[English] 日本語
Yorodumi
- PDB-2n9b: Solution NMR Structure of Antiparallel Myosin-10:GCN4 Tandem Coil... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2n9b
TitleSolution NMR Structure of Antiparallel Myosin-10:GCN4 Tandem Coiled-Coil
ComponentsUnconventional myosin-X, General control protein GCN4 fusion
KeywordsMOTOR PROTEIN/TRANSCRIPTION / anti-parallel coiled-coil / coiled-coil / MOTOR PROTEIN-TRANSCRIPTION complex
Function / homology
Function and homology information


plus-end directed microfilament motor activity / cytoskeleton-dependent intracellular transport / filopodium tip / FCERI mediated MAPK activation / protein localization to nuclear periphery / Activation of the AP-1 family of transcription factors / regulation of filopodium assembly / response to amino acid starvation / negative regulation of ribosomal protein gene transcription by RNA polymerase II / positive regulation of cellular response to amino acid starvation ...plus-end directed microfilament motor activity / cytoskeleton-dependent intracellular transport / filopodium tip / FCERI mediated MAPK activation / protein localization to nuclear periphery / Activation of the AP-1 family of transcription factors / regulation of filopodium assembly / response to amino acid starvation / negative regulation of ribosomal protein gene transcription by RNA polymerase II / positive regulation of cellular response to amino acid starvation / mediator complex binding / Oxidative Stress Induced Senescence / filopodium membrane / myosin complex / microfilament motor activity / phosphatidylinositol-3,4,5-trisphosphate binding / TFIID-class transcription factor complex binding / amino acid biosynthetic process / positive regulation of RNA polymerase II transcription preinitiation complex assembly / positive regulation of transcription initiation by RNA polymerase II / cellular response to nutrient levels / ruffle / cellular response to amino acid starvation / filopodium / RNA polymerase II transcription regulator complex / actin filament binding / regulation of cell shape / lamellipodium / DNA-binding transcription activator activity, RNA polymerase II-specific / cell cortex / transcription regulator complex / sequence-specific DNA binding / RNA polymerase II-specific DNA-binding transcription factor binding / DNA-binding transcription factor activity, RNA polymerase II-specific / calmodulin binding / intracellular signal transduction / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / chromatin binding / negative regulation of transcription by RNA polymerase II / signal transduction / positive regulation of transcription by RNA polymerase II / ATP binding / identical protein binding / nucleus / 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 / RA like domain / Ras-associating (RA) domain / : / Basic region leucine zipper / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #170 / IQ calmodulin-binding motif / Basic-leucine zipper (bZIP) domain signature. / Basic-leucine zipper (bZIP) domain profile. / basic region leucin zipper / Basic-leucine zipper domain / Basic-leucine zipper domain superfamily / FERM central domain / FERM/acyl-CoA-binding protein superfamily / Short calmodulin-binding motif containing conserved Ile and Gln residues. / IQ motif, EF-hand binding site / Myosin motor domain profile. / Myosin head, motor domain / Myosin head (motor domain) / Myosin. Large ATPases. / IQ motif profile. / FERM central domain / FERM superfamily, second domain / FERM domain / FERM domain profile. / Band 4.1 domain / Band 4.1 homologues / PH domain / Kinesin motor domain superfamily / 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
General control transcription factor GCN4 / Unconventional myosin-X
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
Saccharomyces cerevisiae (brewer's yeast)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model1
AuthorsVavra, K.C. / Xia, Y. / Rock, R.S.
Citation
Journal: Biophys.J. / Year: 2016
Title: Competition between Coiled-Coil Structures and the Impact on Myosin-10 Bundle Selection
Authors: Vavra, K.C. / Xia, Y. / Rock, R.S.
#1: Journal: 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.
#2: Journal: Science / Year: 1991
Title: X-ray structure of the GCN4 leucine zipper, a two-stranded, parallel coiled coil
Authors: Klemm, J.D. / Kim, P.S. / Alber, T.
#3: Journal: Proc.Natl.Acad.Sci.USA / Year: 2008
Title: A myosin motor that selects bundled actin for motility
Authors: Nagy, S. / Ricca, B.L. / Norstrom, M.F. / Courson, D.F. / Brawley, C.M. / Smithback, P.A. / Rock, R.S.
#4: Journal: Proc.Natl.Acad.Sci.USA / Year: 1997
Title: Spare the rod, spoil the regulation: necessity for a myosin rod
Authors: Trybus, K.M. / Freyzon, Y. / Faust, L.Z. / Sweeney, H.
History
DepositionNov 12, 2015Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jun 15, 2016Provider: repository / Type: Initial release
Revision 1.1Oct 10, 2018Group: Data collection / Database references ...Data collection / Database references / Experimental preparation / Source and taxonomy / Structure summary
Category: citation / entity ...citation / entity / entity_name_com / entity_src_gen / pdbx_nmr_sample_details / struct_ref_seq_dif
Item: _citation.pdbx_database_id_PubMed / _entity.formula_weight ..._citation.pdbx_database_id_PubMed / _entity.formula_weight / _entity_name_com.name / _pdbx_nmr_sample_details.contents / _struct_ref_seq_dif.details
Revision 1.2Jun 14, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Structure summary
Category: database_2 / entity ...database_2 / entity / pdbx_database_status / pdbx_nmr_spectrometer
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.formula_weight / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_spectrometer.model
Revision 1.3May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Unconventional myosin-X, General control protein GCN4 fusion
B: Unconventional myosin-X, General control protein GCN4 fusion


