[English] 日本語
Yorodumi
- PDB-2x9h: CRYSTAL STRUCTURE OF MYOSIN-2 MOTOR DOMAIN IN COMPLEX WITH ADP- M... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2x9h
TitleCRYSTAL STRUCTURE OF MYOSIN-2 MOTOR DOMAIN IN COMPLEX WITH ADP- METAVANADATE AND PENTACHLOROCARBAZOLE
ComponentsMYOSIN-2 HEAVY CHAIN
KeywordsCONTRACTILE PROTEIN / NUCLEOTIDE-BINDING / MOTOR PROTEIN / ACTIN-BINDING
Function / homology
Function and homology information


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 / pseudopodium retraction / cell trailing edge / contractile vacuole organization ...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 / pseudopodium retraction / 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 / calcium-dependent ATPase activity / hypotonic response / actomyosin contractile ring / uropod / apical cortex / detection of mechanical stimulus / negative regulation of actin filament polymerization / actin-myosin filament sliding / substrate-dependent cell migration, cell extension / bleb assembly / actomyosin / filopodium assembly / myosin filament / early phagosome / myosin II complex / cortical actin cytoskeleton organization / cortical actin cytoskeleton / microfilament motor activity / pseudopodium / cleavage furrow / cytoskeletal motor activity / mitotic cytokinesis / response to cAMP / response to mechanical stimulus / 14-3-3 protein binding / extracellular matrix / cell motility / response to hydrogen peroxide / chemotaxis / actin filament binding / intracellular protein localization / regulation of cell shape / cytoplasmic vesicle / cell cortex / cytoskeleton / calmodulin binding / ATP binding / identical protein binding / cytoplasm / cytosol
Similarity search - Function
Myosin S1 fragment, N-terminal / Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #530 / 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 S1 fragment, N-terminal / Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #530 / 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 / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / SH3 type barrels. / Roll / Up-down Bundle / P-loop containing nucleoside triphosphate hydrolase / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
ADP METAVANADATE / 2,3,4,6,8-PENTACHLORO-9H-CARBAZOL-1-OL / Myosin-2 heavy chain
Similarity search - Component
Biological speciesDICTYOSTELIUM DISCOIDEUM (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsSelvadurai, J. / Kirst, J. / Knoelker, H.J. / Manstein, D.J.
Citation
Journal: To be Published
Title: Crystal Structure of Myosin-2 Motor Domain in Complex with Adp-Metavanadate and Pentachlorocarbazole
Authors: Fedrov, R. / Boehl, M. / Tsiavaliaris, G. / Hartmann, F.K. / Baruch, P. / Brenner, B. / Martin, R. / Knoelker, H.J. / Gutzeit, H.O. / Manstein, D.J.
#1: Journal: Nat.Struct.Mol.Biol. / Year: 2009
Title: The Mechanism of Pentabromopseudilin Inhibition of Myosin Motor Activity.
Authors: Fedorov, R. / Bohl, M. / Tsiavaliaris, G. / Hartmann, F.K. / Taft, M.H. / Baruch, P. / Brenner, B. / Martin, R. / Knolker, H. / Gutzeit, H.O. / Manstein, D.J.
History
DepositionMar 19, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 11, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...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_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_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_asym_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 / _struct_conn.pdbx_dist_value / _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-2 HEAVY CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,8484
Polymers78,9411
Non-polymers9073
Water3,567198
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)89.160, 146.630, 153.680
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

-
Components

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


Mass: 78941.242 Da / Num. of mol.: 1 / Fragment: MYOSIN MOTOR DOMAIN, RESIDUES 2-696
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) DICTYOSTELIUM DISCOIDEUM (eukaryote) / Strain: AX3 / Production host: DICTYOSTELIUM DISCOIDEUM (eukaryote) / References: UniProt: P08799, EC: 3.6.4.1
#2: Chemical ChemComp-AD9 / ADP METAVANADATE


Mass: 527.149 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P2V
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-KI9 / 2,3,4,6,8-PENTACHLORO-9H-CARBAZOL-1-OL


Mass: 355.431 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H4Cl5NO
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 198 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsADP METAVANADATE (AMV): NON-HYDROLYSABLE ATP-ANALOG ADP-METAVANADATE

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.21 Å3/Da / Density % sol: 61 % / Description: NONE
Crystal growpH: 7.4
Details: 50 MM TRIS-HCL PH 7.4, 140 MM NACL, 9% W/V PEG8000, 2% (V/V) MPD, 5 MM MGCL2, 5 MM DTT, 1 MM EGTA

-
Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.939
DetectorType: ADSC CCD / Detector: CCD / Date: Feb 24, 2010
Details: SINGLE SILICON (111) MONOCHROMATOR AND TOROIDAL FOCUSING MIRROR
RadiationMonochromator: SINGLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.939 Å / Relative weight: 1
ReflectionResolution: 2.7→19.77 Å / Num. obs: 26158 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 5 % / Biso Wilson estimate: 38 Å2 / Rmerge(I) obs: 0.4 / Net I/σ(I): 2.4
Reflection shellResolution: 2.7→2.769 Å / % possible all: 100

-
Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
XDSdata reduction
XDSdata scaling
ARPWARP CNS REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2JHR

2jhr


Resolution: 2.7→19.77 Å / Cor.coef. Fo:Fc: 0.907 / Cor.coef. Fo:Fc free: 0.826 / SU B: 0.001 / SU ML: 0 / Cross valid method: THROUGHOUT / ESU R: 0.263 / ESU R Free: 0.373
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.RESIDUES 202-207 ARE DISORDERED. DISORDERED REGIONS COULD NOT BE MODELED DUE TO POOR DENSITY
RfactorNum. reflection% reflectionSelection details
Rfree0.28871 1377 5 %RANDOM
Rwork0.20338 ---
obs0.20751 26158 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: 20.946 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.7→19.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5532 0 51 198 5781
LS refinement shellResolution: 2.7→2.769 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.347 99 -
Rwork0.218 1881 -
obs--100 %

+
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