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BMRB: 25891

1H, 13C and 15N chemical shift assignments for PARP-1 F1F2F3 domains in complex with a DNA single-strand break

Authors

Neuhaus, D., Eustermann, S., Yang, J., Wu, W.

Assembly

PARP-1 F1F2F3-DNA complex

Entity

1. PARP-1 1-362 (polymer, Thiol state: free and other bound), 362 monomers, 40934.54 Da Detail

MAESSDKLYR VEYAKSGRAS CKKCSESIPK DSLRMAIMVQ SPMFDGKVPH WYHFSCFWKV GHSIRHPDVE VDGFSELRWD DQQKVKKTAE AGGVTGKGQD GIGSKAEKTL GDFAAEYAKS NRSTCKGCME KIEKGQVRLS KKMVDPEKPQ LGMIDRWYHP GCFVKNREEL GFRPEYSASQ LKGFSLLATE DKEALKKQLP GVKSEGKRKG DEVDGVDEVA KKKSKKEKDK DSKLEKALKA QNDLIWNIKD ELKKVCSTND LKELLIFNKQ QVPSGESAIL DRVADGMVFG ALLPCEECSG QLVFKSDAYY CTGDVTAWTK CMVKTQTPNR KEWVTPKEFR EISYLKKLKV KKQDRIFPPE TS

2. ZINC ION (non-polymer), 65.409 × 3 Da
3. DNA (45-MER) (polymer, Thiol state: not present), 45 monomers, 13934.83 Da Detail

GCTGGCTTCG TAAGAAGCCA GCTCGCGGTC AGCTTGCTGA CCGCG

Total weight

55065.594 Da

Max. entity weight

40934.54 Da

Entity Connection

metal coordination 12 Detail

ID	Type	Value order	Atom ID 1	Atom ID 2
1	metal coordination	sing	1:CYS21:SG	2:ZN1:ZN
2	metal coordination	sing	1:CYS24:SG	2:ZN1:ZN
3	metal coordination	sing	1:HIS53:ND1	2:ZN1:ZN
4	metal coordination	sing	1:CYS56:SG	2:ZN1:ZN
5	metal coordination	sing	1:CYS125:SG	2:ZN1:ZN
6	metal coordination	sing	1:CYS128:SG	2:ZN1:ZN
7	metal coordination	sing	1:HIS159:ND1	2:ZN1:ZN
8	metal coordination	sing	1:CYS162:SG	2:ZN1:ZN
9	metal coordination	sing	1:CYS295:SG	2:ZN1:ZN
10	metal coordination	sing	1:CYS298:SG	2:ZN1:ZN
11	metal coordination	sing	1:CYS311:SG	2:ZN1:ZN
12	metal coordination	sing	1:CYS321:SG	2:ZN1:ZN

Source organism

Homo sapiens

Exptl. method

solution NMR

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 87.5 %, Completeness: 31.2 %, Completeness (bb): 48.7 % Detail

Polymer type: polypeptide(L) polydeoxyribonucleotide

	Total	¹H	¹³C	¹⁵N
All	31.2 % (1486 of 4760)	22.3 % (607 of 2726)	32.3 % (536 of 1659)	91.5 % (343 of 375)
Backbone	48.7 % (1197 of 2457)	37.5 % (394 of 1050)	43.9 % (465 of 1060)	97.4 % (338 of 347)
Sidechain	13.2 % (348 of 2639)	12.8 % (214 of 1676)	13.8 % (129 of 935)	17.9 % (5 of 28)
Aromatic	6.8 % (27 of 396)	5.8 % (14 of 243)	6.8 % (10 of 146)	42.9 % (3 of 7)
Methyl	15.3 % (49 of 321)	15.2 % (25 of 165)	15.4 % (24 of 156)

