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- PDB-6g8o: Solution structure of the cross-linked SAM domain dimer of murine SLy1 -

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Basic information

Entry
Database: PDB / ID: 6g8o
TitleSolution structure of the cross-linked SAM domain dimer of murine SLy1
ComponentsSAM and SH3 domain-containing protein 3
KeywordsSIGNALING PROTEIN / SLy1 / SAM / adapter protein / scaffold protein
Function / homology
Function and homology information


positive regulation of lymphocyte activation / positive regulation of CD4-positive, alpha-beta T cell differentiation / positive regulation of adaptive immune response / CD4-positive, alpha-beta T cell differentiation / positive regulation of organ growth / positive regulation of immunoglobulin production / positive regulation of interleukin-4 production / B cell proliferation / positive regulation of interleukin-10 production / B cell homeostasis ...positive regulation of lymphocyte activation / positive regulation of CD4-positive, alpha-beta T cell differentiation / positive regulation of adaptive immune response / CD4-positive, alpha-beta T cell differentiation / positive regulation of organ growth / positive regulation of immunoglobulin production / positive regulation of interleukin-4 production / B cell proliferation / positive regulation of interleukin-10 production / B cell homeostasis / T cell proliferation / positive regulation of T cell proliferation / positive regulation of B cell proliferation / homeostasis of number of cells within a tissue / positive regulation of interleukin-2 production / positive regulation of T cell cytokine production / positive regulation of tumor necrosis factor production / positive regulation of type II interferon production / nucleus / cytoplasm
Similarity search - Function
SAM and SH3 domain-containing protein 3, SH3 domain / SAM and SH3 domain-containing protein 3 / SAM/SH3 domain-containing / SLy Proteins Associated Disordered Region / Transcription Factor, Ets-1 / Variant SH3 domain / SAM domain (Sterile alpha motif) / SAM domain profile. / Sterile alpha motif. / Sterile alpha motif domain ...SAM and SH3 domain-containing protein 3, SH3 domain / SAM and SH3 domain-containing protein 3 / SAM/SH3 domain-containing / SLy Proteins Associated Disordered Region / Transcription Factor, Ets-1 / Variant SH3 domain / SAM domain (Sterile alpha motif) / SAM domain profile. / Sterile alpha motif. / Sterile alpha motif domain / Sterile alpha motif/pointed domain superfamily / Src homology 3 domains / DNA polymerase; domain 1 / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
SAM and SH3 domain-containing protein 3
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodSOLUTION NMR / simulated annealing
AuthorsKukuk, L.K. / Dingley, A.J. / Koenig, B.W.
CitationJournal: Sci Rep / Year: 2019
Title: Structure of the SLy1 SAM homodimer reveals a new interface for SAM domain self-association.
Authors: Kukuk, L. / Dingley, A.J. / Granzin, J. / Nagel-Steger, L. / Thiagarajan-Rosenkranz, P. / Ciupka, D. / Hanel, K. / Batra-Safferling, R. / Pacheco, V. / Stoldt, M. / Pfeffer, K. / Beer- ...Authors: Kukuk, L. / Dingley, A.J. / Granzin, J. / Nagel-Steger, L. / Thiagarajan-Rosenkranz, P. / Ciupka, D. / Hanel, K. / Batra-Safferling, R. / Pacheco, V. / Stoldt, M. / Pfeffer, K. / Beer-Hammer, S. / Willbold, D. / Koenig, B.W.
History
DepositionApr 9, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 30, 2019Provider: repository / Type: Initial release
Revision 1.1May 8, 2019Group: Data collection / Category: pdbx_nmr_software / Item: _pdbx_nmr_software.name
Revision 1.2Jun 14, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_spectrometer / struct_conn
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_spectrometer.model / _struct_conn.pdbx_dist_value

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: SAM and SH3 domain-containing protein 3
B: SAM and SH3 domain-containing protein 3


Theoretical massNumber of molelcules
Total (without water)15,9102
Polymers15,9102
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: equilibrium centrifugation, gel filtration, native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area2360 Å2
ΔGint-13 kcal/mol
Surface area6940 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)15 / 100structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

#1: Protein SAM and SH3 domain-containing protein 3 / SH3 protein expressed in lymphocytes


Mass: 7954.952 Da / Num. of mol.: 2 / Fragment: SAM domain, UNP residues 253-321 / Mutation: K1G, S68C
Source method: isolated from a genetically manipulated source
Details: The two chains A and B are cross-linked by an artificial intermonomer disulfide bond at position 68 (320)
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Sash3, Sly / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8K352

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic22D 1H-15N HSQC
121isotropic22D 1H-13C HSQC aliphatic
131isotropic13D HNCO
141isotropic13D HNCA
151isotropic13D HN(CA)CB
171isotropic13D CBCA(CO)NH
161isotropic13D H(CCO)NH
191isotropic13D C(CO)NH
181isotropic23D (H)CCH-TOCSY
1101isotropic23D 1H-15N NOESY
1112isotropic23D 1H-15N NOESY
1131isotropic23D 1H-13C NOESY aliphatic
1121isotropic23D 1H-13C NOESY aromatic
1142isotropic23D 1H-13C NOESY aliphatic

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution11.4 mM [U-99% 13C; U-99% 15N] SLy1 SAM domain, 50 mM potassium phosphate, 20 mM NaCl, 0.2 mM EDTA, 0.03 % sodium azide, 93% H2O/7% D2OSample_193% H2O/7% D2O
solution20.8 mM [U-99% 13C; U-99% 15N] SLy1 SAM domain, 0.8 mM SLy1 SAM domain, 50 mM potassium phosphate, 20 mM sodium chloride, 0.2 mM EDTA, 0.03 % sodium azide, 93% H2O/7% D2OSample_293% H2O/7% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.4 mMSLy1 SAM domain[U-99% 13C; U-99% 15N]1
50 mMpotassium phosphatenatural abundance1
20 mMNaClnatural abundance1
0.2 mMEDTAnatural abundance1
0.03 %sodium azidenatural abundance1
0.8 mMSLy1 SAM domain[U-99% 13C; U-99% 15N]2
50 mMpotassium phosphatenatural abundance2
20 mMsodium chloridenatural abundance2
0.2 mMEDTAnatural abundance2
0.03 %sodium azidenatural abundance2
Sample conditionsIonic strength: 0.098 M / Label: Standard_conditions / pH: 6.4 / Pressure: 1 bar / Temperature: 308 K

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NMR measurement

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

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Processing

NMR software
NameDeveloperClassification
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRDrawDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
CcpNmr AnalysisCCPNchemical shift assignment
ARIALinge, O'Donoghue and Nilgeschemical shift assignment
CNSBrunger, Adams, Clore, Gros, Nilges and Readstructure calculation
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
RefinementMethod: simulated annealing / Software ordinal: 6
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 15

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