. / Trybus, K.M. / Taylor, K.A.
CitationJournal: Nature / Year: 2006
Title: Three-dimensional structure of the myosin V inhibited state by cryoelectron tomography.
Authors: Jun Liu / Dianne W Taylor / Elena B Krementsova / Kathleen M Trybus / Kenneth A Taylor /
Abstract: Unconventional myosin V (myoV) is an actin-based molecular motor that has a key function in organelle and mRNA transport, as well as in membrane trafficking. MyoV was the first member of the myosin ...Unconventional myosin V (myoV) is an actin-based molecular motor that has a key function in organelle and mRNA transport, as well as in membrane trafficking. MyoV was the first member of the myosin superfamily shown to be processive, meaning that a single motor protein can 'walk' hand-over-hand along an actin filament for many steps before detaching. Full-length myoV has a low actin-activated MgATPase activity at low [Ca2+], whereas expressed constructs lacking the cargo-binding domain have a high activity regardless of [Ca2+] (refs 5-7). Hydrodynamic data and electron micrographs indicate that the active state is extended, whereas the inactive state is compact. Here we show the first three-dimensional structure of the myoV inactive state. Each myoV molecule consists of two heads that contain an amino-terminal motor domain followed by a lever arm that binds six calmodulins. The heads are followed by a coiled-coil dimerization domain (S2) and a carboxy-terminal globular cargo-binding domain. In the inactive structure, bending of myoV at the head-S2 junction places the cargo-binding domain near the motor domain's ATP-binding pocket, indicating that ATPase inhibition might occur through decreased rates of nucleotide exchange. The actin-binding interfaces are unobstructed, and the lever arm is oriented in a position typical of strong actin-binding states. This structure indicates that motor recycling after cargo delivery might occur through transport on actively treadmilling actin filaments rather than by diffusion.
History
DepositionMar 3, 2006Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 25, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 18, 2019Group: Author supporting evidence / Data collection / Database references
Category: database_2 / em_image_scans ...database_2 / em_image_scans / em_single_particle_entity / em_software
Item: _em_software.image_processing_id
Revision 1.4Mar 13, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_3d_fitting_list / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type

-
Structure visualization

Movie
  • Deposited structure unit
  • Imaged by Jmol
  • Download
  • Simplified surface model + fitted atomic model
  • EMDB-1201
  • Imaged by Jmol
  • Download
  • Superimposition on EM map
  • EMDB-1201
  • Imaged by UCSF Chimera
  • Download
  • Superimposition on EM map
  • EMDB-1201
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Myosin-5A
B: Calmodulin
C: Calmodulin
D: Calmodulin
E: Calmodulin
F: Calmodulin
G: Calmodulin
M: Myosin-5A
N: Calmodulin
O: Calmodulin
P: Calmodulin
Q: Calmodulin
R: Calmodulin
S: Calmodulin


Theoretical massNumber of molelcules
Total (without water)453,48814
Polymers453,48814
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)653.000, 653.000, 200.000
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number168
Space group name H-MP6

-
Components

#1: Protein Myosin-5A / Myosin Va / Dilute myosin heavy chain / non-muscle / Myosin heavy chain p190 / Myosin-V


Mass: 126415.695 Da / Num. of mol.: 2 / Fragment: residues 1-1080
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Cell line (production host): SF9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q02440
#2: Protein
Calmodulin / / CaM


Mass: 16721.350 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Cell line (production host): SF9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P62204, UniProt: P0DP26*PLUS

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON CRYSTALLOGRAPHY
EM experimentAggregation state: TISSUE / 3D reconstruction method: electron tomography

-
Sample preparation

ComponentName: Myosin-V / Type: TISSUE / Details: myosin-V inhibited state
Buffer solutionName: 20mM Na2HPO4, 80-100mM NaCl, 2mM MgCl2, 1mM ADP, 1mM EGTA, 8-9% PEG 8000
Details: 20mM Na2HPO4, 80-100mM NaCl, 2mM MgCl2, 1mM ADP, 1mM EGTA, 8-9% PEG 8000
SpecimenConc.: 0.2 mg/ml / Embedding applied: YES / Shadowing applied: NO / Staining applied: NO / Vitrification applied: NO
Specimen supportDetails: 200 mesh copper grids covered with a reticulated carbon film
VitrificationInstrument: HOMEMADE PLUNGER / Cryogen name: ETHANE / Details: liquid ethane

-
Data collection

MicroscopyModel: FEI/PHILIPS CM300FEG/ST / Date: Feb 1, 2004
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 24000 X / Calibrated magnification: 24000 X / Nominal defocus max: 4000 nm / Nominal defocus min: 12000 nm / Cs: 2 mm
Specimen holderTemperature: 103 K / Tilt angle max: 70 ° / Tilt angle min: -70 °
Image recordingElectron dose: 30 e/Å2 / Film or detector model: TVIPS TEMCAM-F224 (2k x 2k) / Details: 2048x2048
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: electron
Radiation wavelengthRelative weight: 1

-
Processing

EM software
IDNameCategory
1NMFFmodel fitting
2Situsmodel fitting
3PROTOMO3D reconstruction
CTF correctionDetails: CTF gradient correction
3D reconstructionMethod: electron tomography and 3-D average / Resolution: 24 Å / Num. of particles: 4029 / Nominal pixel size: 5.56 Å / Actual pixel size: 5.56 Å
Details: Tilt series images were aligned using marker-free alignment. Molecular volumes extracted from the cryotomograms, aligned in 3-D. Marker-free alignment is described in the reference: ...Details: Tilt series images were aligned using marker-free alignment. Molecular volumes extracted from the cryotomograms, aligned in 3-D. Marker-free alignment is described in the reference: Winkler,H. and Taylor,K.A. Accurate marker-free alignment with simultaneous geometry determination and reconstruction of tilt series in electron tomography. Ultramicroscopy, 106, 240-254 (2006)
Symmetry type: 2D CRYSTAL
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL / Target criteria: Cross correlation
Details: METHOD--Rigid body docking first and then refined with normal mode flexible fitting. REFINEMENT PROTOCOL--Rigid body docking and normal mode flexible fitting. For the fitting the density ...Details: METHOD--Rigid body docking first and then refined with normal mode flexible fitting. REFINEMENT PROTOCOL--Rigid body docking and normal mode flexible fitting. For the fitting the density corresponding to the two myosin V heads within the asymmetric unit was segmented from the rest of the map using the watershed transform (Volkman 2002. J.STRUCT.BIOL. 138, 123-129). After fitting the atomic model against the head density, the coordinates were not refined further against the nearest neighbor myosin V heads to remove bad crystal contacts. The alpha-helical coiled-coil domain was manually fit to the and not refined further.
Atomic model building
IDPDB-ID 3D fitting-IDAccession codeInitial refinement model-IDSource nameType
11W7I

1w7i

11W7I1PDBexperimental model
21N2D

1n2d

11N2D2PDBexperimental model
Refinement stepCycle: LAST
ProteinNucleic acidLigandSolventTotal
Num. atoms29614 0 0 0 29614

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more