2N8A

1H, 13C and 15N chemical shift assignments and solution structure for PARP-1 F1F2 domains in complex with a DNA single-strand break


SOLUTION NMR
NMR Experiment
ExperimentTypeSample ContentsSolventIonic StrengthpHPressureTemperature (K)Spectrometer
12D 1H-15N TROSYSample 1: 0.2 mM [U-15N; U-13C; U-2H] PARP-1 1, 0.2 mM DNA (45-MER), 50 mM [U-2H] TRIS, 1 mM [U-2H] DTT, 0.1 mM ZnSO495% H2O/5% D2O0.00047.2ambient310
22D 1H-13C HMQCSample 1: 0.2 mM [U-15N; U-13C; U-2H] PARP-1 1, 0.2 mM DNA (45-MER), 50 mM [U-2H] TRIS, 1 mM [U-2H] DTT, 0.1 mM ZnSO495% H2O/5% D2O0.00047.2ambient310
3TROSY-NHCACB (optimized for CB)Sample 1: 0.2 mM [U-15N; U-13C; U-2H] PARP-1 1, 0.2 mM DNA (45-MER), 50 mM [U-2H] TRIS, 1 mM [U-2H] DTT, 0.1 mM ZnSO495% H2O/5% D2O0.00047.2ambient310
4TROSY-HNCASample 1: 0.2 mM [U-15N; U-13C; U-2H] PARP-1 1, 0.2 mM DNA (45-MER), 50 mM [U-2H] TRIS, 1 mM [U-2H] DTT, 0.1 mM ZnSO495% H2O/5% D2O0.00047.2ambient310
5TROSY-HN(CO)CASample 1: 0.2 mM [U-15N; U-13C; U-2H] PARP-1 1, 0.2 mM DNA (45-MER), 50 mM [U-2H] TRIS, 1 mM [U-2H] DTT, 0.1 mM ZnSO495% H2O/5% D2O0.00047.2ambient310
62D 1H-15N TROSYSample 2: 0.2 mM [U-15N; U-13C; U-70% 2H] PARP-1 1, 0.2 mM DNA (45-MER), 50 mM [U-2H] TRIS, 1 mM [U-2H] DTT, 0.1 mM ZnSO495% H2O/5% D2O0.00047.2ambient310
72D 1H-13C HMQCSample 2: 0.2 mM [U-15N; U-13C; U-70% 2H] PARP-1 1, 0.2 mM DNA (45-MER), 50 mM [U-2H] TRIS, 1 mM [U-2H] DTT, 0.1 mM ZnSO495% H2O/5% D2O0.00047.2ambient310
8TROSY-HNCASample 2: 0.2 mM [U-15N; U-13C; U-70% 2H] PARP-1 1, 0.2 mM DNA (45-MER), 50 mM [U-2H] TRIS, 1 mM [U-2H] DTT, 0.1 mM ZnSO495% H2O/5% D2O0.00047.2ambient310
9TROSY-HN(CO)CASample 2: 0.2 mM [U-15N; U-13C; U-70% 2H] PARP-1 1, 0.2 mM DNA (45-MER), 50 mM [U-2H] TRIS, 1 mM [U-2H] DTT, 0.1 mM ZnSO495% H2O/5% D2O0.00047.2ambient310
102D 1H-15N TROSYSample 3: 0.2 mM [U-98% 2H; U-98% 15N] PARP-1 1, 0.2 mM DNA (45-MER), 50 mM [U-2H] TRIS, 1 mM [U-2H] DTT, 0.1 mM ZnSO495% H2O/5% D2O0.00047.2ambient310
113D 1H-13C-1H NOESY-HMQCSample 4a: 0.2 MM PARP-1 1-214, Uniform [2H,15N,13C], back-labeled with [1H,13C] in the delta-methyl groups of Ile and all methyl groups of Leu and Val residues, using sodium [4-13C, 3,3-2H2] alpha-ketobutyrate and sodium [3- 2H, 4,4'-13C2] alpha-ketoisovalerate as precursors to maximize protonation of methyl groups, for use in NOE experiments; sodium [3-2H, 4,4'-13C2] alpha-ketoisovalerate was prepared from sodium [4,4'-13C2] alpha-ketoisovalerate by exchange with 2H2O at pH 12.5 and 45 C for 3 hrs. 0.2 mM DNA (45-MER), 50 mM [U-2H] TRIS, 1 mM [U-2H] DTT, 0.1 mM ZnSO495% H2O/5% D2O0.00047.2ambient310
12HMCM(CG)CBCASample 4b: 0.2 MM PARP-1 1-214, Uniform [2H,15N,13C], back-labeled with [1H,13C] in the delta-methyl groups of Ile and all methyl groups of Leu and Val residues, using sodium [3,3-2H2,13C4] alpha-ketobutyrate and sodium [3- 2H,13C5] alpha-ketoisovalerate as precursors to produce linear chains of 13C in the sidechains of Val and Leu, for use in assignment experiments to link methyl signals to C-alpha signals. 0.2 mM DNA (45-MER), 50 mM [U-2H] TRIS, 1 mM [U-2H] DTT, 0.1 mM ZnSO4100% D2O0.00047.2ambient310