Theoretical massNumber of molelcules
Total (without water)16,4012
Polymers16,4012
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)10 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

-
Components

#1: Protein Unconventional myosin-X, General control protein GCN4 fusion / Unconventional myosin-10 / Amino acid biosynthesis regulatory protein


Mass: 8200.290 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (domestic cattle), (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Gene: MYO10, GCN4, AAS3, ARG9, YEL009C / Strain: ATCC 204508 / S288c / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / Variant (production host): DE3 pLysS / References: UniProt: P79114, UniProt: P03069

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
Details: Tandem antiparallel coiled-coil fusion derived from Bos taurus myosin-10 coiled-coil and GCN4-p1. Structure solved by solution NMR. Tertiary structure supported by Small-Angle X-ray scattering (see reference).
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1213D HCACO
1313D HNCO
1413D HN(CO)CA
1513D HNCA
1613D CBCA(CO)NH
1713D CBCANH
1812D (HB)CB(CGCD)HD
1913D H(CCO)NH
11013D (H)CCH-TOCSY
11113D (H)CCH-COSY
11212D 1H-13C HSQC aliphatic
11312D 1H-13C HSQC
11412D 1H-15N HSQC NH2 only
11513D 1H-15N NOESY
11613D 1H-13C NOESY

-
Sample preparation

DetailsContents: 1.1 mM [U-100% 13C; U-100% 15N] entity-1, 100 mM potassium phosphate-2, 1 mM EDTA-3, 0.03 % sodium azide-4, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.1 mMentity-1[U-100% 13C; U-100% 15N]1
100 mMpotassium phosphate-21
1 mMEDTA-31
0.03 %sodium azide-41
Sample conditionsIonic strength: 0.6 / pH: 6.5 / Pressure: ambient / Temperature: 308 K

-
NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE8501
Varian INOVAVarianINOVA6002

-
Processing

NMR software
NameVersionDeveloperClassification
Xplor-NIH2.38Schwieters, Kuszewski, Tjandra and Clorestructure solution
Xplor-NIH2.38Schwieters, Kuszewski, Tjandra and Clorerefinement
CCPN2.4.1CCPNchemical shift assignment
CCPN2.4.1CCPNdata analysis
CCPN2.4.1CCPNpeak picking
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
RefinementMethod: simulated annealing / Software ordinal: 1
NMR constraintsNOE constraints total: 1561 / NOE intraresidue total count: 332 / NOE long range total count: 149 / NOE medium range total count: 610 / NOE sequential total count: 470 / Hydrogen bond constraints total count: 294 / Protein phi angle constraints total count: 147 / Protein psi angle constraints total count: 147
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 10

+
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