[English] 日本語
Yorodumi
- PDB-5vt9: Myosin Light chain 1 and MyoA complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5vt9
TitleMyosin Light chain 1 and MyoA complex
Components
  • Myosin light chain TgMLC1
  • Myosin-A
KeywordsMOTOR PROTEIN / Myosin light chain
Function / homology
Function and homology information


mitotic actomyosin contractile ring assembly / vesicle transport along actin filament / myosin complex / myosin II complex / microfilament motor activity / myosin heavy chain binding / actin filament organization / actin filament binding / vesicle / calcium ion binding ...mitotic actomyosin contractile ring assembly / vesicle transport along actin filament / myosin complex / myosin II complex / microfilament motor activity / myosin heavy chain binding / actin filament organization / actin filament binding / vesicle / calcium ion binding / ATP binding / plasma membrane / cytoplasm
Similarity search - Function
: / Myosin A tail domain interacting protein, N-terminal / Class XIV myosin, motor domain / Myosin head, motor domain / Myosin head (motor domain) / Myosin motor domain profile. / Myosin. Large ATPases. / Kinesin motor domain superfamily / EF-hand / Recoverin; domain 1 ...: / Myosin A tail domain interacting protein, N-terminal / Class XIV myosin, motor domain / Myosin head, motor domain / Myosin head (motor domain) / Myosin motor domain profile. / Myosin. Large ATPases. / Kinesin motor domain superfamily / EF-hand / Recoverin; domain 1 / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair / P-loop containing nucleoside triphosphate hydrolase / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Myosin-A / Myosin light chain MLC1
Similarity search - Component
Biological speciesToxoplasma gondii (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsPowell, C.J. / Parker, M.L. / Boulanger, M.J.
Funding support Canada, 2items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR)MOP82915 Canada
Canadian Institutes of Health Research (CIHR)148596 Canada
CitationJournal: J. Biol. Chem. / Year: 2017
Title: Dissecting the molecular assembly of the Toxoplasma gondii MyoA motility complex.
Authors: Powell, C.J. / Jenkins, M.L. / Parker, M.L. / Ramaswamy, R. / Kelsen, A. / Warshaw, D.M. / Ward, G.E. / Burke, J.E. / Boulanger, M.J.
History
DepositionMay 16, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 4, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2017Group: Database references / Category: citation
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Dec 6, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Myosin light chain TgMLC1
C: Myosin-A
B: Myosin light chain TgMLC1
D: Myosin-A


Theoretical massNumber of molelcules
Total (without water)41,6804
Polymers41,6804
Non-polymers00
Water2,648147
1
A: Myosin light chain TgMLC1
C: Myosin-A


Theoretical massNumber of molelcules
Total (without water)20,8402
Polymers20,8402
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3020 Å2
ΔGint-22 kcal/mol
Surface area8520 Å2
MethodPISA
2
B: Myosin light chain TgMLC1
D: Myosin-A


Theoretical massNumber of molelcules
Total (without water)20,8402
Polymers20,8402
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3010 Å2
ΔGint-19 kcal/mol
Surface area8800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.990, 64.390, 65.150
Angle α, β, γ (deg.)90.00, 97.72, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Myosin light chain TgMLC1 / MLC1


Mass: 16878.602 Da / Num. of mol.: 2 / Fragment: UNP residues 66-210
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Toxoplasma gondii (eukaryote) / Production host: Escherichia coli (E. coli) / References: UniProt: Q95UJ7
#2: Protein/peptide Myosin-A / MyoA / TgM-A


Mass: 3961.553 Da / Num. of mol.: 2 / Fragment: UNP residues 801-831
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Toxoplasma gondii (eukaryote) / Production host: Escherichia coli (E. coli) / References: UniProt: O00934
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 147 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.04 Å3/Da / Density % sol: 39.83 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.9 uL 8 mg/mL protein + 1.35 uL reservoir (0.1 M Bis-Tris, pH 5.5, 25% PEG3350)

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.127 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 1, 2016
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.127 Å / Relative weight: 1
ReflectionResolution: 1.85→64.56 Å / Num. obs: 28665 / % possible obs: 99.6 % / Redundancy: 6 % / Rmerge(I) obs: 0.076 / Net I/σ(I): 15.3
Reflection shellResolution: 1.85→1.89 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.627 / Mean I/σ(I) obs: 2.9 / Num. unique obs: 1749 / % possible all: 99.8

-
Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2QAC

2qac


Resolution: 1.85→40.618 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 24.02
RfactorNum. reflection% reflectionSelection details
Rfree0.2294 1440 5.03 %Random selection
Rwork0.1909 ---
obs0.1928 28641 99.51 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.85→40.618 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2608 0 0 147 2755
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0052660
X-RAY DIFFRACTIONf_angle_d0.9493591
X-RAY DIFFRACTIONf_dihedral_angle_d14.675975
X-RAY DIFFRACTIONf_chiral_restr0.036386
X-RAY DIFFRACTIONf_plane_restr0.004477
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.85-1.91610.28671480.24132701X-RAY DIFFRACTION100
1.9161-1.99280.26271440.22562695X-RAY DIFFRACTION100
1.9928-2.08350.25951300.21462746X-RAY DIFFRACTION100
2.0835-2.19340.23961360.19962713X-RAY DIFFRACTION100
2.1934-2.33080.21821630.19922695X-RAY DIFFRACTION100
2.3308-2.51070.24761160.19082737X-RAY DIFFRACTION100
2.5107-2.76330.25091560.20132710X-RAY DIFFRACTION100
2.7633-3.16310.25271340.20552744X-RAY DIFFRACTION99
3.1631-3.98460.2331520.17172699X-RAY DIFFRACTION99
3.9846-40.6280.1811610.16752761X-RAY DIFFRACTION99

+
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://pdbjlvh1.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