132D 1H-1H NOESYSample 5: 0.2 MM PARP-1 1-214, Uniform [2H,15N,13C], back-labeled with [1H,13C] in the methyl groups of Met residues in addition to Ile, Leu and Val methyl groups as in sample 4a. 0.2 mM DNA (45-MER), 50 mM [U-2H] TRIS, 1 mM [U-2H] DTT, 0.1 mM ZnSO4100% D2O0.00047.2ambient310
143D 13C-13C-1H HMQC-NOESY-HMQCSample 5: 0.2 MM PARP-1 1-214, Uniform [2H,15N,13C], back-labeled with [1H,13C] in the methyl groups of Met residues in addition to Ile, Leu and Val methyl groups as in sample 4a. 0.2 mM DNA (45-MER), 50 mM [U-2H] TRIS, 1 mM [U-2H] DTT, 0.1 mM ZnSO4100% D2O0.00047.2ambient310
153D 1H-13C-1H NOESY-HMQCSample 5: 0.2 MM PARP-1 1-214, Uniform [2H,15N,13C], back-labeled with [1H,13C] in the methyl groups of Met residues in addition to Ile, Leu and Val methyl groups as in sample 4a. 0.2 mM DNA (45-MER), 50 mM [U-2H] TRIS, 1 mM [U-2H] DTT, 0.1 mM ZnSO4100% D2O0.00047.2ambient310
162D 1H-13C HSQC aromaticSample 6: 0.2 MM PARP-1 1-214, Uniform [2H,15N,13C]; back-labeled with [1H,13C] in the methyl groups of Ile, Leu and Val methyl groups as in sample 4a and [1H,13C,15N] Phe residues. 0.2 mM DNA (45-MER), 50 mM [U-2H] TRIS, 1 mM [U-2H] DTT, 0.1 mM ZnSO4100% D2O0.00047.2ambient310
172D 1H-1H NOESY filtered to accept 13C-1H in w2Sample 7: 0.2 MM PARP-1 1-214, Sortase ligated, block-labelled sample. (N.B. residues 103 and 104 of WT sequence deleted, additional residues LPETGGG inserted between residues 102 and 105; this sample was not used for making any assignments of residues in this region, which is in the flexible linker between domains). Labelling for residues 1-102 (and LPET of insertion): uniform [1H,12C,15N]. Labelling for residues 105-214 (and GGG of insertion): [2H,15N,13C] back-labeled with [1H,13C] Ile, Leu Val and Met methyl groups labeled as in sample 5. 0.2 mM DNA (45-MER), 50 mM [U-2H] TRIS, 1 mM [U-2H] DTT, 0.1 mM ZnSO4100% D2O0.00047.2ambient310
182D 1H-1H NOESY filtered to accept 13C-1H in w2 (no decoupling in w1)Sample 7: 0.2 MM PARP-1 1-214, Sortase ligated, block-labelled sample. (N.B. residues 103 and 104 of WT sequence deleted, additional residues LPETGGG inserted between residues 102 and 105; this sample was not used for making any assignments of residues in this region, which is in the flexible linker between domains). Labelling for residues 1-102 (and LPET of insertion): uniform [1H,12C,15N]. Labelling for residues 105-214 (and GGG of insertion): [2H,15N,13C] back-labeled with [1H,13C] Ile, Leu Val and Met methyl groups labeled as in sample 5. 0.2 mM DNA (45-MER), 50 mM [U-2H] TRIS, 1 mM [U-2H] DTT, 0.1 mM ZnSO4100% D2O0.00047.2ambient310
