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- PDB-2n34: NMR assignments and solution structure of the JAK interaction reg... -

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Basic information

Entry
Database: PDB / ID: 2n34
TitleNMR assignments and solution structure of the JAK interaction region of SOCS5
ComponentsSuppressor of cytokine signaling 5
KeywordsSIGNALING PROTEIN / Suppressor of cytokine Signalling / JAK interaction region / Intrinsically unstructured protein
Function / homology
Function and homology information


vascular endothelial cell response to fluid shear stress / negative regulation of endothelial cell activation / Interleukin-4 and Interleukin-13 signaling / negative regulation of epidermal growth factor-activated receptor activity / positive regulation of T-helper 1 cell differentiation / kinase inhibitor activity / Neddylation / negative regulation of monocyte chemotactic protein-1 production / negative regulation of T-helper 2 cell differentiation / epidermal growth factor receptor binding ...vascular endothelial cell response to fluid shear stress / negative regulation of endothelial cell activation / Interleukin-4 and Interleukin-13 signaling / negative regulation of epidermal growth factor-activated receptor activity / positive regulation of T-helper 1 cell differentiation / kinase inhibitor activity / Neddylation / negative regulation of monocyte chemotactic protein-1 production / negative regulation of T-helper 2 cell differentiation / epidermal growth factor receptor binding / negative regulation of interleukin-6 production / cellular response to low-density lipoprotein particle stimulus / cell surface receptor signaling pathway via JAK-STAT / negative regulation of signal transduction / cytokine-mediated signaling pathway / receptor tyrosine kinase binding / negative regulation of inflammatory response / epidermal growth factor receptor signaling pathway / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / intracellular signal transduction / protein ubiquitination / cytoplasm
Similarity search - Function
SOCS5, SOCS box domain / SOCS4/SOCS5 domain / Suppressor of cytokine signalling / suppressors of cytokine signalling / SOCS box / SOCS box-like domain superfamily / SOCS box domain / SOCS box domain profile. / SOCS_box / SH2 domain ...SOCS5, SOCS box domain / SOCS4/SOCS5 domain / Suppressor of cytokine signalling / suppressors of cytokine signalling / SOCS box / SOCS box-like domain superfamily / SOCS box domain / SOCS box domain profile. / SOCS_box / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains / SH2 domain / SH2 domain superfamily
Similarity search - Domain/homology
Suppressor of cytokine signaling 5
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsChandrashekaran, I.R. / Mohanty, B. / Linossi, E.M. / Nicholson, S.E. / Babon, J. / Norton, R.S. / Dagley, L.F. / Leung, E.W.W. / Murphy, J.M.
CitationJournal: Biochemistry / Year: 2015
Title: Structure and Functional Characterization of the Conserved JAK Interaction Region in the Intrinsically Disordered N-Terminus of SOCS5.
Authors: Chandrashekaran, I.R. / Mohanty, B. / Linossi, E.M. / Dagley, L.F. / Leung, E.W. / Murphy, J.M. / Babon, J.J. / Nicholson, S.E. / Norton, R.S.
History
DepositionMay 21, 2015Deposition site: BMRB / Processing site: RCSB
SupersessionJul 29, 2015ID: 2MP6
Revision 1.0Jul 29, 2015Provider: repository / Type: Initial release
Revision 1.1Aug 26, 2015Group: Database references
Revision 1.2Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_software.name / _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: Suppressor of cytokine signaling 5


Theoretical massNumber of molelcules
Total (without water)8,1171
Polymers8,1171
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 / 40structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

#1: Protein Suppressor of cytokine signaling 5 / SOCS-5 / Cytokine-inducible SH2-containing protein 5


Mass: 8116.516 Da / Num. of mol.: 1 / Fragment: JAK interaction region (UNP residues 175-244)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Cish5, Socs5 / Plasmid: pGEX2T / Production host: Escherichia coli (E. coli) / References: UniProt: O54928

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-13C HSQC
1313D HNCA
1413D HN(CO)CA
1513D HN(CA)CB
1613D CBCA(CO)NH
1713D HBHA(CO)NH
1813D H(CCO)NH
1913D C(CO)NH
11013D 1H-15N NOESY
11113D 1H-13C NOESY aliphatic
11213D 1H-13C NOESY aromatic
11312D 1H-15N HSQC

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Sample preparation

DetailsContents: 0.3 mM [U-100% 13C; U-100% 15N] SOCS5 JIR, 5 mM TCEP, 20 mM Sodium citrate, 0.02 % sodium azide, 94% H2O/6% D2O
Solvent system: 94% H2O/6% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.3 mMSOCS5 JIR-1[U-100% 13C; U-100% 15N]1
5 mMTCEP-21
20 mMSodium citrate-31
0.02 %sodium azide-41
Sample conditionsIonic strength: 0.02 / pH: 4.5 / Pressure: ambient / Temperature: 303 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE6001
Bruker AvanceBrukerAVANCE8002

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Processing

NMR software
NameVersionDeveloperClassification
TopSpin3.2Bruker Biospinprocessing
TopSpin3.2Bruker Biospincollection
NMRPipe3Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRViewv8.2.33Johnson, One Moon Scientificpeak picking
NMRViewv8.2.33Johnson, One Moon Scientificchemical shift assignment
CARAKeller and Wuthrichpeak picking
CARAKeller and Wuthrichchemical shift assignment
CARAKeller and Wuthrichdata analysis
TALOSCornilescu, Delaglio and Baxdata analysis
SparkyGoddarddata analysis
CYANA3Guntert, Mumenthaler and Wuthrichstructure solution
ATNOSHerrmann,Guntert,Wuthrichdata analysis
CANDIDHerrmann, Guntert and Wuthrichdata analysis
CANDIDHerrmann, Guntert and Wuthrichnoe assignment
OPALpLuginbuhl, Guntert, Billeter and Wuthrichrefinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR constraintsNOE constraints total: 450 / NOE intraresidue total count: 189 / NOE long range total count: 18 / NOE medium range total count: 45 / NOE sequential total count: 198
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 40 / Conformers submitted total number: 20

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