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BMRB: 25892

1H, 13C and 15N chemical shift assignments for PARP-1 F1F2F3 domains

Authors

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

Assembly

PARP-1 F1F2F3

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

Total weight

41130.766 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: 98.3 %, Completeness: 33.7 %, Completeness (bb): 56.4 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	33.7 % (1457 of 4318)	25.8 % (589 of 2284)	31.8 % (528 of 1659)	90.7 % (340 of 375)
Backbone	56.4 % (1208 of 2142)	55.8 % (410 of 735)	43.4 % (460 of 1060)	97.4 % (338 of 347)
Sidechain	12.1 % (304 of 2512)	11.7 % (181 of 1549)	12.9 % (121 of 935)	7.1 % (2 of 28)
Aromatic	2.0 % (6 of 306)	2.0 % (3 of 153)	1.4 % (2 of 146)	14.3 % (1 of 7)
Methyl	16.7 % (52 of 312)	17.3 % (27 of 156)	16.0 % (25 of 156)

1. PARP-1 1-362

Show sample condition

Sample #1

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 303 K, pH 7.2, Details PARP-1 F1F2F3 free protein. 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	TRIS	[U-2H]	buffer	50 mM
3	DTT	[U-2H]		1 mM
4	ZnSO4	natural abundance		0.1 mM
5	H2O	natural abundance	solvent	95 %
6	D2O	[U-2H]	solvent	5 %
7	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 free protein. 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
8	PARP-1_1-362	[natural abundance]-1_214, [U-13C; U-15N; U-2H]-215_362	protein	0.2 mM
9	TRIS	[U-2H]	buffer	50 mM
10	DTT	[U-2H]		1 mM
11	ZnSO4	natural abundance		0.1 mM
12	H2O	natural abundance	solvent	95 %
13	D2O	[U-2H]	solvent	5 %
14	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 free protein. Uniformly 15N,13C,2H labelled

#	Name	Isotope labeling	Type	Concentration
15	PARP-1_1-362	[U-13C; U-15N; U-2H]	protein	0.2 mM
16	TRIS	[U-2H]	buffer	50 mM
17	DTT	[U-2H]		1 mM
18	ZnSO4	natural abundance		0.1 mM
19	H2O	natural abundance	solvent	95 %
20	D2O	[U-2H]	solvent	5 %
21	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

Interaction partners 1. PARP-1 1-362, : 182 interactors Detail

More details for 182 interactors identified by 72 citations

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 free protein. 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	TRIS	[U-2H]	buffer	50 mM
3	DTT	[U-2H]		1 mM
4	ZnSO4	natural abundance		0.1 mM
5	H2O	natural abundance	solvent	95 %
6	D2O	[U-2H]	solvent	5 %
7	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	TRIS	[U-2H]	buffer	50 mM
3	DTT	[U-2H]		1 mM
4	ZnSO4	natural abundance		0.1 mM
5	H2O	natural abundance	solvent	95 %
6	D2O	[U-2H]	solvent	5 %
7	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 free protein. 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
8	PARP-1_1-362	[natural abundance]-1_214, [U-13C; U-15N; U-2H]-215_362	protein	0.2 mM
9	TRIS	[U-2H]	buffer	50 mM
10	DTT	[U-2H]		1 mM
11	ZnSO4	natural abundance		0.1 mM
12	H2O	natural abundance	solvent	95 %
13	D2O	[U-2H]	solvent	5 %
14	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 free protein. 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
8	PARP-1_1-362	[natural abundance]-1_214, [U-13C; U-15N; U-2H]-215_362	protein	0.2 mM
9	TRIS	[U-2H]	buffer	50 mM
10	DTT	[U-2H]		1 mM
11	ZnSO4	natural abundance		0.1 mM
12	H2O	natural abundance	solvent	95 %
13	D2O	[U-2H]	solvent	5 %
14	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 free protein. Uniformly 15N,13C,2H labelled

#	Name	Isotope labeling	Type	Concentration
15	PARP-1_1-362	[U-13C; U-15N; U-2H]	protein	0.2 mM
16	TRIS	[U-2H]	buffer	50 mM
17	DTT	[U-2H]		1 mM
18	ZnSO4	natural abundance		0.1 mM
19	H2O	natural abundance	solvent	95 %
20	D2O	[U-2H]	solvent	5 %
21	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 free protein. Uniformly 15N,13C,2H labelled

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

Chemical shift validation 4 contents Detail

Properties

Input source #1: Assigned chemical shifts - Assigned chemical shifts	bmr25892_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	2:1:ZN:ZN	unknown, CA 58.017 ppm	unknown	n/a
1:24:CYS:SG	2:1:ZN:ZN	unknown, CA 58.88 ppm	unknown	n/a
1:53:HIS:ND1	2:1:ZN:ZN	unknown	unknown	n/a
1:56:CYS:SG	2:1:ZN:ZN	unknown, CA 62.73 ppm	unknown	n/a
1:125:CYS:SG	3:1:ZN:ZN	unknown, CA 57.162 ppm	unknown	n/a
1:128:CYS:SG	3:1:ZN:ZN	unknown, CA 58.145 ppm	unknown	n/a
1:159:HIS:ND1	3:1:ZN:ZN	unknown	unknown	n/a
1:162:CYS:SG	3:1:ZN:ZN	unknown, CA 62.019 ppm	unknown	n/a
1:295:CYS:SG	4:1:ZN:ZN	unknown, CA 60.006 ppm	unknown	n/a
1:298:CYS:SG	4:1:ZN:ZN	unknown, CA 58.549 ppm	unknown	n/a
1:311:CYS:SG	4:1:ZN:ZN	unknown, CA 61.666 ppm	unknown	n/a
1:321:CYS:SG	4:1:ZN:ZN	unknown, CA 60.836 ppm	unknown	n/a

Non-standard residues

None

Content subtype: bmr25892_3.str

#	Content subtype	Saveframe	Status	# of rows	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	free_F1F2F3	Warning	1014		97.2 (chain: 1, length: 362)
1	Chemical shift references	chemical_shift_reference_1	OK	3		No information

Assigned chemical shifts

Saveframe: free_F1F2F3
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: 1, Chain length: 362, Sequence coverage: 97.2%
- Total number of assignments
  - ¹H chemical shifts: 332
  - ¹³C chemical shifts: 350
  - ¹⁵N chemical shifts: 332
- 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	332	14.5
¹³C chemical shifts	1659	350	21.1
¹⁵N chemical shifts	390	332	85.1

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	735	331	45.0
¹³C chemical shifts	724	350	48.3
¹⁵N chemical shifts	347	331	95.4

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	1549	1	0.1
¹³C chemical shifts	935	0	0.0
¹⁵N chemical shifts	43	1	2.3

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	1	0.7
¹³C chemical shifts	146	0	0.0
¹⁵N chemical shifts	7	1	14.3

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 (6.971 seconds)

BMRB: 25892

Sample #1

Sample #2

Sample #3

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

Interaction partners 1. PARP-1 1-362, : 182 interactors Detail

Experiments performed 6 experiments Detail

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Chemical shift validation 4 contents Detail