BMRB Entry 25894

Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR25894

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Title:
1H and 15N chemical shift assignments for PARP-1 F1F2F3 domains in complex with PARP-1 WGR domain and a DNA single-strand break
Deposition date:
2015-10-08
Original release date:
2015-11-25
Authors:
Neuhaus, David; Eustermann, Sebastian; Yang, Ji-Chun; Wu, Wing-Fung
Citation:

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).
PubMed: 26626479

Assembly members:

Assembly members:
PARP-1_1-362, polymer, 362 residues, 24106.734 Da.
PARP-1_525-645, polymer, 127 residues, Formula weight is not available
DNA_(45-MER), polymer, 45 residues, 13871.971 Da.
ZINC ION, non-polymer, 65.409 Da.

Natural source:

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

Experimental source:

Experimental source:   Production method: recombinant technology   Host organism: Escherichia coli   Vector: Pet13

Entity Sequences (FASTA):

Entity Sequences (FASTA):
PARP-1_1-362: MAESSDKLYRVEYAKSGRAS CKKCSESIPKDSLRMAIMVQ SPMFDGKVPHWYHFSCFWKV GHSIRHPDVEVDGFSELRWD DQQKVKKTAEAGGVTGKGQD GIGSKAEKTLGDFAAEYAKS NRSTCKGCMEKIEKGQVRLS KKMVDPEKPQLGMIDRWYHP GCFVKNREELGFRPEYSASQ LKGFSLLATEDKEALKKQLP GVKSEGKRKGDEVDGVDEVA KKKSKKEKDKDSKLEKALKA QNDLIWNIKDELKKVCSTND LKELLIFNKQQVPSGESAIL DRVADGMVFGALLPCEECSG QLVFKSDAYYCTGDVTAWTK CMVKTQTPNRKEWVTPKEFR EISYLKKLKVKKQDRIFPPE TS
PARP-1_525-645: MKLTLKGGAAVDPDSGLEHS AHVLEKGGKVFSATLGLVDI VKGTNSYYKLQLLEDDKENR YWIFRSWGRVGTVIGSNKLE QMPSKEDAIEHFMKLYEEKT GNAWHSKNFTKYPKKFYPLE IDYGQDE
DNA_(45-MER): GCTGGCTTCGTAAGAAGCCA GCTCGCGGTCAGCTTGCTGA CCGCG

Data sets:
Data typeCount
15N chemical shifts444
1H chemical shifts444

Additional metadata:

  • Assembly
  • Samples and Experiments
  • Software
  • Spectrometers
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Assembly:

Entity Assembly IDEntity NameEntity ID
1PARP-1_1-3621
2PARP-1_525-6452
3DNA (45-MER)3
4ZN14
5ZN24
6ZN34

Entities:

Entity 1, PARP-1_1-362 362 residues - 24106.734 Da.

1   METALAGLUSERSERASPLYSLEUTYRARG
2   VALGLUTYRALALYSSERGLYARGALASER
3   CYSLYSLYSCYSSERGLUSERILEPROLYS
4   ASPSERLEUARGMETALAILEMETVALGLN
5   SERPROMETPHEASPGLYLYSVALPROHIS
6   TRPTYRHISPHESERCYSPHETRPLYSVAL
7   GLYHISSERILEARGHISPROASPVALGLU
8   VALASPGLYPHESERGLULEUARGTRPASP
9   ASPGLNGLNLYSVALLYSLYSTHRALAGLU
10   ALAGLYGLYVALTHRGLYLYSGLYGLNASP
11   GLYILEGLYSERLYSALAGLULYSTHRLEU
12   GLYASPPHEALAALAGLUTYRALALYSSER
13   ASNARGSERTHRCYSLYSGLYCYSMETGLU
14   LYSILEGLULYSGLYGLNVALARGLEUSER
15   LYSLYSMETVALASPPROGLULYSPROGLN
16   LEUGLYMETILEASPARGTRPTYRHISPRO
17   GLYCYSPHEVALLYSASNARGGLUGLULEU
18   GLYPHEARGPROGLUTYRSERALASERGLN
19   LEULYSGLYPHESERLEULEUALATHRGLU
20   ASPLYSGLUALALEULYSLYSGLNLEUPRO
21   GLYVALLYSSERGLUGLYLYSARGLYSGLY
22   ASPGLUVALASPGLYVALASPGLUVALALA
23   LYSLYSLYSSERLYSLYSGLULYSASPLYS
24   ASPSERLYSLEUGLULYSALALEULYSALA
25   GLNASNASPLEUILETRPASNILELYSASP
26   GLULEULYSLYSVALCYSSERTHRASNASP
27   LEULYSGLULEULEUILEPHEASNLYSGLN
28   GLNVALPROSERGLYGLUSERALAILELEU
29   ASPARGVALALAASPGLYMETVALPHEGLY
30   ALALEULEUPROCYSGLUGLUCYSSERGLY
31   GLNLEUVALPHELYSSERASPALATYRTYR
32   CYSTHRGLYASPVALTHRALATRPTHRLYS
33   CYSMETVALLYSTHRGLNTHRPROASNARG
34   LYSGLUTRPVALTHRPROLYSGLUPHEARG
35   GLUILESERTYRLEULYSLYSLEULYSVAL
36   LYSLYSGLNASPARGILEPHEPROPROGLU
37   THRSER

