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- PDB-2i0n: Structure of Dictyostelium discoideum Myosin VII SH3 domain with ... -

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Basic information

Entry
Database: PDB / ID: 2i0n
TitleStructure of Dictyostelium discoideum Myosin VII SH3 domain with adjacent proline rich region
ComponentsClass VII unconventional myosin
KeywordsSTRUCTURAL PROTEIN / BETA-SHEET LOOP
Function / homology
Function and homology information


spore germination / actin filament-based movement / filopodium tip / filopodium assembly / myosin complex / microfilament motor activity / cell-substrate adhesion / cell leading edge / cytoskeletal motor activity / phagocytic cup ...spore germination / actin filament-based movement / filopodium tip / filopodium assembly / myosin complex / microfilament motor activity / cell-substrate adhesion / cell leading edge / cytoskeletal motor activity / phagocytic cup / phagocytosis / filopodium / actin filament organization / cell morphogenesis / endocytosis / : / actin filament binding / actin cytoskeleton / actin binding / cell cortex / microtubule binding / ATP binding / membrane / cytoplasm / cytosol
Similarity search - Function
MyTH4 domain / MyTH4 domain superfamily / MyTH4 domain / MyTH4 domain profile. / Domain in Myosin and Kinesin Tails / Variant SH3 domain / FERM central domain / FERM/acyl-CoA-binding protein superfamily / Short calmodulin-binding motif containing conserved Ile and Gln residues. / Myosin head, motor domain ...MyTH4 domain / MyTH4 domain superfamily / MyTH4 domain / MyTH4 domain profile. / Domain in Myosin and Kinesin Tails / Variant SH3 domain / 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 profile. / IQ motif, EF-hand binding site / SH3 Domains / FERM central domain / FERM superfamily, second domain / FERM domain / FERM domain profile. / Band 4.1 domain / Band 4.1 homologues / Kinesin motor domain superfamily / SH3 type barrels. / Src homology 3 domains / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / PH-like domain superfamily / Ubiquitin-like domain superfamily / Roll / P-loop containing nucleoside triphosphate hydrolase / Mainly Beta
Similarity search - Domain/homology
Myosin-I heavy chain
Similarity search - Component
Biological speciesDictyostelium discoideum (eukaryote)
MethodSOLUTION NMR / Simulated annealing in XPLOR
AuthorsWang, Q. / Deloia, M.A. / Kang, Y. / Litchke, C. / Titus, M.A. / Walters, K.J.
CitationJournal: Protein Sci. / Year: 2007
Title: The SH3 domain of a M7 interacts with its C-terminal proline-rich region.
Authors: Wang, Q. / Deloia, M.A. / Kang, Y. / Litchke, C. / Zhang, N. / Titus, M.A. / Walters, K.J.
History
DepositionAug 10, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 9, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 9, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly ...database_2 / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Class VII unconventional myosin


Theoretical massNumber of molelcules
Total (without water)8,9641
Polymers8,9641
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 / 21structures with the lowest energy
RepresentativeModel #1fewest violations

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Components

#1: Protein Class VII unconventional myosin


Mass: 8964.195 Da / Num. of mol.: 1 / Fragment: SH3 domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Dictyostelium discoideum (eukaryote) / Gene: myoI / Plasmid: pGEX-6p-1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q9U1M8

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
11115N-edited NOESY-HSQC
12213C-edited NOESY-HSQC
1342D NOESY
14315N-13C HNCA
15315N-13C HN(CO)CA
16315N-13C HNCO

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Sample preparation

Details
Solution-IDContentsSolvent system
1protein U-15N, 20mM phosphate buffer, 100mM NaCl, 90% H2O, 10% D2O90% H2O/10% D2O
2protein U-13C, 20mM phosphate buffer, 100mM NaCl, 90% H2O, 10% D2O90% H2O/10% D2O
3protein U-15N,13C, 20mM phosphate buffer, 100mM NaCl, 90% H2O, 10% D2O90% H2O/10% D2O
4unlabeled sample, 20mM phosphate buffer, 100mM NaCl, 100% D2O100% D2O
Sample conditionsIonic strength: 20mM NaPO4, 100mM NaCl / pH: 6.5 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA8001
Varian INOVAVarianINOVA6002

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Processing

NMR software
NameVersionDeveloperClassification
NMRPipe1995Delaglio et al.processing
X-PLOR3.851Brungerrefinement
RefinementMethod: Simulated annealing in XPLOR / Software ordinal: 1
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 21 / Conformers submitted total number: 20

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