[English] 日本語
Yorodumi
- PDB-2vas: Myosin VI (MD-insert2-CaM, Delta-Insert1) Post-rigor state -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2vas
TitleMyosin VI (MD-insert2-CaM, Delta-Insert1) Post-rigor state
Components
  • CALMODULIN
  • MYOSIN VI
KeywordsMOTOR PROTEIN / CALMODULIN-BINDING / NUCLEOTIDE-BINDING / TRANSPORT / CALMODULIN / ENDOCYTOSIS / MG.ADP.BEFX / CAM / MYOSIN / NUCLEUS / MEMBRANE / MYOSIN VI / CYTOPLASM / GOLGI APPARATUS / PHOSPHORYLATION / MOLECULAR MOTOR / ATP-BINDING / COILED COIL / ACTIN-BINDING / POST-RIGOR STATE / PROTEIN TRANSPORT
Function / homology
Function and homology information


metarhodopsin inactivation / regulation of light-activated channel activity / myosin VI head/neck binding / CaMK IV-mediated phosphorylation of CREB / Calmodulin induced events / Cam-PDE 1 activation / Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / PKA activation / myosin VI complex / eNOS activation ...metarhodopsin inactivation / regulation of light-activated channel activity / myosin VI head/neck binding / CaMK IV-mediated phosphorylation of CREB / Calmodulin induced events / Cam-PDE 1 activation / Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / PKA activation / myosin VI complex / eNOS activation / Inactivation, recovery and regulation of the phototransduction cascade / CREB1 phosphorylation through the activation of CaMKII/CaMKK/CaMKIV cascasde / VEGFR2 mediated vascular permeability / CLEC7A (Dectin-1) induces NFAT activation / Glycogen breakdown (glycogenolysis) / Extra-nuclear estrogen signaling / Activation of RAC1 downstream of NMDARs / Calcineurin activates NFAT / adaptation of rhodopsin mediated signaling / myosin VII complex / Synthesis of IP3 and IP4 in the cytosol / Ion transport by P-type ATPases / Ca2+ pathway / RAF activation / Platelet degranulation / photoreceptor cell axon guidance / FCERI mediated Ca+2 mobilization / Ion homeostasis / deactivation of rhodopsin mediated signaling / RAS processing / Protein methylation / Activation of Ca-permeable Kainate Receptor / rhabdomere development / Unblocking of NMDA receptors, glutamate binding and activation / regulation of secretion / myosin V complex / salivary gland cell autophagic cell death / kinetochore organization / rhabdomere / RNA polymerase II, holoenzyme / Neutrophil degranulation / actin filament-based movement / rhodopsin mediated signaling pathway / inner ear auditory receptor cell differentiation / myosin V binding / cellular response to ethanol / positive regulation of cation channel activity / vesicle transport along actin filament / inner ear morphogenesis / myosin complex / microfilament motor activity / clathrin-coated vesicle / muscle cell cellular homeostasis / myosin heavy chain binding / mitotic spindle pole / filamentous actin / DNA damage response, signal transduction by p53 class mediator / microvillus / centriole replication / cytoskeletal motor activity / centriole / enzyme regulator activity / ruffle / actin filament organization / filopodium / actin filament / calcium-mediated signaling / ADP binding / sensory perception of sound / intracellular protein transport / spindle / ruffle membrane / mitotic spindle / cell cortex / sensory perception of smell / endocytosis / actin cytoskeleton / actin filament binding / midbody / nuclear membrane / cytoplasmic vesicle / calmodulin binding / vesicle / centrosome / protein phosphorylation / calcium ion binding / perinuclear region of cytoplasm / Golgi apparatus / positive regulation of transcription by RNA polymerase II / nucleoplasm / ATP binding / plasma membrane / nucleus / cytosol / cytoplasm
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #2980 / Alpha-Beta Plaits - #1590 / Arc Repressor Mutant, subunit A - #820 / Myosin VI head, motor domain, U50 subdomain / Myosin VI, cargo binding domain / Class VI myosin, motor domain / Myosin VI cargo binding domain / Myosin S1 fragment, N-terminal / Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #530 / Calmodulin ...Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #2980 / Alpha-Beta Plaits - #1590 / Arc Repressor Mutant, subunit A - #820 / Myosin VI head, motor domain, U50 subdomain / Myosin VI, cargo binding domain / Class VI myosin, motor domain / Myosin VI cargo binding domain / Myosin S1 fragment, N-terminal / Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #530 / Calmodulin / Kinesin motor domain / Kinesin / Myosin S1 fragment, N-terminal / Myosin, N-terminal, SH3-like / Myosin N-terminal SH3-like domain profile. / Myosin head (motor domain) / Myosin motor domain profile. / Myosin head, motor domain / Myosin. Large ATPases. / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Kinesin motor domain superfamily / EF-hand domain pair / Four Helix Bundle (Hemerythrin (Met), subunit A) / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / EF-hand, calcium binding motif / Helix non-globular / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / EF-hand domain / Special / SH3 type barrels. / EF-hand domain pair / Arc Repressor Mutant, subunit A / Roll / Alpha-Beta Plaits / Up-down Bundle / P-loop containing nucleoside triphosphate hydrolase / 2-Layer Sandwich / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Calmodulin / ADENOSINE-5'-DIPHOSPHATE / BERYLLIUM TRIFLUORIDE ION / Unconventional myosin-VI
Similarity search - Component
Biological speciesSUS SCROFA (pig)
DROSOPHILA MELANOGASTER (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsMenetrey, J. / Llinas, P. / Cicolari, J. / Squires, G. / Liu, X. / Li, A. / Sweeney, H.L. / Houdusse, A.
CitationJournal: Embo J. / Year: 2008
Title: The Post-Rigor Structure of Myosin Vi and Implications for the Recovery Stroke.
Authors: Menetrey, J. / Llinas, P. / Cicolari, J. / Squires, G. / Liu, X. / Li, A. / Sweeney, H.L. / Houdusse, A.
History
DepositionSep 4, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 11, 2007Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: MYOSIN VI
B: CALMODULIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,4039
Polymers106,7252
Non-polymers6787
Water2,774154
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5200 Å2
ΔGint-32.9 kcal/mol
Surface area49100 Å2
MethodPQS
Unit cell
Length a, b, c (Å)73.420, 100.470, 174.070
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

