BMRB Entry 25888

Name: 1H, 13C and 15N chemical shift assignments and solution structure for PARP-1 F1F2 domains in complex with a DNA single-strand break
Published: 2015-11-25

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PDB ID: 2n8a
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full, SPARTA
BMRB Entry DOI: doi:10.13018/BMR25888
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Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

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Title: 1H, 13C and 15N chemical shift assignments and solution structure for PARP-1 F1F2 domains in complex with a DNA single-strand break PubMed: 26626479

Deposition date: 2015-10-08 Original release date: 2015-11-25

Authors: Neuhaus, David; Eustermann, Sebastian; Yang, Ji-Chun; Wu, Wing-Fung

Citation: Eustermann, Sebastian; Wu, Wing-Fung; Langelier, Marie-France; Yang, Ji-Chun; Easton, Laura; Riccio, Amanda; Pascal, John; Neuhaus, David. "Structural basis of detection and signaling of DNA single-strand breaks by human PARP 1" Mol. Cell 60, 742-754 (2015).

Assembly members:
F1F2, polymer, 214 residues, 24106.734 Da.
DNA_(45-MER), polymer, . residues, 13871.971 Da.
entity_ZN, non-polymer, 65.409 Da.

Natural source: Common Name: Human Taxonomy ID: 9606 Superkingdom: Eukaryota Kingdom: Metazoa Genus/species: Homo sapiens

Experimental source: Production method: recombinant technology Host organism: Escherichia coli

Entity Sequences (FASTA):
F1F2: MAESSDKLYRVEYAKSGRAS CKKCSESIPKDSLRMAIMVQ SPMFDGKVPHWYHFSCFWKV GHSIRHPDVEVDGFSELRWD DQQKVKKTAEAGGVTGKGQD GIGSKAEKTLGDFAAEYAKS NRSTCKGCMEKIEKGQVRLS KKMVDPEKPQLGMIDRWYHP GCFVKNREELGFRPEYSASQ LKGFSLLATEDKEALKKQLP GVKSEGKRKGDEVD
DNA_(45-MER): GCTGGCTTCGTAAGAAGCCA GCTCGCGGTCAGCTTGCTGA CCGCG

Data sets:

assigned_chemical_shifts

Data type	Count
13C chemical shifts	272
15N chemical shifts	396
1H chemical shifts	896

Additional metadata:

Assembly
Samples and Experiments
Software
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Entity Assembly ID	Entity Name	Entity ID
1	F1F2	1
2	DNA (45-MER)	2
3	ZN, 1	3
4	ZN, 2	3

Samples:

sample_1: PARP-1 1-214, [U-15N; U-13C; U-2H], 0.2 mM; DNA (45-MER) 0.2 mM; TRIS, [U-2H], 50 mM; DTT, [U-2H], 1 mM; ZnSO4 0.1 mM; H2O 95%; D2O, [U-2H], 5%

sample_2: PARP-1 1-214, [U-15N; U-13C; U-70% 2H], 0.2 mM; DNA (45-MER) 0.2 mM; TRIS, [U-2H], 50 mM; DTT, [U-2H], 1 mM; ZnSO4 0.1 mM; H2O 95%; D2O, [U-2H], 5%

sample_3: PARP-1 1-214, [U-98% 2H; U-98% 15N], 0.2 mM; DNA (45-MER) 0.2 mM; TRIS, [U-2H], 50 mM; DTT, [U-2H], 1 mM; ZnSO4 0.1 mM; H2O 95%; D2O, [U-2H], 5%

sample_4a: PARP-1 1-214, see Sample details section, 0.2 mM; DNA (45-MER) 0.2 mM; TRIS, [U-2H], 50 mM; DTT, [U-2H], 1 mM; ZnSO4 0.1 mM; H2O 95%; D2O, [U-2H], 5%

sample_4b: PARP-1 1-214, see Sample details section, 0.2 mM; DNA (45-MER) 0.2 mM; TRIS, [U-2H], 50 mM; DTT, [U-2H], 1 mM; ZnSO4 0.1 mM; D2O, [U-2H], 100%

sample_5: PARP-1 1-214, see Sample details section, 0.2 mM; DNA (45-MER) 0.2 mM; TRIS, [U-2H], 50 mM; DTT, [U-2H], 1 mM; ZnSO4 0.1 mM; D2O, [U-2H], 100%

sample_6: PARP-1 1-214, see Sample details section, 0.2 mM; DNA (45-MER) 0.2 mM; TRIS, [U-2H], 50 mM; DTT, [U-2H], 1 mM; ZnSO4 0.1 mM; D2O, [U-2H], 100%

sample_7: PARP-1 1-214, see Sample details section, 0.2 mM; DNA (45-MER) 0.2 mM; TRIS, [U-2H], 50 mM; DTT, [U-2H], 1 mM; ZnSO4 0.1 mM; D2O, [U-2H], 100%

