BMRB

Biological Magnetic Resonance Data Bank


A Repository for Data from NMR Spectroscopy on Proteins, Peptides, Nucleic Acids, and other Biomolecules
Member of WWPDB

BMRB Entry 16449

Title: Structure of the XPF-single strand DNA complex   PubMed: 22483113

Authors: Das, Devashish; Folkers, Gert; Dijk, Marc; Jaspers, Nicolaas; Hoeijmakers, Jan; Kaptein, Robert; Boelens, Rolf

Citation: Das, Devashish; Folkers, Gert; van Dijk, Marc; Jaspers, Nicolaas; Hoeijmakers, Jan; Kaptein, Robert; Boelens, Rolf. "The structure of the XPF-ssDNA complex underscores the distinct roles of the XPF and ERCC1 helix- hairpin-helix domains in ss/ds DNA recognition."  Structure 20, 667-675 (2012).

Assembly members:
entity_1, polymer, 134 residues, 14828.994 Da.
DNA, polymer, 10 residues, Formula weight is not available

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):
entity_1: EKYNPGPQDFLLKMPGVNAK NCRSLMHHVKNIAELAALSQ DELTSILGNAANAKQLYDFI HTSFAEVEKYNPGPKDFLLK MPGVNAKNCRSLMHHVKNIA ELAALSQDELTSILGNAANA KQLYDFIHTSFAEV
DNA: CAGTGGCTGA

Data sets:
Data typeCount
13C chemical shifts199
15N chemical shifts73
1H chemical shifts435

Additional metadata:

  • Assembly
  • Samples and Experiments
  • Software
  • Spectrometers
  • Hide all

Assembly:

Entity Assembly IDEntity NameEntity ID
1XPF1
2DNA chain2

Entities:

Entity 1, XPF 134 residues - 14828.994 Da.

1   GLULYSTYRASNPROGLYPROGLNASPPHE
2   LEULEULYSMETPROGLYVALASNALALYS
3   ASNCYSARGSERLEUMETHISHISVALLYS
4   ASNILEALAGLULEUALAALALEUSERGLN
5   ASPGLULEUTHRSERILELEUGLYASNALA
6   ALAASNALALYSGLNLEUTYRASPPHEILE
7   HISTHRSERPHEALAGLUVALGLULYSTYR
8   ASNPROGLYPROLYSASPPHELEULEULYS
9   METPROGLYVALASNALALYSASNCYSARG
10   SERLEUMETHISHISVALLYSASNILEALA
11   GLULEUALAALALEUSERGLNASPGLULEU
12   THRSERILELEUGLYASNALAALAASNALA
13   LYSGLNLEUTYRASPPHEILEHISTHRSER
14   PHEALAGLUVAL

Entity 2, DNA chain 10 residues - Formula weight is not available

1   DCDADGDTDGDGDCDTDGDA

Samples:

XPF-ssDNAcomplex: sodium phosphate 80 mM; sodium chloride 2 mM; AEBSF protease inhibitor5 – 10 uM

sample_conditions_1: ionic strength: 100 mM; pH: 5.2; pressure: 1 atm; temperature: 293.6 K

Experiments:

NameSampleSample stateSample conditions
3D 1H-13C NOESYXPF-ssDNAcomplexisotropicsample_conditions_1
3D 1H-15N NOESYXPF-ssDNAcomplexisotropicsample_conditions_1
3D CBCA(CO)NHXPF-ssDNAcomplexisotropicsample_conditions_1
2D 1H-15N HSQCXPF-ssDNAcomplexisotropicsample_conditions_1
2D 1H-13C HSQCXPF-ssDNAcomplexisotropicsample_conditions_1
3D HCCH-TOCSYXPF-ssDNAcomplexisotropicsample_conditions_1
3D C(CO)NHXPF-ssDNAcomplexisotropicsample_conditions_1

Software:

xwinnmr v3.5, Bruker Biospin - processing

CYANA, Herrmann, Guntert and Wuthrich - structure solution

CNS, Brunger, Adams, Clore, Gros, Nilges and Read - refinement

NMR spectrometers:

  • Bruker Avance 900 MHz
  • Bruker DRX 600 MHz

Related Database Links:

PDB