BMRB Entry 18015

Name: Chemical shift assignments for the homeodomain of Pitx2 in complex with a TAATCC DNA binding site
Published: 2011-11-28

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PDB ID: 2lkx
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_anomalous, AVS_full, LACS, SPARTA
BMRB Entry DOI: doi:10.13018/BMR18015
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Nicholas Rego and David Koes
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Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

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Title:

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

Deposition date:

2011-10-21

Original release date:

2011-11-28

Authors:

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

Citation:

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:

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:

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: pGEX-1lambdat-PITX2HD

Entity Sequences (FASTA):

Entity Sequences (FASTA):
PITX2: GSQRRQRTHFTSQQLQELEA TFQRNRYPDMSTREEIAVWT NLTEARVRVWFKNRRAKWRK REEFIVTD
DNA_1: CTCTAATCCCC
DNA_2: GGGGATTAGAG

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
13C chemical shifts	225
15N chemical shifts	89
1H chemical shifts	519

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	PITX2	1
2	DNA_1	2
3	DNA_2	3

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

GLY

SER

GLN

ARG

GLN

ARG

THR

HIS

PHE

2

THR

SER

GLN

LEU

GLN

GLU

LEU

GLU

ALA

3

THR

PHE

GLN

ARG

ASN

ARG

TYR

PRO

ASP

MET

4

SER

THR

ARG

GLU

ILE

ALA

VAL

TRP

THR

5

ASN

LEU

THR

GLU

ALA

ARG

VAL

ARG

VAL

TRP

6

PHE

LYS

ASN

ARG

ALA

LYS

TRP

ARG

LYS

7

ARG

GLU

PHE

ILE

VAL

THR

ASP

Entity 2, DNA_1 11 residues - 3229.152 Da.

1

DC

DT

DC

DT

DA

DT

DC

2

DC

Entity 3, DNA_2 11 residues - 3478.311 Da.

1

DG

DA

DT

DA

DG

DA

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:

Name	Sample	Sample state	Sample conditions
2D 1H-15N HSQC	sample_2	isotropic	sample_conditions_1
3D 1H-15N NOESY	sample_2	isotropic	sample_conditions_1
2D 1H-13C HSQC aliphatic	sample_1	isotropic	sample_conditions_1
2D 1H-13C HSQC aromatic	sample_1	isotropic	sample_conditions_1
3D CBCA(CO)NH	sample_1	isotropic	sample_conditions_1
3D C(CO)NH	sample_1	isotropic	sample_conditions_1
3D HNCO	sample_1	isotropic	sample_conditions_1
3D HNCA	sample_1	isotropic	sample_conditions_1
3D HNCACB	sample_1	isotropic	sample_conditions_1
3D H(CCO)NH	sample_1	isotropic	sample_conditions_1
3D HCCH-TOCSY	sample_1	isotropic	sample_conditions_1
3D 1H-13C NOESY aliphatic	sample_1	isotropic	sample_conditions_1
3D 1H-13C NOESY aromatic	sample_1	isotropic	sample_conditions_1
3D HBHA(CO)NH	sample_1	isotropic	sample_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

BMRB	17145 17147 17452
PDB	2L7F 2L7M 2LKX
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
AlphaFold	O35160 O75364 O93385 P81062 P97474