1. PARP-1 1-362

3. DNA (45-MER)

GCTGGCTTCG TAAGAAGCCA GCTCGCGGTC AGCTTGCTGA CCGCG

Show sample condition

Sample #1

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 303 K, pH 7.2, Details PARP-1 F1F2F3 DNA complex. F1F2F3 was sortase ligated (N.B. additional residues LPETGG inserted between residues 214 and 215; 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 1-214 (and LPET of insertion): uniform [2H,15N,13C] Labelling for residues 215-362 (and GG of insertion): natural abundance

#	Name	Isotope labeling	Type	Concentration
1	PARP-1_1-362	[U-13C; U-15N; U-2H]-1_214, [natural abundance]-215_362	protein	0.2 mM
2	DNA (45-MER)	natural abundance	DNA	0.2 mM
3	TRIS	[U-2H]	buffer	50 mM
4	DTT	[U-2H]		1 mM
5	ZnSO4	natural abundance		0.1 mM
6	H2O	natural abundance	solvent	95 %
7	D2O	[U-2H]	solvent	5 %
8	sodium chloride	natural abundance		200 mM

Sample #2

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 303 K, pH 7.2, Details PARP-1 F1F2F3 DNA complex. F1F2F3 was sortase ligated (N.B. additional residues LPETGG inserted between residues 214 and 215; 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 1-214 (and LPET of insertion): natural abundance Labelling for residues 215-362 (and GG of insertion): uniform [2H,15N,13C]

#	Name	Isotope labeling	Type	Concentration
9	PARP-1_1-362	[natural abundance]-1_214, [U-13C; U-15N; U-2H]-215_362	protein	0.2 mM
10	DNA (45-MER)	natural abundance	DNA	0.2 mM
11	TRIS	[U-2H]	buffer	50 mM
12	DTT	[U-2H]		1 mM
13	ZnSO4	natural abundance		0.1 mM
14	H2O	natural abundance	solvent	95 %
15	D2O	[U-2H]	solvent	5 %
16	sodium chloride	natural abundance		200 mM

Sample #3

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 303 K, pH 7.2, Details PARP-1 F1F2F3 DNA complex. F1F2F3 15N,13C,2H labelled

#	Name	Isotope labeling	Type	Concentration
17	PARP-1_1-362	[U-13C; U-15N; U-2H]	protein	0.2 mM
18	DNA (45-MER)	natural abundance	DNA	0.2 mM
19	TRIS	[U-2H]	buffer	50 mM
20	DTT	[U-2H]		1 mM
21	ZnSO4	natural abundance		0.1 mM
22	H2O	natural abundance	solvent	95 %
23	D2O	[U-2H]	solvent	5 %
24	sodium chloride	natural abundance		200 mM

Release date

2015-11-24

Citation

Structural Basis of Detection and Signaling of DNA Single-Strand Breaks by Human PARP-1
Eustermann, S., Wu, W., Langelier, M., Yang, J., Easton, L.E., Riccio, A., Pascal, J.M., Neuhaus, D.
Mol. Cell (2015), 60, 742-754, PubMed 26626479 , DOI 10.1016/j.molcel.2015.10.032 , Abstract

Related entities 1. PARP-1 1-362, : 2 : 22 entities Detail

Experiments performed 6 experiments Detail

1 2D 1H-15N TROSY

Instrument

Bruker Avance I - 800 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 303 K, pH 7.2, Details PARP-1 F1F2F3 DNA complex. F1F2F3 was sortase ligated (N.B. additional residues LPETGG inserted between residues 214 and 215; 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 1-214 (and LPET of insertion): uniform [2H,15N,13C] Labelling for residues 215-362 (and GG of insertion): natural abundance

#	Name	Isotope labeling	Type	Concentration
1	PARP-1_1-362	[U-13C; U-15N; U-2H]-1_214, [natural abundance]-215_362	protein	0.2 mM
2	DNA (45-MER)	natural abundance	DNA	0.2 mM
3	TRIS	[U-2H]	buffer	50 mM
4	DTT	[U-2H]		1 mM
5	ZnSO4	natural abundance		0.1 mM
6	H2O	natural abundance	solvent	95 %
7	D2O	[U-2H]	solvent	5 %
8	sodium chloride	natural abundance		200 mM