Entity 2, PARP-1_525-645 127 residues - Formula weight is not available

1   METLYSLEUTHRLEULYSGLYGLYALAALA
2   VALASPPROASPSERGLYLEUGLUHISSER
3   ALAHISVALLEUGLULYSGLYGLYLYSVAL
4   PHESERALATHRLEUGLYLEUVALASPILE
5   VALLYSGLYTHRASNSERTYRTYRLYSLEU
6   GLNLEULEUGLUASPASPLYSGLUASNARG
7   TYRTRPILEPHEARGSERTRPGLYARGVAL
8   GLYTHRVALILEGLYSERASNLYSLEUGLU
9   GLNMETPROSERLYSGLUASPALAILEGLU
10   HISPHEMETLYSLEUTYRGLUGLULYSTHR
11   GLYASNALATRPHISSERLYSASNPHETHR
12   LYSTYRPROLYSLYSPHETYRPROLEUGLU
13   ILEASPTYRGLYGLNASPGLU

Entity 3, DNA (45-MER) 45 residues - 13871.971 Da.

1   DGDCDTDGDGDCDTDTDCDG
2   DTDADADGDADADGDCDCDA
3   DGDCDTDCDGDCDGDGDTDC
4   DADGDCDTDTDGDCDTDGDA
5   DCDCDGDCDG

Entity 4, ZN1 - Zn - 65.409 Da.

1   ZN

Samples:

sample_1: PARP-1_1-362, [U-13C; U-15N; U-2H]-1_214, [natural abundance]-215_362, 0.2 mM; PARP-1_525-645 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%; sodium chloride 200 mM

sample_2: PARP-1_1-362, [natural abundance]-1_214, [U-13C; U-15N; U-2H]-215_362, 0.2 mM; PARP-1_525-645 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%; sodium chloride 200 mM

sample_3: PARP-1_1-362 0.2 mM; PARP-1_525-645, [U-13C; U-15N; 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%; sodium chloride 200 mM

sample_conditions_1: ionic strength: 0.25 M; pH: 7.2; pressure: 1 atm; temperature: 303 K

Experiments:

NameSampleSample stateSample conditions
2D 1H-15N TROSYsample_1isotropicsample_conditions_1
3D TROSY-HNCAsample_1isotropicsample_conditions_1
2D 1H-15N TROSYsample_2isotropicsample_conditions_1
3D TROSY-HNCAsample_2isotropicsample_conditions_1
2D 1H-15N HSQCsample_3isotropicsample_conditions_1

Software:

SPARKY v3.115, Goddard - chemical shift assignment

TOPSPIN v2.1, Bruker Biospin - processing

Analysis v2.4.1, CCPN - chemical shift assignment, data analysis

NMRPipe, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - data analysis

NMR spectrometers:

  • Bruker Avance I 800 MHz
  • Bruker Avance II+ 700 MHz
  • Bruker DMX 600 MHz
  • Bruker DRX 500 MHz

Download HSQC peak lists in one of the following formats:
CSV: Backbone or all simulated peaks
SPARKY: Backbone or all simulated peaks