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Biological Magnetic Resonance Data Bank


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BMRB Entry 16744

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PDB ID:
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full, LACS
BMRB Entry DOI: doi:10.13018/BMR16744
MolProbity Validation Chart

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Title: Structure and identification of ADP-ribose recognition motifs of APLF and role in the DNA damage response   PubMed: 20439749

Deposition date: 2010-02-23 Original release date: 2010-05-18

Authors: Li, Guang-Yao; McCulloch, Richard; Fenton, Amanda; Cheung, Melissa; Meng, Li; Ikura, Mitsuhiko; Koch, C. Anne

Citation: Li, Guang-Yao; McCulloch, Richard; Fenton, Amanda; Cheung, Melissa; Meng, Li; Ikura, Mitsuhiko; Koch, C. Anne. "Structure and identification of ADP-ribose recognition motifs of APLF and role in the DNA damage response."  Proc. Natl. Acad. Sci. U.S.A. 107, 9129-9134 (2010).

Assembly members:
APLF_Tandem_ZF, polymer, 91 residues, 10272.400 Da.
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):
APLF_Tandem_ZF: GSKATDSVLQGSEGNKVKRT SCMYGANCYRKNPVHFQHFS HPGDSDYGGVQIVGQDETDD RPECPYGPSCYRKNPQHKIE YRHNTLPVRNV

Data sets:
Data typeCount
13C chemical shifts302
15N chemical shifts95
1H chemical shifts608

Additional metadata:

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

Entity Assembly IDEntity NameEntity ID
1entity_11
2ZINC ION_12
3ZINC ION_22

Entities:

Entity 1, entity_1 91 residues - 10272.400 Da.

The first two residues (GS)are from the experssion vector.The sequence of APLF used in this study is from K360 to V448.

1   GLYSERLYSALATHRASPSERVALLEUGLN
2   GLYSERGLUGLYASNLYSVALLYSARGTHR
3   SERCYSMETTYRGLYALAASNCYSTYRARG
4   LYSASNPROVALHISPHEGLNHISPHESER
5   HISPROGLYASPSERASPTYRGLYGLYVAL
6   GLNILEVALGLYGLNASPGLUTHRASPASP
7   ARGPROGLUCYSPROTYRGLYPROSERCYS
8   TYRARGLYSASNPROGLNHISLYSILEGLU
9   TYRARGHISASNTHRLEUPROVALARGASN
10   VAL

Entity 2, ZINC ION_1 - Zn - 65.409 Da.

1   ZN

Samples:

sample_1_h2o: APLF Tandem ZF, [U-100% 13C; U-100% 15N], 0.5 – 0.8 mM; Bis-tris 20 mM; sodium chloride 50 mM; sodium azide 1 mM; zinc chloride 0.05 mM; H2O 93%; D2O 7%

sample_1_d2o: APLF Tandem ZF, [U-100% 13C; U-100% 15N], 0.5 – 0.8 mM; Bis-tris 20 mM; sodium chloride 50 mM; sodium azide 1 mM; zinc chloride 0.05 mM; D2O 99%

sample_2_h2o: APLF Tandem ZF, [U-100% 15N], 0.1 mM; Bis-tris 20 mM; sodium chloride 50 mM; sodium azide 1 mM; zinc chloride 0.05 mM; H2O 93%; D2O 7%

sample_3_h2o: APLF Tandem ZF, [U-100% 15N], 0.1 mM; sodium phosphate 20 mM; potassium chloride 150 mM; sodium azide 1 mM; zinc chloride 0.05 mM; magnesium chloride 2 mM; H2O 93%; D2O 7%

sample_4_high_salt: APLF Tandem ZF, [U-100% 15N], 0.5 mM; Bis-tris 20 mM; sodium chloride 500 mM; sodium azide 1 mM; zinc chloride 0.05 mM; Pf1 phage 10 mg/ml; H2O 93%; D2O 7%

sample_conditions_1: ionic strength: 50 mM; pH: 6.0; pressure: 1 atm; temperature: 298 K

sample_conditions_2: ionic strength: 150 mM; pH: 7.4; pressure: 1 atm; temperature: 298 K

sample_conditions_3: ionic strength: 500 mM; pH: 6.0; pressure: 1 atm; temperature: 298 K

Experiments:

NameSampleSample stateSample conditions
2D 1H-15N HSQCsample_1_h2oisotropicsample_conditions_1
2D 1H-13C HSQCsample_1_d2oisotropicsample_conditions_1
2D 1H-1H NOESYsample_1_d2oisotropicsample_conditions_1
3D CBCA(CO)NHsample_1_h2oisotropicsample_conditions_1
3D HNCACBsample_1_h2oisotropicsample_conditions_1
3D HBHA(CO)NHsample_1_h2oisotropicsample_conditions_1
3D H(CCO)NHsample_1_h2oisotropicsample_conditions_1
3D C(CO)NHsample_1_h2oisotropicsample_conditions_1
3D HCCH-TOCSYsample_1_d2oisotropicsample_conditions_1
3D HCCH-COSYsample_1_h2oisotropicsample_conditions_1
3D 1H-15N NOESYsample_1_h2oisotropicsample_conditions_1
3D 1H-13C NOESYsample_1_d2oisotropicsample_conditions_1
2D 1H-15N IPAP HSQCsample_4_high_saltisotropicsample_conditions_3
2D 1H-15N HSQCsample_2_h2oisotropicsample_conditions_1
2D 1H-15N HSQCsample_3_h2oisotropicsample_conditions_2

Software:

CYANA v2.1, Guntert, Mumenthaler and Wuthrich - structure solution

CNS v1.1, Brunger, Adams, Clore, Gros, Nilges and Read - refinement

Molmol v2k, Koradi, Billeter and Wuthrich - data analysis

NMRPipe, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - processing

TALOS, Cornilescu, Delaglio and Bax - chemical shift based dihedral angle calculation

TOPSPIN, Bruker Biospin - collection

XEASY, Bartels et al. - chemical shift assignment, data analysis, peak picking

NMR spectrometers:

  • Bruker Avance 600 MHz
  • Bruker Avance 800 MHz

Related Database Links:

BMRB 16596
PDB
DBJ BAF83530
GB AAH41144 AAY24113 ADZ15607 AIC53375 EAW99871
REF NP_775816 XP_003830966 XP_005575759 XP_009235504 XP_009440878
SP Q8IW19

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