Mass: 8660.873 Da / Num. of mol.: 1 / Mutation: K11R, K48R, K63R Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: UBB / Production host: Escherichia coli (E. coli) / References: UniProt: P0CG47
#2: Protein
Ubiquitin
Mass: 8604.845 Da / Num. of mol.: 1 / Mutation: K48R Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: UBB / Production host: Escherichia coli (E. coli) / References: UniProt: P0CG47
#3: Protein
Ubiquitin
Mass: 8691.918 Da / Num. of mol.: 1 / Mutation: M77D Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: UBB / Production host: Escherichia coli (E. coli) / References: UniProt: P0CG47
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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
2
isotropic
1
2D 1H-15N HSQC
1
3
3
isotropic
2
2D 1H-15N HSQC
1
4
4
isotropic
1
2D 1H-15N HSQC
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Sample preparation
Details
Type
Solution-ID
Contents
Details
Label
Solvent system
solution
1
120 uM [U-15N-distal11] Branched K11/K48-Linked Tri-Ubiquitin, 95% H2O/5% D2O
The distal K11-linked Ub was uniformly 15N-enriched, while the distal K48-linked Ub and the proximal Ub were not isotopically enriched.
15N_distal11
95% H2O/5% D2O
solution
2
100 uM [U-15N-distal48] Branched K11/K48-Linked Tri-Ubiquitin, 95% H2O/5% D2O
The distal K48-linked Ub was uniformly 15N-enriched, while the distal K11-linked Ub and the proximal Ub were not isotopically enriched.
15N_distal48
95% H2O/5% D2O
solution
3
60 uM [U-15N-distal11] Branched K11/K48-Linked Tri-Ubiquitin, 95% H2O/5% D2O
The distal K11-linked Ub was uniformly 15N-enriched, while the distal K48-linked Ub and the proximal Ub were not isotopically enriched. MTSL was attached to residue C48 in the distal K48-linked Ub.
15N_distal11_MTSL48
95% H2O/5% D2O
solution
4
110 uM [U-15N-distal48] Branched K11/K48-Linked Tri-Ubiquitin, 95% H2O/5% D2O
The distal K48-linked Ub was uniformly 15N-enriched, while the distal K11-linked Ub and the proximal Ub were not isotopically enriched. MTSL was attached to residue C48 in the distal K11-linked Ub.
15N_distal48_MTSL11
95% H2O/5% D2O
Sample
Conc. (mg/ml)
Component
Isotopic labeling
Solution-ID
120uM
Branched K11/K48-Linked Tri-Ubiquitin
[U-15N-distal11]
1
100uM
Branched K11/K48-Linked Tri-Ubiquitin
[U-15N-distal48]
2
60uM
Branched K11/K48-Linked Tri-Ubiquitin
[U-15N-distal11]
3
110uM
Branched K11/K48-Linked Tri-Ubiquitin
[U-15N-distal48]
4
Sample conditions
Details: Buffer: 20 mM sodium phosphate, pH 6.8. / Ionic strength: 0 M / Label: sample_conditions / pH: 6.8 / Pressure: 1 atm / Temperature: 298 K
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NMR measurement
NMR spectrometer
Type
Manufacturer
Model
Field strength (MHz)
Spectrometer-ID
Bruker AVANCE III
Bruker
AVANCEIII
800
1
Bruker AVANCE III
Bruker
AVANCEIII
600
2
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Processing
NMR software
Name
Developer
Classification
TopSpin
BrukerBiospin
processing
Sparky
Goddard
peakpicking
HADDOCK
Bonvin
refinement
HADDOCK
Bonvin
structurecalculation
Refinement
Method: simulated annealing / Software ordinal: 3 Details: THE INITIAL HADDOCK INPUT WAS THE CRYSTAL STRUCTURE OF BRANCHED K11/K48-LINKED TRI-UBIQUITIN (PDB ID 6OQ1). AMBIGUOUS DISTANCE RESTRAINTS WERE FROM CHEMICAL SHIFT PERTURBATIONS AND DISTANCE ...Details: THE INITIAL HADDOCK INPUT WAS THE CRYSTAL STRUCTURE OF BRANCHED K11/K48-LINKED TRI-UBIQUITIN (PDB ID 6OQ1). AMBIGUOUS DISTANCE RESTRAINTS WERE FROM CHEMICAL SHIFT PERTURBATIONS AND DISTANCE RESTRAINTS WERE BASED ON PRES.
NMR representative
Selection criteria: lowest energy
NMR ensemble
Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 400 / Conformers submitted total number: 10
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