sample_8: PARP-1 1-214, see Sample details section, 0.2 mM; DNA (45-MER) 0.2 mM; TRIS, [U-2H], 50 mM; DTT, [U-2H], 1 mM; ZnSO4 0.1 mM; D2O, [U-2H], 100%

sample_9: PARP-1 1-214, see Sample details section, 0.2 mM; DNA (45-MER) 0.2 mM; TRIS, [U-2H], 50 mM; DTT, [U-2H], 1 mM; ZnSO4 0.1 mM; H2O 95%; D2O, [U-2H], 5%

sample_10: PARP-1 1-214, see Sample details section, 0.2 mM; DNA (45-MER) 0.2 mM; TRIS, [U-2H], 50 mM; DTT, [U-2H], 1 mM; ZnSO4 0.1 mM; D2O, [U-2H], 100%

sample_11: PARP-1 1-214, see Sample details section, 0.2 mM; DNA (45-MER) 0.2 mM; TRIS, [U-2H], 50 mM; DTT, [U-2H], 1 mM; ZnSO4 0.1 mM; D2O, [U-2H], 100%

sample_1_D2O: PARP-1 1-214, [U-15N; U-13C; U-2H], 0.2 mM; DNA (45-MER) 0.2 mM; TRIS, [U-2H], 50 mM; DTT, [U-2H], 1 mM; ZnSO4 0.1 mM; D2O, [U-2H], 100%

bound_F1F2_high_salt: PARP-1 1-214, [U-15N; U-13C; U-2H], 0.2 mM; DNA (45-MER) 0.2 mM; TRIS, [U-2H], 50 mM; DTT, [U-2H], 1 mM; ZnSO4 0.1 uM; sodium chloride 200 mM; H2O 95%; D2O, [U-2H], 5%

sample_conditions_1: ionic strength: 0.05 M; pH: 7.2; pressure: 1 atm; temperature: 273 K

sample_conditions_2: ionic strength: 0.05 M; pH: 7.2; pressure: 1 atm; temperature: 273 K

sample_conditions_3: ionic strength: 0.25 M; pH: 7.2; pressure: 1 atm; temperature: 273 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-15N TROSY	sample_1	isotropic	sample_conditions_1
2D 1H-13C HMQC	sample_1	isotropic	sample_conditions_1
TROSY-NHCACB (optimized for CB)	sample_1	isotropic	sample_conditions_1
TROSY-HNCA	sample_1	isotropic	sample_conditions_1
TROSY-HN(CO)CA	sample_1	isotropic	sample_conditions_1
2D 1H-15N TROSY	sample_2	isotropic	sample_conditions_1
2D 1H-13C HMQC	sample_2	isotropic	sample_conditions_1
TROSY-HNCA	sample_2	isotropic	sample_conditions_1
TROSY-HN(CO)CA	sample_2	isotropic	sample_conditions_1
2D 1H-15N TROSY	sample_3	isotropic	sample_conditions_1
3D 1H-13C-1H NOESY-HMQC	sample_4a	isotropic	sample_conditions_1
HMCM(CG)CBCA	sample_4b	isotropic	sample_conditions_1
2D 1H-1H NOESY	sample_5	isotropic	sample_conditions_1
3D 13C-13C-1H HMQC-NOESY-HMQC	sample_5	isotropic	sample_conditions_1
3D 1H-13C-1H NOESY-HMQC	sample_5	isotropic	sample_conditions_1
2D 1H-13C HSQC aromatic	sample_6	isotropic	sample_conditions_1
2D 1H-1H NOESY filtered to accept 13C-1H in w2	sample_7	isotropic	sample_conditions_1
2D 1H-1H NOESY filtered to accept 13C-1H in w2 (no decoupling in w1)	sample_7	isotropic	sample_conditions_1
2D 1H-1H NOESY filtered to accept 13C-1H in w2	sample_8	isotropic	sample_conditions_1
2D 1H-1H NOESY filtered to accept 13C-1H in w2 (no decoupling in w1)	sample_8	isotropic	sample_conditions_1
2D 1H-1H NOESY filtered to accept 13C-1H in w2 (no decoupling in w1)	sample_9	isotropic	sample_conditions_1
2D 1H-1H NOESY filtered to accept 13C-1H in w2	sample_10	isotropic	sample_conditions_1
2D 1H-13C HSQC aliphatic	sample_11	isotropic	sample_conditions_1
2D 1H-1H NOESY filtered to accept 13C-1H in w2	sample_11	isotropic	sample_conditions_1
2D 1H-1H NOESY	sample_1_D2O	isotropic	sample_conditions_1
2D 1H-15N TROSY	bound_F1F2_high_salt	isotropic	sample_conditions_3

Download simulated HSQC data in one of the following formats:
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Biological Magnetic Resonance Data Bank

BMRB Entry 25888

Title: 1H, 13C and 15N chemical shift assignments and solution structure for PARP-1 F1F2 domains in complex with a DNA single-strand break PubMed: 26626479

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