[English] 日本語
Yorodumi
- PDB-2lw9: NMR solution structure of Myo10 anti-CC -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2lw9
TitleNMR solution structure of Myo10 anti-CC
ComponentsUnconventionnal myosin-X
KeywordsMOTOR PROTEIN / Myo10 anti-CC
Function / homology
Function and homology information


plus-end directed microfilament motor activity / Netrin-1 signaling / positive regulation of cell-cell adhesion / filopodium tip / cytoskeleton-dependent intracellular transport / regulation of filopodium assembly / filopodium membrane / myosin complex / microfilament motor activity / spectrin binding ...plus-end directed microfilament motor activity / Netrin-1 signaling / positive regulation of cell-cell adhesion / filopodium tip / cytoskeleton-dependent intracellular transport / regulation of filopodium assembly / filopodium membrane / myosin complex / microfilament motor activity / spectrin binding / phosphatidylinositol-3,4,5-trisphosphate binding / ruffle / filopodium / FCGR3A-mediated phagocytosis / Regulation of actin dynamics for phagocytic cup formation / actin filament binding / lamellipodium / regulation of cell shape / cell cortex / calmodulin binding / neuron projection / neuronal cell body / nucleolus / signal transduction / ATP binding / plasma membrane / cytosol
Similarity search - Function
Unconventional myosin-X, coiled coil domain / Class X myosin, motor domain / Myosin X, N-terminal SH3 domain / Myosin X, FERM domain C-lobe / Unconventional myosin-X coiled coil domain / Myosin X N-terminal SH3 domain / : / MyTH4 domain / MyTH4 domain superfamily / MyTH4 domain ...Unconventional myosin-X, coiled coil domain / Class X myosin, motor domain / Myosin X, N-terminal SH3 domain / Myosin X, FERM domain C-lobe / Unconventional myosin-X coiled coil domain / Myosin X N-terminal SH3 domain / : / MyTH4 domain / MyTH4 domain superfamily / MyTH4 domain / MyTH4 domain profile. / Domain in Myosin and Kinesin Tails / Ras association (RalGDS/AF-6) domain / Ras-associating (RA) domain / IQ calmodulin-binding motif / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #170 / FERM central domain / FERM/acyl-CoA-binding protein superfamily / Short calmodulin-binding motif containing conserved Ile and Gln residues. / Myosin head, motor domain / Myosin head (motor domain) / Myosin motor domain profile. / Myosin. Large ATPases. / IQ motif, EF-hand binding site / IQ motif profile. / FERM central domain / FERM superfamily, second domain / FERM domain / FERM domain profile. / Band 4.1 domain / Band 4.1 homologues / Kinesin motor domain superfamily / PH domain / PH domain profile. / Pleckstrin homology domain. / Pleckstrin homology domain / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / PH-like domain superfamily / Up-down Bundle / P-loop containing nucleoside triphosphate hydrolase / Mainly Alpha
Similarity search - Domain/homology
Unconventional myosin-X
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / DGSA-distance geometry simulated annealing
Model detailslowest energy, model1
AuthorsYe, F. / Lu, Q. / Zhang, M.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2012
Title: Antiparallel coiled-coil-mediated dimerization of myosin X
Authors: Lu, Q. / Ye, F. / Wei, Z. / Wen, Z. / Zhang, M.
History
DepositionJul 25, 2012Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Sep 26, 2012Provider: repository / Type: Initial release
Revision 1.1Jun 12, 2013Group: Database references
Revision 1.2May 1, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Unconventionnal myosin-X
B: Unconventionnal myosin-X


Theoretical massNumber of molelcules
Total (without water)12,6962
Polymers12,6962
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 61structures with the lowest energy
RepresentativeModel #1lowest energy

-
Components

#1: Protein Unconventionnal myosin-X / Unconventional myosin-10


Mass: 6348.069 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MYO10, KIAA0799 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9HD67

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-13C HSQC
1313D HN(CA)CB
1413D CBCA(CO)NH
1513D 1H-15N NOESY
1613D 1H-13C NOESY

-
Sample preparation

DetailsContents: 0.8 mM [U-100% 13C; U-100% 15N] entity-1, 100% D2O
Solvent system: 100% D2O
SampleConc.: 0.8 mM / Component: entity-1 / Isotopic labeling: [U-100% 13C; U-100% 15N]
Sample conditionsIonic strength: 100 / pH: 6.5 / Temperature: 303 K

-
NMR measurement

NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 800 MHz

-
Processing

NMR software
NameDeveloperClassification
CNSBrunger, Adams, Clore, Gros, Nilges and Readstructure solution
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxdata analysis
SparkyGoddardchemical shift assignment
PIPPGarrettchemical shift assignment
MOLMOLKoradi, Billeter and Wuthrichstructure solution
CNSrefinement
RefinementMethod: DGSA-distance geometry simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 61 / Conformers submitted total number: 20 / Representative conformer: 1

+
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