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BMRB: 25894

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

Authors

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

Assembly

PARP-1 F1F2F3-WGR-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. PARP-1 525-645 (polymer, Thiol state: not present), 127 monomers, 14504.24 Da Detail

MKLTLKGGAA VDPDSGLEHS AHVLEKGGKV FSATLGLVDI VKGTNSYYKL QLLEDDKENR YWIFRSWGRV GTVIGSNKLE QMPSKEDAIE HFMKLYEEKT GNAWHSKNFT KYPKKFYPLE IDYGQDE

3. DNA (45-MER) (polymer, Thiol state: not present), 45 monomers, 13934.83 Da Detail

GCTGGCTTCG TAAGAAGCCA GCTCGCGGTC AGCTTGCTGA CCGCG

4. ZINC ION (non-polymer), 65.409 × 3 Da

Total weight

69569.836 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	4:ZN1:ZN
2	metal coordination	sing	1:CYS24:SG	4:ZN1:ZN
3	metal coordination	sing	1:HIS53:ND1	4:ZN1:ZN
4	metal coordination	sing	1:CYS56:SG	4:ZN1:ZN
5	metal coordination	sing	1:CYS125:SG	4:ZN1:ZN
6	metal coordination	sing	1:CYS128:SG	4:ZN1:ZN
7	metal coordination	sing	1:HIS159:ND1	4:ZN1:ZN
8	metal coordination	sing	1:CYS162:SG	4:ZN1:ZN
9	metal coordination	sing	1:CYS295:SG	4:ZN1:ZN
10	metal coordination	sing	1:CYS298:SG	4:ZN1:ZN
11	metal coordination	sing	1:CYS311:SG	4:ZN1:ZN
12	metal coordination	sing	1:CYS321:SG	4:ZN1:ZN

Source organism

Homo sapiens

Exptl. method

solution NMR

Data set

assigned_chemical_shifts

Chem. Shift Complete1

Sequence coverage: 63.7 %, Completeness: 20.9 %, Completeness (bb): 40.1 % Detail

Polymer type: polypeptide(L) polydeoxyribonucleotide

	Total	¹H	¹⁵N
All	20.9 % (841 of 4032)	14.2 % (500 of 3523)	67.0 % (341 of 509)
Backbone	40.1 % (715 of 1782)	28.7 % (377 of 1312)	71.9 % (338 of 470)
Sidechain	5.6 % (126 of 2250)	5.6 % (123 of 2211)	7.7 % (3 of 39)
Aromatic	3.0 % (10 of 332)	2.2 % (7 of 322)	30.0 % (3 of 10)
Methyl	9.8 % (22 of 225)	9.8 % (22 of 225)

1. PARP-1 1-362

2. PARP-1 525-645

MKLTLKGGAA VDPDSGLEHS AHVLEKGGKV FSATLGLVDI VKGTNSYYKL QLLEDDKENR YWIFRSWGRV GTVIGSNKLE QMPSKEDAIE HFMKLYEEKT GNAWHSKNFT KYPKKFYPLE IDYGQDE

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, PARP-1 WGR, DNA ternary 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	PARP-1_525-645	natural abundance	protein	0.2 mM
3	DNA (45-MER)	natural abundance	DNA	0.2 mM
4	TRIS	[U-2H]	buffer	50 mM
5	DTT	[U-2H]		1 mM
6	ZnSO4	natural abundance		0.1 mM
7	H2O	natural abundance	solvent	95 %
8	D2O	[U-2H]	solvent	5 %
9	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, PARP-1 WGR, DNA ternary 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
10	PARP-1_1-362	[natural abundance]-1_214, [U-13C; U-15N; U-2H]-215_362	protein	0.2 mM
11	PARP-1_525-645	natural abundance	protein	0.2 mM
12	DNA (45-MER)	natural abundance	DNA	0.2 mM
13	TRIS	[U-2H]	buffer	50 mM
14	DTT	[U-2H]		1 mM
15	ZnSO4	natural abundance		0.1 mM
16	H2O	natural abundance	solvent	95 %
17	D2O	[U-2H]	solvent	5 %
18	sodium chloride	natural abundance		200 mM