-
Protein , 2 types, 2 molecules AB

#1: Protein MYOSIN VI / / UNCONVENTIONAL MYOSIN VI


Mass: 89899.477 Da / Num. of mol.: 1
Fragment: MOTOR DOMAIN-INSERT2,RESIDUES 2-277,304-377,379-816
Source method: isolated from a genetically manipulated source
Details: INSERT1 DELETION (C278-A303) / Source: (gene. exp.) SUS SCROFA (pig) / Plasmid: SF9 / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) / References: UniProt: Q29122
#2: Protein CALMODULIN / / CAM


Mass: 16825.520 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) DROSOPHILA MELANOGASTER (fruit fly) / Plasmid: SF9 / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) / References: UniProt: P62152

-
Non-polymers , 5 types, 161 molecules

#3: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#4: Chemical ChemComp-BEF / BERYLLIUM TRIFLUORIDE ION


Mass: 66.007 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: BeF3
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#6: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 154 / Source method: isolated from a natural source / Formula: H2O

-
Details

Sequence detailsTHE AUTHORS STATE THAT THE ORIGINAL SEQUENCE (UNIPROT Q29122) OF MYOSIN VI FROM PIG WAS MOST LIKELY ...THE AUTHORS STATE THAT THE ORIGINAL SEQUENCE (UNIPROT Q29122) OF MYOSIN VI FROM PIG WAS MOST LIKELY INCORRECT BECAUSE THE CHANGES THAT ARE IN THEIR CLONE (LYS DELETION AND THE 6 MUTATIONS) ARE CONSERVED ACROSS THE MYOSIN VI FAMILY.

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 3.18 Å3/Da / Density % sol: 53.1 % / Description: NONE
Crystal growDetails: 8% PEG 8000, 50MM GLYCINE PH 9.5, 6% MPD

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726
DetectorType: ADSC CCD / Detector: CCD / Date: Jun 29, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 2.4→48.97 Å / Num. obs: 51218 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 8.2 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 17.2
Reflection shellResolution: 2.4→2.53 Å / Redundancy: 8.3 % / Rmerge(I) obs: 0.38 / Mean I/σ(I) obs: 6.6 / % possible all: 100

-
Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2BKH
Resolution: 2.4→48.28 Å / Cor.coef. Fo:Fc: 0.919 / Cor.coef. Fo:Fc free: 0.89 / SU B: 7.393 / SU ML: 0.175 / Cross valid method: THROUGHOUT / ESU R: 0.311 / ESU R Free: 0.238 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.256 2628 5.1 %RANDOM
Rwork0.217 ---
obs0.219 48522 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 31.35 Å2
Baniso -1Baniso -2Baniso -3
1--0.97 Å20 Å20 Å2
2---0.89 Å20 Å2
3---1.86 Å2
Refinement stepCycle: LAST / Resolution: 2.4→48.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7023 0 36 154 7213
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0227012
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2221.9589452
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5545866
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.1624.327342
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.872151205
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.771541
X-RAY DIFFRACTIONr_chiral_restr0.1260.21027
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.025328
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1930.22949
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2990.24814
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1310.2244
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2170.238
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1230.210
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8061.54432
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.03426893
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.54832887
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.4714.52559
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.4→2.46 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.326 185
Rwork0.255 3544

+
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