- PDB-6g8o: Solution structure of the cross-linked SAM domain dimer of murine SLy1 -
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Open data
ID or keywords:
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Basic information
Entry
Database: PDB / ID: 6g8o
Title
Solution structure of the cross-linked SAM domain dimer of murine SLy1
Components
SAM and SH3 domain-containing protein 3
Keywords
SIGNALING 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
Evidence: equilibrium centrifugation, gel filtration, native gel electrophoresis
Type
Name
Symmetry operation
Number
identity operation
1_555
1
Buried area
2360 Å2
ΔGint
-13 kcal/mol
Surface area
6940 Å2
Method
PISA
NMR ensembles
Data
Criteria
Number of conformers (submitted / calculated)
15 / 100
structures with the lowest energy
Representative
Model #1
closest to the average
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Components
#1: Protein
SAMandSH3domain-containingprotein3 / 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
Experiment
Method: SOLUTION NMR
NMR experiment
Conditions-ID
Experiment-ID
Solution-ID
Sample state
Spectrometer-ID
Type
1
1
1
isotropic
2
2D 1H-15N HSQC
1
2
1
isotropic
2
2D 1H-13C HSQC aliphatic
1
3
1
isotropic
1
3D HNCO
1
4
1
isotropic
1
3D HNCA
1
5
1
isotropic
1
3D HN(CA)CB
1
7
1
isotropic
1
3DCBCA(CO)NH
1
6
1
isotropic
1
3DH(CCO)NH
1
9
1
isotropic
1
3DC(CO)NH
1
8
1
isotropic
2
3D (H)CCH-TOCSY
1
10
1
isotropic
2
3D 1H-15N NOESY
1
11
2
isotropic
2
3D 1H-15N NOESY
1
13
1
isotropic
2
3D 1H-13C NOESY aliphatic
1
12
1
isotropic
2
3D 1H-13C NOESY aromatic
1
14
2
isotropic
2
3D 1H-13C NOESY aliphatic
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Sample preparation
Details
Type
Solution-ID
Contents
Label
Solvent system
solution
1
1.4 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% D2O
Sample_1
93% H2O/7% D2O
solution
2
0.8 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% D2O
Sample_2
93% H2O/7% D2O
Sample
Conc. (mg/ml)
Component
Isotopic labeling
Solution-ID
1.4mM
SLy1SAMdomain
[U-99% 13C; U-99% 15N]
1
50mM
potassiumphosphate
naturalabundance
1
20mM
NaCl
naturalabundance
1
0.2mM
EDTA
naturalabundance
1
0.03 %
sodiumazide
naturalabundance
1
0.8mM
SLy1SAMdomain
[U-99% 13C; U-99% 15N]
2
50mM
potassiumphosphate
naturalabundance
2
20mM
sodiumchloride
naturalabundance
2
0.2mM
EDTA
naturalabundance
2
0.03 %
sodiumazide
naturalabundance
2
Sample conditions
Ionic strength: 0.098 M / Label: Standard_conditions / pH: 6.4 / Pressure: 1 bar / Temperature: 308 K
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NMR measurement
NMR spectrometer
Type
Manufacturer
Model
Field strength (MHz)
Spectrometer-ID
Bruker AVANCE
Bruker
AVANCE
600
1
Bruker AVANCE
Bruker
AVANCE
700
2
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Processing
NMR software
Name
Developer
Classification
NMRPipe
Delaglio, Grzesiek, Vuister, Zhu, PfeiferandBax
processing
NMRDraw
Delaglio, Grzesiek, Vuister, Zhu, PfeiferandBax
processing
CcpNmr Analysis
CCPN
chemicalshiftassignment
ARIA
Linge, O'DonoghueandNilges
chemicalshiftassignment
CNS
Brunger, Adams, Clore, Gros, NilgesandRead
structurecalculation
CNS
Brunger, Adams, Clore, Gros, NilgesandRead
refinement
Refinement
Method: simulated annealing / Software ordinal: 6
NMR representative
Selection criteria: closest to the average
NMR ensemble
Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 100 / Conformers submitted total number: 15
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