Chem. Shift Complete2

Sequence coverage: 32.4 %, Completeness: 17.4 %, Completeness (bb): 30.6 % Detail

Polymer type: polypeptide(L) polydeoxyribonucleotide

	Total	¹H	¹⁵N
All	17.4 % (1406 of 8064)	12.8 % (904 of 7046)	49.3 % (502 of 1018)
Backbone	30.6 % (1091 of 3564)	22.6 % (593 of 2624)	53.0 % (498 of 940)
Sidechain	7.0 % (316 of 4500)	7.1 % (312 of 4422)	5.1 % (4 of 78)
Aromatic	5.4 % (36 of 664)	5.1 % (33 of 644)	15.0 % (3 of 20)
Methyl	8.4 % (38 of 450)	8.4 % (38 of 450)

1. PARP-1 1-362

2. PARP-1 525-645

MKLTLKGGAA VDPDSGLEHS AHVLEKGGKV FSATLGLVDI VKGTNSYYKL QLLEDDKENR YWIFRSWGRV GTVIGSNKLE QMPSKEDAIE HFMKLYEEKT GNAWHSKNFT KYPKKFYPLE IDYGQDE

3. DNA (45-MER)

GCTGGCTTCG TAAGAAGCCA GCTCGCGGTC AGCTTGCTGA CCGCG

Show sample condition

Sample

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

#	Name	Isotope labeling	Type	Concentration
19	PARP-1_1-362	natural abundance	protein	0.2 mM
20	PARP-1_525-645	[U-13C; U-15N; U-2H]	protein	0.2 mM
21	DNA (45-MER)	natural abundance	DNA	0.2 mM
22	TRIS	[U-2H]	buffer	50 mM
23	DTT	[U-2H]		1 mM
24	ZnSO4	natural abundance		0.1 mM
25	H2O	natural abundance	solvent	95 %
26	D2O	[U-2H]	solvent	5 %
27	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

Related entities 2. PARP-1 525-645, : 2 : 2 : 48 entities Detail

Experiments performed 5 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, PARP-1 WGR, DNA ternary 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	PARP-1_525-645	natural abundance	protein	0.2 mM
3	DNA (45-MER)	natural abundance	DNA	0.2 mM
4	TRIS	[U-2H]	buffer	50 mM
5	DTT	[U-2H]		1 mM
6	ZnSO4	natural abundance		0.1 mM
7	H2O	natural abundance	solvent	95 %
8	D2O	[U-2H]	solvent	5 %
9	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	PARP-1_525-645	natural abundance	protein	0.2 mM
3	DNA (45-MER)	natural abundance	DNA	0.2 mM
4	TRIS	[U-2H]	buffer	50 mM
5	DTT	[U-2H]		1 mM
6	ZnSO4	natural abundance		0.1 mM
7	H2O	natural abundance	solvent	95 %
8	D2O	[U-2H]	solvent	5 %
9	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, PARP-1 WGR, DNA ternary 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
10	PARP-1_1-362	[natural abundance]-1_214, [U-13C; U-15N; U-2H]-215_362	protein	0.2 mM
11	PARP-1_525-645	natural abundance	protein	0.2 mM
12	DNA (45-MER)	natural abundance	DNA	0.2 mM
13	TRIS	[U-2H]	buffer	50 mM
14	DTT	[U-2H]		1 mM
15	ZnSO4	natural abundance		0.1 mM
16	H2O	natural abundance	solvent	95 %
17	D2O	[U-2H]	solvent	5 %
18	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, PARP-1 WGR, DNA ternary 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
10	PARP-1_1-362	[natural abundance]-1_214, [U-13C; U-15N; U-2H]-215_362	protein	0.2 mM
11	PARP-1_525-645	natural abundance	protein	0.2 mM
12	DNA (45-MER)	natural abundance	DNA	0.2 mM
13	TRIS	[U-2H]	buffer	50 mM
14	DTT	[U-2H]		1 mM
15	ZnSO4	natural abundance		0.1 mM
16	H2O	natural abundance	solvent	95 %
17	D2O	[U-2H]	solvent	5 %
18	sodium chloride	natural abundance		200 mM