2 3D TROSY-HNCA

Instrument

Bruker Avance I - 800 MHz

Sample

#	Name	Isotope labeling	Type	Concentration
1	PARP-1_1-362	[U-13C; U-15N; U-2H]-1_214, [natural abundance]-215_362	protein	0.2 mM
2	DNA (45-MER)	natural abundance	DNA	0.2 mM
3	TRIS	[U-2H]	buffer	50 mM
4	DTT	[U-2H]		1 mM
5	ZnSO4	natural abundance		0.1 mM
6	H2O	natural abundance	solvent	95 %
7	D2O	[U-2H]	solvent	5 %
8	sodium chloride	natural abundance		200 mM

3 2D 1H-15N TROSY

Instrument

Bruker Avance I - 800 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 303 K, pH 7.2, Details PARP-1 F1F2F3 DNA complex. F1F2F3 was sortase ligated (N.B. additional residues LPETGG inserted between residues 214 and 215; 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 1-214 (and LPET of insertion): natural abundance Labelling for residues 215-362 (and GG of insertion): uniform [2H,15N,13C]

#	Name	Isotope labeling	Type	Concentration
9	PARP-1_1-362	[natural abundance]-1_214, [U-13C; U-15N; U-2H]-215_362	protein	0.2 mM
10	DNA (45-MER)	natural abundance	DNA	0.2 mM
11	TRIS	[U-2H]	buffer	50 mM
12	DTT	[U-2H]		1 mM
13	ZnSO4	natural abundance		0.1 mM
14	H2O	natural abundance	solvent	95 %
15	D2O	[U-2H]	solvent	5 %
16	sodium chloride	natural abundance		200 mM

4 3D TROSY-HNCA

Instrument

Bruker Avance I - 800 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 303 K, pH 7.2, Details PARP-1 F1F2F3 DNA complex. F1F2F3 was sortase ligated (N.B. additional residues LPETGG inserted between residues 214 and 215; 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 1-214 (and LPET of insertion): natural abundance Labelling for residues 215-362 (and GG of insertion): uniform [2H,15N,13C]

#	Name	Isotope labeling	Type	Concentration
9	PARP-1_1-362	[natural abundance]-1_214, [U-13C; U-15N; U-2H]-215_362	protein	0.2 mM
10	DNA (45-MER)	natural abundance	DNA	0.2 mM
11	TRIS	[U-2H]	buffer	50 mM
12	DTT	[U-2H]		1 mM
13	ZnSO4	natural abundance		0.1 mM
14	H2O	natural abundance	solvent	95 %
15	D2O	[U-2H]	solvent	5 %
16	sodium chloride	natural abundance		200 mM

5 2D 1H-15N TROSY

Instrument

Bruker Avance I - 800 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 303 K, pH 7.2, Details PARP-1 F1F2F3 DNA complex. F1F2F3 15N,13C,2H labelled

#	Name	Isotope labeling	Type	Concentration
17	PARP-1_1-362	[U-13C; U-15N; U-2H]	protein	0.2 mM
18	DNA (45-MER)	natural abundance	DNA	0.2 mM
19	TRIS	[U-2H]	buffer	50 mM
20	DTT	[U-2H]		1 mM
21	ZnSO4	natural abundance		0.1 mM
22	H2O	natural abundance	solvent	95 %
23	D2O	[U-2H]	solvent	5 %
24	sodium chloride	natural abundance		200 mM

6 3D TROSY-HNCA

Instrument

Bruker Avance I - 800 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 303 K, pH 7.2, Details PARP-1 F1F2F3 DNA complex. F1F2F3 15N,13C,2H labelled

#	Name	Isotope labeling	Type	Concentration
17	PARP-1_1-362	[U-13C; U-15N; U-2H]	protein	0.2 mM
18	DNA (45-MER)	natural abundance	DNA	0.2 mM
19	TRIS	[U-2H]	buffer	50 mM
20	DTT	[U-2H]		1 mM
21	ZnSO4	natural abundance		0.1 mM
22	H2O	natural abundance	solvent	95 %
23	D2O	[U-2H]	solvent	5 %
24	sodium chloride	natural abundance		200 mM

