BMRB Entry 18462

Name: Solution NMR structure of Kaiso zinc finger DNA binding domain in complex with Kaiso binding site DNA
Published: 2012-09-04

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PDB ID: 2lt7
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/BMR18462
MolProbity Validation Chart

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Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

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Title: Solution NMR structure of Kaiso zinc finger DNA binding domain in complex with Kaiso binding site DNA PubMed: 22949637

Deposition date: 2012-05-15 Original release date: 2012-09-04

Authors: Buck-Koehntop, Bethany; Stanfield, Robyn; Ekiert, Damian; Martinez-Yamout, Maria; Dyson, H. Jane; Wilson, Ian; Wright, Peter

Citation: Buck-Koehntop, Bethany; Stanfield, Robyn; Ekiert, Damian; Martinez-Yamout, Maria; Dyson, H. Jane; Wilson, Ian; Wright, Peter. "Molecular basis for recognition of methylated and specific DNA sequences by the zinc finger protein Kaiso." Proc. Natl. Acad. Sci. U.S.A. 109, 15229-15234 (2012).

Assembly members:
Kaiso, polymer, 133 residues, 16086.681 Da.
DNA_strand_1, polymer, 19 residues, 5780.795 Da.
DNA_strand_2, polymer, 19 residues, 5869.857 Da.
ZINC ION, non-polymer, 65.409 Da.

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

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

Entity Sequences (FASTA):
Kaiso: ANKRMKVKHDDHYELIVDGR VYYICIVCKRSYVCLTSLRR HFNIHSWEKKYPCRYCEKVF PLAEYRTKHEIHHTGERRYQ CLACGKSFINYQFMSSHIKS VHSQDPSGDSKLYRLHPCRS LQIRQYAYLSDRS
DNA_strand_1: GTGCTTCCTGCCAATAACG
DNA_strand_2: CGTTATTGGCAGGAAGCAC

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_KBS

Data type	Count
13C chemical shifts	609
15N chemical shifts	164
1H chemical shifts	1288

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	Kaiso	1
2	DNA_strand_1	2
3	DNA_strand_2	3
4	ZINC ION_1	4
5	ZINC ION_2	4
6	ZINC ION_3	4

Entities:

Entity 1, Kaiso 133 residues - 16086.681 Da.

1

ALA

ASN

LYS

ARG

MET

LYS

VAL

LYS

HIS

ASP

2

ASP

HIS

TYR

GLU

LEU

ILE

VAL

ASP

GLY

ARG

3

VAL

TYR

ILE

CYS

ILE

VAL

CYS

LYS

ARG

4

SER

TYR

VAL

CYS

LEU

THR

SER

LEU

ARG

5

HIS

PHE

ASN

ILE

HIS

SER

TRP

GLU

LYS

6

TYR

PRO

CYS

ARG

TYR

CYS

GLU

LYS

VAL

PHE

7

PRO

LEU

ALA

GLU

TYR

ARG

THR

LYS

HIS

GLU

8

ILE

HIS

THR

GLY

GLU

ARG

TYR

GLN

9

CYS

LEU

ALA

CYS

GLY

LYS

SER

PHE

ILE

ASN

10

TYR

GLN

PHE

MET

SER

HIS

ILE

LYS

SER

11

VAL

HIS

SER

GLN

ASP

PRO

SER

GLY

ASP

SER

12

LYS

LEU

TYR

ARG

LEU

HIS

PRO

CYS

ARG

SER

13

LEU

GLN

ILE

ARG

GLN

TYR

ALA

TYR

LEU

SER

14

ASP

ARG

SER

Entity 2, DNA_strand_1 19 residues - 5780.795 Da.

1

DG

DT

DG

DC

DT

DC

DT

DG

2

DC

DA

DT

DA

DC

DG

Entity 3, DNA_strand_2 19 residues - 5869.857 Da.

1

DC

DG

DT

DA

DT

DG

DC

2

DA

DG

DA

DG

DC

DA

DC

Entity 4, ZINC ION_1 - Zn - 65.409 Da.

1

ZN

Samples:

sample_1: Kaiso, [U-13C; U-15N], 500 uM; Kaiso binding sequence (KBS) 500 uM; Tris 10 mM; TCEP 1 mM; H2O 95%; D2O 5%

sample_2: Kaiso, [U-100% 13C; U-100% 15N; U-80% 2H], 500 uM; Kaiso binding sequence (KBS) 500 uM; Tris 10 mM; TCEP 1 mM; H2O 95%; D2O 5%

sample_3: Kaiso, [U-13C; U-15N], 500 uM; Kaiso binding sequence (KBS) 500 uM; Tris 10 mM; TCEP 1 mM; D2O 100%

sample_conditions_1: pH: 7.0; pressure: 1 atm; temperature: 298 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-15N HSQC	sample_1	isotropic	sample_conditions_1
2D 1H-13C HSQC	sample_3	isotropic	sample_conditions_1
3D HNCO	sample_2	isotropic	sample_conditions_1
3D HNCA	sample_2	isotropic	sample_conditions_1
3D HNCACB	sample_2	isotropic	sample_conditions_1
3D CBCA(CO)NH	sample_2	isotropic	sample_conditions_1
3D HN(CO)CA	sample_2	isotropic	sample_conditions_1
3D HCCH-COSY	sample_3	isotropic	sample_conditions_1
3D CBCGCD	sample_3	isotropic	sample_conditions_1
3D 1H-15N NOESY	sample_1	isotropic	sample_conditions_1
3D 1H-13C NOESY	sample_3	isotropic	sample_conditions_1
2D 1H-1H NOESY	sample_2	isotropic	sample_conditions_1

Software:

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

CYANA, