BMRB

Biological Magnetic Resonance Data Bank


A Repository for Data from NMR Spectroscopy on Proteins, Peptides, Nucleic Acids, and other Biomolecules
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BMRB Entry 18015

Title: Chemical shift assignments for the homeodomain of Pitx2 in complex with a TAATCC DNA binding site

Authors: Baird-Titus, Jamie; Doerdelmann, Thomas; Chaney, Beth; Clark-Baldwin, Kimber; Dave, Vrushank; Ma, Jun

Citation: Chaney, Beth; Clark-Baldwin, Kimber; Dave, Vrushank; Ma, Jun; Rance, Mark. "Solution structure of the K50 class homeodomain PITX2 bound to DNA and implications for mutations that cause Rieger syndrome"  Biochemistry 44, 7497-7511 (2005).

Assembly members:
PITX2, polymer, 68 residues, 8486.608 Da.
DNA_1, polymer, 11 residues, 3229.152 Da.
DNA_2, polymer, 11 residues, 3478.311 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):
PITX2: GSQRRQRTHFTSQQLQELEA TFQRNRYPDMSTREEIAVWT NLTEARVRVWFKNRRAKWRK REEFIVTD
DNA_1: CTCTAATCCCC
DNA_2: GGGGATTAGAG

Data sets:
Data typeCount
13C chemical shifts225
15N chemical shifts89
1H chemical shifts519

Additional metadata:

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

Assembly:

Entity Assembly IDEntity NameEntity ID
1PITX21
2DNA_12
3DNA_23

Entities:

Entity 1, PITX2 68 residues - 8486.608 Da.

Residues 61-66 represent a non-native cloning artifact. Residues -2, -1 represent are non-native, cloning artifact.

1   GLYSERGLNARGARGGLNARGTHRHISPHE
2   THRSERGLNGLNLEUGLNGLULEUGLUALA
3   THRPHEGLNARGASNARGTYRPROASPMET
4   SERTHRARGGLUGLUILEALAVALTRPTHR
5   ASNLEUTHRGLUALAARGVALARGVALTRP
6   PHELYSASNARGARGALALYSTRPARGLYS
7   ARGGLUGLUPHEILEVALTHRASP

Entity 2, DNA_1 11 residues - 3229.152 Da.

1   DCDTDCDTDADADTDCDCDC
2   DC

Entity 3, DNA_2 11 residues - 3478.311 Da.

1   DGDGDGDGDADTDTDADGDA
2   DG

Samples:

sample_1: PITX2, [U-99% 13C; U-99% 15N], 1 mM; DNA_1 1 mM; DNA_2 1 mM; H2O, [U-99% 13C; U-99% 15N], 90%; D2O, [U-99% 13C; U-99% 15N], 10%

sample_2: PITX2, [U-99% 15N], 1 mM; DNA_1 1 mM; DNA_2 1 mM; H2O, [U-99% 13C; U-99% 15N], 90%; D2O, [U-99% 13C; U-99% 15N], 10%

sample_conditions_1: pH: 7.0; pressure: 1 atm; temperature: 295 K

Experiments:

NameSampleSample stateSample conditions
2D 1H-15N HSQCsample_2isotropicsample_conditions_1
3D 1H-15N NOESYsample_2isotropicsample_conditions_1
2D 1H-13C HSQC aliphaticsample_1isotropicsample_conditions_1
2D 1H-13C HSQC aromaticsample_1isotropicsample_conditions_1
3D CBCA(CO)NHsample_1isotropicsample_conditions_1
3D C(CO)NHsample_1isotropicsample_conditions_1
3D HNCOsample_1isotropicsample_conditions_1
3D HNCAsample_1isotropicsample_conditions_1
3D HNCACBsample_1isotropicsample_conditions_1
3D H(CCO)NHsample_1isotropicsample_conditions_1
3D HCCH-TOCSYsample_1isotropicsample_conditions_1
3D 1H-13C NOESY aliphaticsample_1isotropicsample_conditions_1
3D 1H-13C NOESY aromaticsample_1isotropicsample_conditions_1
3D HBHA(CO)NHsample_1isotropicsample_conditions_1

Software:

CYANA, Guntert, Mumenthaler and Wuthrich - structure solution

AMBER, Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollm - refinement

NMR spectrometers:

  • Varian INOVA 800 MHz
  • Varian INOVA 600 MHz
  • Varian INOVA 500 MHz

Related Database Links:

BMRB 17145 17147 17452
PDB
DBJ BAA75247 BAA75248 BAB69053 BAD12775 BAF84280
EMBL CAA06696 CAA06697 CAA09455 CAB52283 CAB52284
GB AAB38505 AAB38864 AAB87380 AAC16257 AAC24502
REF NP_000316 NP_001007500 NP_001017227 NP_001035436 NP_001035967
SP O35160 O75364 O93385 P81062 P97474
TPG DAA14908 DAA28868