192D 1H-1H NOESY filtered to accept 13C-1H in w2Sample 8: 0.2 MM PARP-1 1-214, Sortase ligated, block-labelled sample. (N.B. residues 103 and 104 of WT sequence deleted, additional residues LPETGGG inserted between residues 102 and 105; this sample was not used for making any assignments of residues in this region, which is in the flexible linker between domains). Labelling for residues 1-102 (and LPET of insertion): uniform [1H,12C,15N]. Labelling for residues 105-214 (and GGG of insertion): [2H,15N,13C] back labeled with [1H,13C] Met methyl groups as in sample 5 and [13C,15N,1H] Arg residues. 0.2 mM DNA (45-MER), 50 mM [U-2H] TRIS, 1 mM [U-2H] DTT, 0.1 mM ZnSO4100% D2O0.00047.2ambient310
202D 1H-1H NOESY filtered to accept 13C-1H in w2 (no decoupling in w1)Sample 8: 0.2 MM PARP-1 1-214, Sortase ligated, block-labelled sample. (N.B. residues 103 and 104 of WT sequence deleted, additional residues LPETGGG inserted between residues 102 and 105; this sample was not used for making any assignments of residues in this region, which is in the flexible linker between domains). Labelling for residues 1-102 (and LPET of insertion): uniform [1H,12C,15N]. Labelling for residues 105-214 (and GGG of insertion): [2H,15N,13C] back labeled with [1H,13C] Met methyl groups as in sample 5 and [13C,15N,1H] Arg residues. 0.2 mM DNA (45-MER), 50 mM [U-2H] TRIS, 1 mM [U-2H] DTT, 0.1 mM ZnSO4100% D2O0.00047.2ambient310
212D 1H-1H NOESY filtered to accept 13C-1H in w2 (no decoupling in w1)Sample 9: 0.2 MM PARP-1 1-214, Sortase ligated, block-labelled sample. (N.B. residues 103 and 104 of WT sequence deleted, additional residues LPETGGG inserted between residues 102 and 105; this sample was not used for making any assignments of residues in this region, which is in the flexible linker between domains). Labelling for residues 1-102 (and LPET of insertion): [2H,15N,13C] back-labeled with Ile, Leu and Val methyl groups labeled as in sample 4a and [1H,13C,15N] Arg residues. Labelling for residues 105-214 (and GGG of insertion): uniform [1H,12C,15N]. 0.2 mM DNA (45-MER), 50 mM [U-2H] TRIS, 1 mM [U-2H] DTT, 0.1 mM ZnSO495% H2O/5% D2O0.00047.2ambient310
222D 1H-1H NOESY filtered to accept 13C-1H in w2Sample 10: 0.2 MM PARP-1 1-214, Sortase ligated, block-labelled sample. (N.B. residues 103 and 104 of WT sequence deleted, additional residues LPETGGG inserted between residues 102 and 105; this sample was not used for making any assignments of residues in this region, which is in the flexible linker between domains). Labelling for residues 1-102 (and LPET of insertion): [2H,15N,13C] back-labeled with Ile, Leu and Val methyl groups labeled as in sample 4a and [1H,13C,15N] Phe residues. Labelling for residues 105-214 (and GGG of insertion): uniform [1H,12C,15N]. 0.2 mM DNA (45-MER), 50 mM [U-2H] TRIS, 1 mM [U-2H] DTT, 0.1 mM ZnSO4100% D2O0.00047.2ambient310
232D 1H-13C HSQC aliphaticSample 11: 0.2 mM see Sample details section PARP-1 1, 0.2 mM DNA (45-MER), 50 mM [U-2H] TRIS, 1 mM [U-2H] DTT, 0.1 mM ZnSO4100% D2O0.00047.2ambient310
242D 1H-1H NOESY filtered to accept 13C-1H in w2Sample 11: 0.2 mM see Sample details section PARP-1 1, 0.2 mM DNA (45-MER), 50 mM [U-2H] TRIS, 1 mM [U-2H] DTT, 0.1 mM ZnSO4100% D2O0.00047.2ambient310
