[English] 日本語
Yorodumi
- PDB-2y8i: Structural basis for the allosteric interference of myosin functi... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2y8i
TitleStructural basis for the allosteric interference of myosin function by mutants G680A and G680V of Dictyostelium myosin-2
ComponentsMYOSIN-2 HEAVY CHAIN
KeywordsMOTOR PROTEIN / ADP COMPLEX
Function / homology
Function and homology information


calcium-dependent ATPase activity / pseudopodium retraction / uropod retraction / cytoplasmic actin-based contraction involved in forward cell motility / phagocytic cup base / pathogen-containing vacuole / response to differentiation-inducing factor 1 / equatorial cell cortex / contractile actin filament bundle assembly / cell trailing edge ...calcium-dependent ATPase activity / pseudopodium retraction / uropod retraction / cytoplasmic actin-based contraction involved in forward cell motility / phagocytic cup base / pathogen-containing vacuole / response to differentiation-inducing factor 1 / equatorial cell cortex / contractile actin filament bundle assembly / cell trailing edge / contractile vacuole organization / myosin filament assembly / aggregation involved in sorocarp development / culmination involved in sorocarp development / RHO GTPases activate PAKs / adenyl nucleotide binding / actomyosin contractile ring / hypotonic response / uropod / actin-myosin filament sliding / detection of mechanical stimulus / negative regulation of actin filament polymerization / apical cortex / bleb assembly / actomyosin / substrate-dependent cell migration, cell extension / myosin filament / filopodium assembly / early phagosome / myosin II complex / cortical actin cytoskeleton organization / microfilament motor activity / cortical actin cytoskeleton / pseudopodium / cytoskeletal motor activity / cleavage furrow / mitotic cytokinesis / response to mechanical stimulus / 14-3-3 protein binding / response to cAMP / extracellular matrix / cell motility / response to hydrogen peroxide / chemotaxis / actin filament binding / protein localization / regulation of cell shape / cell cortex / cytoplasmic vesicle / cytoskeleton / calmodulin binding / ATP binding / identical protein binding / cytosol / cytoplasm
Similarity search - Function
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. / Myosin head, motor domain / Myosin head (motor domain) / Myosin motor domain profile. / Myosin. Large ATPases. ...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. / Myosin head, motor domain / Myosin head (motor domain) / Myosin motor domain profile. / Myosin. Large ATPases. / IQ motif profile. / Kinesin motor domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / Myosin-2 heavy chain
Similarity search - Component
Biological speciesDICTYOSTELIUM DISCOIDEUM (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.132 Å
AuthorsPreller, M. / Bauer, S. / Adamek, N. / Fujita-Becker, S. / Fedorov, R. / Geeves, M.A. / Manstein, D.J.
CitationJournal: J.Biol.Chem. / Year: 2011
Title: Structural Basis for the Allosteric Interference of Myosin Function by Reactive Thiol Region Mutations G680A and G680V.
Authors: Preller, M. / Bauer, S. / Adamek, N. / Fujita-Becker, S. / Fedorov, R. / Geeves, M.A. / Manstein, D.J.
History
DepositionFeb 7, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 20, 2011Provider: repository / Type: Initial release
Revision 1.1Oct 12, 2011Group: Database references
Revision 1.2Jun 20, 2018Group: Advisory / Data collection / Category: pdbx_unobs_or_zero_occ_residues
Revision 1.3Jul 31, 2019Group: Advisory / Data collection / Derived calculations
Category: pdbx_struct_conn_angle / pdbx_validate_close_contact ...pdbx_struct_conn_angle / pdbx_validate_close_contact / struct_conn / struct_conn_type
Item: _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id ..._pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value
Revision 1.4Dec 20, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_residues / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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
X: MYOSIN-2 HEAVY CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,8313
Polymers86,3801
Non-polymers4522
Water4,648258
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)55.000, 105.800, 180.500
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121

-
Components

#1: Protein MYOSIN-2 HEAVY CHAIN / MYOSIN II HEAVY CHAIN


Mass: 86379.703 Da / Num. of mol.: 1 / Fragment: MOTOR DOMAIN, RESIDUES 2-759 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) DICTYOSTELIUM DISCOIDEUM (eukaryote) / Production host: DICTYOSTELIUM DISCOIDEUM (eukaryote) / References: UniProt: P08799, EC: 3.6.4.1
#2: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


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


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 258 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN X, GLY 680 TO ALA

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.2 Å3/Da / Density % sol: 61 % / Description: NONE
Crystal growpH: 7 / Details: 13% PEG 6000, 4% GLYCEROL., pH 7.0

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.9175
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jan 28, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9175 Å / Relative weight: 1
ReflectionResolution: 3.13→20.22 Å / Num. obs: 20093 / % possible obs: 96.4 % / Observed criterion σ(I): 3 / Redundancy: 11.1 % / Rmerge(I) obs: 0.17 / Net I/σ(I): 9.23
Reflection shellResolution: 3.13→3.19 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.46 / Mean I/σ(I) obs: 2.37 / % possible all: 83.4

-
Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XDSdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1MMD

1mmd


Resolution: 3.132→20.215 Å / SU ML: 0.56 / σ(F): 1.33 / Phase error: 34.32 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3365 942 5.1 %
Rwork0.2447 --
obs0.2494 18481 96.35 %
Solvent computationShrinkage radii: 1.17 Å / VDW probe radii: 1.4 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 30.699 Å2 / ksol: 0.153 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--5.0714 Å20 Å20 Å2
2---9.7729 Å20 Å2
3----3.9893 Å2
Refinement stepCycle: LAST / Resolution: 3.132→20.215 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6090 0 28 258 6376
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.016237
X-RAY DIFFRACTIONf_angle_d1.368428
X-RAY DIFFRACTIONf_dihedral_angle_d23.9882338
X-RAY DIFFRACTIONf_chiral_restr0.089918
X-RAY DIFFRACTIONf_plane_restr0.0041104
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1324-3.29690.38910.29041891X-RAY DIFFRACTION83
3.2969-3.50250.3581300.25742563X-RAY DIFFRACTION100
3.5025-3.77130.37381430.22982559X-RAY DIFFRACTION100
3.7713-4.14780.311590.22162552X-RAY DIFFRACTION100
4.1478-4.74130.3041400.18762595X-RAY DIFFRACTION100
4.7413-5.94810.2761480.23292618X-RAY DIFFRACTION100
5.9481-20.21590.38631310.29552761X-RAY DIFFRACTION100

+
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