Chemical shift validation 5 contents Detail

Properties

Input source #1: Assigned chemical shifts - Assigned chemical shifts	bmr25891_3.str
Diamagnetism of the molecular assembly	True (excluding Oxygen atoms)
Whether the assembly has a disulfide bond	None
Whether the assembly has a other bond	True (see coodinates for details)
Whether the assembly contains a cyclic polymer	None
Overall data processing status	Warning

Disulfide bonds

None

Other bonds (neither disulfide, covalent nor hydrogen bonds, e.g. Zinc–sulphur bond)

Ptnr_site_1	Ptnr_site_2	Redox_state_prediction_1	Redox_state_prediction_2	Distance (Å)
1:21:CYS:SG	3:1:ZN:ZN	unknown, CA 57.597 ppm	unknown	n/a
1:24:CYS:SG	3:1:ZN:ZN	unknown, CA 58.743 ppm	unknown	n/a
1:53:HIS:ND1	3:1:ZN:ZN	unknown	unknown	n/a
1:56:CYS:SG	3:1:ZN:ZN	unknown, CA 62.858 ppm	unknown	n/a
1:125:CYS:SG	4:1:ZN:ZN	unknown, CA 57.132 ppm	unknown	n/a
1:128:CYS:SG	4:1:ZN:ZN	unknown, CA 58.115 ppm	unknown	n/a
1:159:HIS:ND1	4:1:ZN:ZN	unknown	unknown	n/a
1:162:CYS:SG	4:1:ZN:ZN	unknown, CA 62.068 ppm	unknown	n/a
1:295:CYS:SG	5:1:ZN:ZN	unknown, CA 60.02 ppm	unknown	n/a
1:298:CYS:SG	5:1:ZN:ZN	unknown, CA 58.532 ppm	unknown	n/a
1:311:CYS:SG	5:1:ZN:ZN	unknown, CA 61.679 ppm	unknown	n/a
1:321:CYS:SG	5:1:ZN:ZN	unknown, CA 60.809 ppm	unknown	n/a

Non-standard residues

None

Content subtype: bmr25891_3.str

#	Content subtype	Saveframe	Status	# of rows	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	bound_F1F2F3	Warning	1018		96.7 (chain: 1, length: 362)
1	Chemical shift references	chemical_shift_reference_1	OK	3		No information

Assigned chemical shifts

Saveframe: bound_F1F2F3
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: 1, Chain length: 362, Sequence coverage: 96.7%
- Total number of assignments
  - ¹H chemical shifts: 335
  - ¹³C chemical shifts: 348
  - ¹⁵N chemical shifts: 335
- Completeness of assignments
  - Entity_assemble_ID: 1
- Redox state of CYS
- Histogram of normalized assigned chemical shifts
- Random coil index and derived parameters (S² and NMR RMSD)
  - Chain_ID: 1

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	2284	335	14.7
¹³C chemical shifts	1659	348	21.0
¹⁵N chemical shifts	390	335	85.9

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	735	332	45.2
¹³C chemical shifts	724	348	48.1
¹⁵N chemical shifts	347	332	95.7

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	1549	3	0.2
¹³C chemical shifts	935	0	0.0
¹⁵N chemical shifts	43	3	7.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	165	0	0.0
¹³C chemical shifts	165	0	0.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	153	3	2.0
¹³C chemical shifts	146	0	0.0
¹⁵N chemical shifts	7	3	42.9

Keywords PROTEIN/DNA, Structural basis of detection and signaling of DNA single-strand breaks by human PARP 1

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Found 1 Document (0.404 seconds)

BMRB: 25891

Sample #1

Sample #2

Sample #3

Related entities 1. PARP-1 1-362, : 2 : 22 entities Detail

Experiments performed 6 experiments Detail

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Chemical shift validation 5 contents Detail