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- PDB-2ruj: Solution structure of MTSL spin-labeled Schizosaccharomyces pombe... -

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Basic information

Entry
Database: PDB / ID: 2ruj
TitleSolution structure of MTSL spin-labeled Schizosaccharomyces pombe Sin1 CRIM domain
ComponentsStress-activated map kinase-interacting protein 1
KeywordsPROTEIN BINDING / Sin1 / CRIM domain / TORC2 / PRE
Function / homology
Function and homology information


PIP3 activates AKT signaling / CD28 dependent PI3K/Akt signaling / VEGFR2 mediated vascular permeability / Regulation of TP53 Degradation / positive regulation of conjugation with cellular fusion / TORC2 signaling / TORC2 complex / p38MAPK cascade / signaling adaptor activity / phosphatidylinositol-4,5-bisphosphate binding ...PIP3 activates AKT signaling / CD28 dependent PI3K/Akt signaling / VEGFR2 mediated vascular permeability / Regulation of TP53 Degradation / positive regulation of conjugation with cellular fusion / TORC2 signaling / TORC2 complex / p38MAPK cascade / signaling adaptor activity / phosphatidylinositol-4,5-bisphosphate binding / positive regulation of G2/M transition of mitotic cell cycle / meiotic cell cycle / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Sin1, N-terminal / Stress-activated map kinase interacting protein 1 (SIN1) / TORC2 component Sin1/Avo1 / SAPK-interacting protein 1, Pleckstrin-homology domain / Sin1, middle CRIM domain / SAPK-interacting protein 1 (Sin1), middle CRIM domain / SAPK-interacting protein 1 (Sin1), Pleckstrin-homology / PH-like domain superfamily
Similarity search - Domain/homology
Target of rapamycin complex 2 subunit sin1
Similarity search - Component
Biological speciesSchizosaccharomyces pombe 972h- (yeast)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model1
AuthorsFuruita, K. / Kataoka, S. / Sugiki, T. / Kobayashi, N. / Ikegami, T. / Shiozaki, K. / Fujiwara, T. / Kojima, C.
CitationJournal: J.Biomol.Nmr / Year: 2015
Title: Utilization of paramagnetic relaxation enhancements for high-resolution NMR structure determination of a soluble loop-rich protein with sparse NOE distance restraints
Authors: Furuita, K. / Kataoka, S. / Sugiki, T. / Hattori, Y. / Kobayashi, N. / Ikegami, T. / Shiozaki, K. / Fujiwara, T. / Kojima, C.
History
DepositionJul 24, 2014Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Jul 29, 2015Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Stress-activated map kinase-interacting protein 1


Theoretical massNumber of molelcules
Total (without water)19,2431
Polymers19,2431
Non-polymers00
Water0
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 Stress-activated map kinase-interacting protein 1 / SAPK-interacting protein 1


Mass: 19243.361 Da / Num. of mol.: 1 / Fragment: UNP residues 247-400
Mutation: T280(R1A), S282(R1A), R291(R1A), S301(R1A), K312(R1A), L322(R1A), S371(R1A), T384(R1A), A394(R1A)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schizosaccharomyces pombe 972h- (yeast)
Strain: 972 / ATCC 24843 / Gene: sin1, SPAPYUG7.02c / Production host: Escherichia coli (E. coli) / References: UniProt: Q9P7Y9

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1222D 1H-13C HSQC
1332D 1H-1H NOESY
1423D C(CO)NH
1523D HNCO
1623D HNCA
1723D HN(CA)CB
1823D HBHA(CO)NH
1923D HN(CO)CA
11023D HN(COCA)CB
11123D H(CCO)NH
11223D (H)CCH-TOCSY
11313D 1H-15N NOESY
11423D 1H-13C NOESY
11542D 1H-15N HSQC
11623D HN(CA)CO

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Sample preparation

Details
Solution-IDContentsSolvent system
10.5 mM [U-100% 15N] entity_1-1, 50 mM potassium phosphate-2, 50 mM potassium chloride-3, 90 % H2O-4, 10 % D2O-5, 1 mM DTT-6, 90% H2O/10% D2O90% H2O/10% D2O
20.5 mM [U-100% 13C; U-100% 15N] entity_1-7, 50 mM potassium phosphate-8, 50 mM potassium chloride-9, 1 mM DTT-10, 90 % H2O-11, 10 % D2O-12, 90% H2O/10% D2O90% H2O/10% D2O
30.5 mM entity_1-13, 50 mM potassium phosphate-14, 50 mM potassium chloride-15, 90 % H2O-16, 10 % D2O-17, 1 mM DTT-18, 90% H2O/10% D2O90% H2O/10% D2O
40.5 mM [U-100% 15N] entity_1-19, 50 mM potassium phosphate-20, 50 mM potassium chloride-21, 90 % H2O-22, 10 % D2O-23, 1 mM DTT-24, 15 mg/mL Pf1 phage-25, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.5 mMentity_1-1[U-100% 15N]1
50 mMpotassium phosphate-21
50 mMpotassium chloride-31
90 %H2O-41
10 %D2O-51
1 mMDTT-61
0.5 mMentity_1-7[U-100% 13C; U-100% 15N]2
50 mMpotassium phosphate-82
50 mMpotassium chloride-92
1 mMDTT-102
90 %H2O-112
10 %D2O-122
0.5 mMentity_1-133
50 mMpotassium phosphate-143
50 mMpotassium chloride-153
90 %H2O-163
10 %D2O-173
1 mMDTT-183
0.5 mMentity_1-19[U-100% 15N]4
50 mMpotassium phosphate-204
50 mMpotassium chloride-214
90 %H2O-224
10 %D2O-234
1 mMDTT-244
15 mg/mLPf1 phage-254
Sample conditionsIonic strength: 0.2 / pH: 6.8 / Pressure: ambient / Temperature: 303 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAvance8001
Bruker AvanceBrukerAvance9502

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Processing

NMR software
NameVersionDeveloperClassification
CYANA3.95Guntert, Mumenthaler and Wuthrichstructure solution
X-PLOR_NIH2.31Schwieters, Kuszewski, Tjandra and Clorerefinement
SPARKYGoddardchemical shift assignment
RefinementMethod: simulated annealing / Software ordinal: 1
NMR constraintsNOE constraints total: 929 / NOE long range total count: 191 / NOE medium range total count: 126
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 10 / Representative conformer: 1

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