252D 1H-1H TOCSYSample 12: 0.2 mM DNA (45-MER), 50 mM [U-2H] TRIS, 1 mM [U-2H] DTT, 0.1 mM ZnSO4100% D2O0.00047.2ambient310
262D 1H-1H NOESYSample 12: 0.2 mM DNA (45-MER), 50 mM [U-2H] TRIS, 1 mM [U-2H] DTT, 0.1 mM ZnSO4100% D2O0.00047.2ambient310
272D 1H-1H TOCSYSample 13: 0.2 mM DNA (45-MER), 50 mM [U-2H] TRIS, 1 mM [U-2H] DTT, 0.1 mM ZnSO495% H2O/5% D2O0.00047.2ambient300
282D 1H-1H NOESYSample 13: 0.2 mM DNA (45-MER), 50 mM [U-2H] TRIS, 1 mM [U-2H] DTT, 0.1 mM ZnSO495% H2O/5% D2O0.00047.2ambient300
292D 1H-1H NOESYSample 14: 0.2 mM [U-15N; U-13C; U-2H] PARP-1 1, 0.2 mM DNA (45-MER), 50 mM [U-2H] TRIS, 1 mM [U-2H] DTT, 0.1 mM ZnSO4100% D2O0.00047.2ambient310
302D 1H-15N TROSYSample 15: 0.2 mM [U-15N; U-13C; U-2H] PARP-1 1, 50 mM [U-2H] TRIS, 1 mM [U-2H] DTT, 0.1 uM ZnSO4, 200 mM sodium chloride95% H2O/5% D2O0.17.2ambient303
312D 1H-15N TROSYSample 16: 0.2 mM [U-15N; U-13C; U-2H] PARP-1 1, 0.2 mM DNA (45-MER), 50 mM [U-2H] TRIS, 1 mM [U-2H] DTT, 0.1 uM ZnSO4, 200 mM sodium chloride95% H2O/5% D2O0.17.2ambient303
NMR Spectrometer Information
SpectrometerManufacturerModelField Strength
1BrukerAvance I800
2BrukerAvance II+700
3BrukerDMX600
4BrukerDRX500
NMR Refinement
MethodDetailsSoftware
simulated annealingTHE STRUCTURE WAS CALCULATED USING A COMBINED NMR/X-RAY PROTOCOL. NMR EVIDENCE ESTABLISHED THE TOPOLOGY OF THE COMPLEX TO BE A MONOMERIC ASSEMBLY IN WHICH DOMAIN F1 (PROTEIN RESIDUES 6-91) IS BOUND TO THE DNA STEM WITH THE 5' TERMINUS AND DOMAIN F2 (PROTEIN RESIDUES 109-200) TO THE DNA STEM WITH THE 3' TERMINUS; NMR FURTHER SHOWED THAT THE INDIVIDUAL BINDING MODES OF F1 AND F2 TO THEIR RESPECTIVE STEMS WAS EQUIVALENT (THOUGH IN A DIFFERENT CONTEXT) TO THOSE SEEN IN CRYSTAL STRUCTURES PDB 3ODA AND 3ODC RESPECTIVELY. TEMPLATE STRUCTURES WERE CREATED FROM 3ODA AND 3ODC (AND 1MSY AND 1RNG FOR THE DNA TETRALOOPS) AND USED TOGETHER WITH NON-CRYSTALLOGRAPHIC SYMMETRY TERMS IN XPLOR-NIH TO RETAIN THESE FEATURES IN THE CALCULATED STRUCTURES, WHILE THE RDC AND NOE DERIVED RESTRAINTS DEFINED THE OVERALL STRUCTURE. FULL DETAILS OF THE APPROACH AND THE CALCULATION PROTOCOL APPEAR IN THE PRIMARY REFERENCE AND CORRESPONDING SUPPLEMENTARY MATERIAL FOR THIS ENTRY.X-PLOR_NIH
NMR Ensemble Information
Conformer Selection CriteriaTotal, Tensor and NOE xplor energies simultaneously below thresholds (6000, 1500 and 2 kcal.mol-1 respectively)
Conformers Calculated Total Number78
Conformers Submitted Total Number78
Representative Model1 (lowest energy)
Additional NMR Experimental Information
DetailsSample numbers used here correspond to those used in the supplementary material for the primary citation
Computation: NMR Software
#ClassificationVersionSoftware NameAuthor
1structure solutionX-PLOR_NIH2.28Schwieters, Kuszewski, Tjandra and Clore
2chemical shift assignmentSPARKY3.115Goddard
3processingTOPSPIN2.1Bruker Biospin
4chemical shift assignmentAnalysis2.4.1CCPN
5data analysisAnalysis2.4.1CCPN
6data analysisNMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax
7refinementX-PLOR_NIHSchwieters, Kuszewski, Tjandra and Clore