5 2D 1H-15N HSQC

Instrument

Bruker Avance I - 800 MHz

Sample

#	Name	Isotope labeling	Type	Concentration
19	PARP-1_1-362	natural abundance	protein	0.2 mM
20	PARP-1_525-645	[U-13C; U-15N; U-2H]	protein	0.2 mM
21	DNA (45-MER)	natural abundance	DNA	0.2 mM
22	TRIS	[U-2H]	buffer	50 mM
23	DTT	[U-2H]		1 mM
24	ZnSO4	natural abundance		0.1 mM
25	H2O	natural abundance	solvent	95 %
26	D2O	[U-2H]	solvent	5 %
27	sodium chloride	natural abundance		200 mM

Chemical shift validation 7 contents Detail

Properties

Input source #1: Assigned chemical shifts - Assigned chemical shifts	bmr25894_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	4:1:ZN:ZN	unknown	unknown	n/a
1:24:CYS:SG	4:1:ZN:ZN	unknown	unknown	n/a
1:53:HIS:ND1	4:1:ZN:ZN	unknown	unknown	n/a
1:56:CYS:SG	4:1:ZN:ZN	unknown	unknown	n/a
1:125:CYS:SG	5:1:ZN:ZN	unknown	unknown	n/a
1:128:CYS:SG	5:1:ZN:ZN	unknown	unknown	n/a
1:159:HIS:ND1	5:1:ZN:ZN	unknown	unknown	n/a
1:162:CYS:SG	5:1:ZN:ZN	unknown	unknown	n/a
1:295:CYS:SG	6:1:ZN:ZN	unknown	unknown	n/a
1:298:CYS:SG	6:1:ZN:ZN	unknown	unknown	n/a
1:311:CYS:SG	6:1:ZN:ZN	unknown	unknown	n/a
1:321:CYS:SG	6:1:ZN:ZN	unknown	unknown	n/a

Non-standard residues

None

Content subtype: bmr25894_3.str

#	Content subtype	Saveframe	Status	# of rows	Sequence coverage (%)
1	Assigned chemical shifts	bound_F1F2F3	Warning	658	90.3 (chain: 1, length: 362)
2	Assigned chemical shifts	bound_WGR	OK	230	90.6 (chain: 2, length: 127)
1	Chemical shift references	chemical_shift_reference_1	OK	2	No information

Assigned chemical shifts

Saveframe: bound_F1F2F3
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: 1, Chain length: 362, Sequence coverage: 90.3%
- Total number of assignments
  - ¹H chemical shifts: 329
  - ¹⁵N chemical shifts: 329
- Completeness of assignments
  - Entity_assemble_ID: 1
- Histogram of normalized assigned chemical shifts
- Random coil index and derived parameters (S² and NMR RMSD)
  - Chain_ID: 1
Saveframe: bound_WGR
- Status: OK
- Sequence coverage of experimental data
  - Entity_assembly_ID: 2, Chain length: 127, Sequence coverage: 90.6%
- Total number of assignments
  - ¹H chemical shifts: 115
  - ¹⁵N chemical shifts: 115
- Completeness of assignments
  - Entity_assemble_ID: 2
- Histogram of normalized assigned chemical shifts
- Random coil index and derived parameters (S² and NMR RMSD)
  - Chain_ID: 2

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	2284	329	14.4
¹⁵N chemical shifts	390	329	84.4

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	735	326	44.4
¹⁵N chemical shifts	347	326	93.9

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

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

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

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	797	115	14.4
¹⁵N chemical shifts	137	115	83.9

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	262	115	43.9
¹⁵N chemical shifts	123	115	93.5

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	535	0	0.0
¹⁵N chemical shifts	14	0	0.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	63	0	0.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	79	0	0.0
¹⁵N chemical shifts	3	0	0.0

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 (0.544 seconds)

BMRB: 25894

Sample #1

Sample #2

Sample

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

Related entities 2. PARP-1 525-645, : 2 : 2 : 48 entities Detail

Experiments performed 5 experiments Detail

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Chemical shift validation 7 contents Detail