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- PDB-5huz: Solution structure of coiled coil domain of myosin binding subuni... -

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Basic information

Entry
Database: PDB / ID: 5huz
TitleSolution structure of coiled coil domain of myosin binding subunit of myosin light chain phosphatase
ComponentsProtein phosphatase 1 regulatory subunit 12A
KeywordsSIGNALING PROTEIN / VASCULAR SMOOTH MUSCLE CELL
Function / homology
Function and homology information


regulation of myosin-light-chain-phosphatase activity / positive regulation of myosin-light-chain-phosphatase activity / phosphatase regulator activity / PTW/PP1 phosphatase complex / contractile muscle fiber / regulation of nucleocytoplasmic transport / negative regulation of catalytic activity / RHO GTPases Activate ROCKs / RHO GTPases activate CIT / enzyme inhibitor activity ...regulation of myosin-light-chain-phosphatase activity / positive regulation of myosin-light-chain-phosphatase activity / phosphatase regulator activity / PTW/PP1 phosphatase complex / contractile muscle fiber / regulation of nucleocytoplasmic transport / negative regulation of catalytic activity / RHO GTPases Activate ROCKs / RHO GTPases activate CIT / enzyme inhibitor activity / centrosome cycle / A band / RHO GTPases activate PAKs / regulation of cell adhesion / stress fiber / RHO GTPases activate PKNs / 14-3-3 protein binding / protein dephosphorylation / kinetochore / Z disc / Regulation of PLK1 Activity at G2/M Transition / cellular response to xenobiotic stimulus / actin cytoskeleton / mitotic cell cycle / focal adhesion / centrosome / nucleolus / protein kinase binding / signal transduction / positive regulation of transcription by RNA polymerase II / nucleoplasm / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Protein phosphatase 1 regulatory subunit 12A/B/C / cGMP-dependent protein kinase, interacting domain / cGMP-dependent protein kinase interacting domain / Ankyrin repeats (3 copies) / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / Ankyrin repeat-containing domain superfamily
Similarity search - Domain/homology
Protein phosphatase 1 regulatory subunit 12A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / torsion angle dynamics, molecular dynamics
AuthorsSharma, A.K. / Birrane, G. / Anklin, C. / Rigby, A.C. / Pollak, M. / Alper, S.L.
Citation
Journal: To Be Published
Title: To be published
Authors: Sharma, A.K. / Rigby, A.C.
#1: Journal: Protein Pept Lett. / Year: 2014
Title: NMR assignment and secondary structure of coiled coil domain of C-terminal myosin binding subunit of myosin phosphatase
Authors: Sharma, A.K. / Rigby, A.C.
History
DepositionJan 27, 2016Deposition site: RCSB / Processing site: RCSB
SupersessionMar 2, 2016ID: 2mxr
Revision 1.0Mar 2, 2016Provider: repository / Type: Initial release
SupersessionAug 10, 2016ID: 2MXR
Revision 1.1Aug 10, 2016Group: Advisory / Database references / Structure summary
Revision 1.2Jun 14, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description / Structure summary
Category: database_2 / entity ...database_2 / entity / pdbx_database_status / pdbx_nmr_exptl / pdbx_nmr_refine / pdbx_nmr_spectrometer
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_number_of_molecules / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_exptl.type / _pdbx_nmr_refine.software_ordinal / _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: Protein phosphatase 1 regulatory subunit 12A
B: Protein phosphatase 1 regulatory subunit 12A


Theoretical massNumber of molelcules
Total (without water)11,5772
Polymers11,5772
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area2270 Å2
ΔGint-20 kcal/mol
Surface area6910 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 20structures with the least restraint violations
RepresentativeModel #1target function

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Components

#1: Protein/peptide Protein phosphatase 1 regulatory subunit 12A / Myosin phosphatase-targeting subunit 1 / Myosin phosphatase target subunit 1 / Protein phosphatase ...Myosin phosphatase-targeting subunit 1 / Myosin phosphatase target subunit 1 / Protein phosphatase myosin-binding subunit


Mass: 5788.542 Da / Num. of mol.: 2 / Fragment: residues 931-978
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line: Bacteria / Gene: PPP1R12A, MBS, MYPT1 / Plasmid: pET28a / Organ (production host): HOMO SAPIENS / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: O14974

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-15N HSQC
121isotropic12D 1H-15N HSQC NH2 only
131isotropic12D 1H-13C HSQC
141isotropic13D CBCA(CO)NH
151isotropic13D C(CO)NH
1101isotropic13D HNCO
191isotropic13D HNCA
181isotropic13D HN(CA)CB
171isotropic13D HBHA(CO)NH
161isotropic13D HN(CO)CA
1111isotropic13D (H)CCH-TOCSY
1121isotropic13D H(CCO)NH
1131isotropic23D 1H-15N NOESY
1141isotropic23D 1H-13C NOESY
1151isotropic22D 1H-1H NOESY
1161anisotropic2isotope filtered 3D 1H-13C NOESY
1171anisotropic2isotope filtered 3D 1H-15N NOESY
1181anisotropic3isotope filtered 2D NOESY
1191isotropic32D 1H-15N HSQC

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Sample preparation

DetailsType: solution
Contents: 1.0 mM [U-99% 13C; U-99% 15N] coiled coil mbs-1, 1.0 mM [U-99% 15N] coiled coil mbs-2, 1.0 mM coiled coil mbs-3, 90% H2O/10% D2O
Details: 8% D2O, 1.0 MM [U-99% 13C; U-99% 15N] PROTEIN, 1 % DSS, 25 MM POTASSIUM PHOSPHATE, 0.05 % SODIUM AZIDE, 10 MM SODIUM CHLORIDE, 92% H2O/8% D2O
Label: 13C,15N_sample, 15N_sample, unlabeled_sample / Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.0 mMcoiled coil mbs-1[U-99% 13C; U-99% 15N]1
1.0 mMcoiled coil mbs-2[U-99% 15N]1
1.0 mMcoiled coil mbs-3natural abundance1
Sample conditionsIonic strength: 10 mM / Ionic strength err: 0.1 / Label: conditions_1 / pH: 7.0 / PH err: 0.05 / Pressure: 1 atm / Pressure err: 0.01 / Temperature: 303 K / Temperature err: 0.2

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCEBrukerAVANCE6001
Bruker AVANCEBrukerAVANCE7002
Bruker AVANCEBrukerAVANCE8003

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Processing

NMR software
NameVersionDeveloperClassification
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
Analysis2.4.0CCPNchemical shift assignment
ANSIGKraulischemical shift assignment
CYANA3.97Guntert, Mumenthaler and Wuthrichstructure calculation
CNS1.3Brunger, Adams, Clore, Gros, Nilges and Readrefinement
RefinementMethod: torsion angle dynamics, molecular dynamics / Software ordinal: 1
NMR representativeSelection criteria: target function
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 20 / Conformers submitted total number: 20

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