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- PDB-2n9b: Solution NMR Structure of Antiparallel Myosin-10:GCN4 Tandem Coil... -

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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 head, motor domain / Myosin head (motor domain) / Myosin motor domain profile. / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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

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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

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Experimental details

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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

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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

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NMR measurement

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

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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

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