[English] 日本語
Yorodumi
- PDB-2os8: Rigor-like structures of muscle myosins reveal key mechanical ele... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2os8
TitleRigor-like structures of muscle myosins reveal key mechanical elements in the transduction pathways of this allosteric motor
Components
  • Myosin essential light chain
  • Myosin heavy chain
  • Myosin regulatory light chain
KeywordsCONTRACTILE PROTEIN / myosin S1 / rigor-like / motor / mechanical elements
Function / homology
Function and homology information


muscle myosin complex / myosin filament / myosin complex / myosin II complex / microfilament motor activity / myofibril / actin filament binding / calcium ion binding / ATP binding / metal ion binding
Similarity search - Function
Alpha-Beta Plaits - #1590 / : / Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #530 / EF-hand domain / DNA repair protein XRCC4-like, C-terminal / Myosin tail / Myosin tail / Myosin N-terminal SH3-like domain / Myosin S1 fragment, N-terminal / Myosin, N-terminal, SH3-like ...Alpha-Beta Plaits - #1590 / : / Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #530 / EF-hand domain / DNA repair protein XRCC4-like, C-terminal / Myosin tail / Myosin tail / Myosin N-terminal SH3-like domain / Myosin S1 fragment, N-terminal / Myosin, N-terminal, SH3-like / Myosin N-terminal SH3-like domain profile. / Short calmodulin-binding motif containing conserved Ile and Gln residues. / IQ motif, EF-hand binding site / Myosin head, motor domain / Myosin head (motor domain) / Myosin motor domain profile. / Myosin. Large ATPases. / IQ motif profile. / Kinesin motor domain superfamily / EF-hand / : / Recoverin; domain 1 / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / 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 / Alpha-Beta Plaits / Up-down Bundle / P-loop containing nucleoside triphosphate hydrolase / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Sulfhydryl light chain / Myosin regulatory light chain / Myosin heavy chain
Similarity search - Component
Biological speciesPlacopecten magellanicus (sea scallop)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.27 Å
AuthorsYang, Y. / Gourinath, S. / Cohen, C. / Brown, J.H.
CitationJournal: Structure / Year: 2007
Title: Rigor-like Structures from Muscle Myosins Reveal Key Mechanical Elements in the Transduction Pathways of This Allosteric Motor.
Authors: Yang, Y. / Gourinath, S. / Kovacs, M. / Nyitray, L. / Reutzel, R. / Himmel, D.M. / O'neall-Hennessey, E. / Reshetnikova, L. / Szent-Gyorgyi, A.G. / Brown, J.H. / Cohen, C.
History
DepositionFeb 5, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 29, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Myosin heavy chain
B: Myosin regulatory light chain
C: Myosin essential light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)131,7855
Polymers131,7203
Non-polymers642
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8170 Å2
ΔGint-75 kcal/mol
Surface area53870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.567, 50.359, 161.621
Angle α, β, γ (deg.)90.000, 98.720, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Myosin heavy chain


Mass: 96139.289 Da / Num. of mol.: 1 / Fragment: Myosin heavy chain / Source method: isolated from a natural source / Source: (natural) Placopecten magellanicus (sea scallop) / References: UniProt: Q26080
#2: Protein Myosin regulatory light chain


Mass: 17769.146 Da / Num. of mol.: 1 / Fragment: Myosin RLC / Source method: isolated from a natural source / Source: (natural) Placopecten magellanicus (sea scallop) / References: UniProt: Q26068
#3: Protein Myosin essential light chain


Mass: 17811.805 Da / Num. of mol.: 1 / Fragment: Myosin ELC / Source method: isolated from a natural source / Source: (natural) Placopecten magellanicus (sea scallop) / References: UniProt: Q26066
#4: Chemical ChemComp-MG / MAGNESIUM ION


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


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

-
Sample preparation

CrystalDensity Matthews: 2.61 Å3/Da / Density % sol: 52.91 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: CaCl2, PEG , pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 3.25→50 Å / Num. all: 16888 / Num. obs: 16888 / % possible obs: 79.6 % / Observed criterion σ(I): -3 / Redundancy: 3.5 % / Biso Wilson estimate: 66 Å2 / Rsym value: 0.085 / Net I/σ(I): 7.2
Reflection shellResolution: 3.25→3.37 Å / Redundancy: 2.5 % / Mean I/σ(I) obs: 1.5 / Num. unique all: 1371 / Rsym value: 0.451 / % possible all: 64.7

-
Processing

Software
NameVersionClassificationNB
CNS1.1refinement
PDB_EXTRACT2data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1SR6

1sr6


Resolution: 3.27→48.03 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 125059.531 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.314 1114 6.9 %RANDOM
Rwork0.281 ---
obs-16224 75.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 117.409 Å2 / ksol: 0.261 e/Å3
Displacement parametersBiso mean: 102.2 Å2
Baniso -1Baniso -2Baniso -3
1--0.92 Å20 Å25.21 Å2
2---22.21 Å20 Å2
3---23.14 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.55 Å0.48 Å
Luzzati d res low-5 Å
Luzzati sigma a0.64 Å0.75 Å
Refinement stepCycle: LAST / Resolution: 3.27→48.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8663 0 2 0 8665
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_angle_deg1.7
X-RAY DIFFRACTIONc_dihedral_angle_d23.4
X-RAY DIFFRACTIONc_improper_angle_d1.07
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 3.25→3.45 Å / Rfactor Rfree error: 0.033 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.378 133 7.8 %
Rwork0.362 1571 -
obs-1704 46.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2ion.paramion.top

+
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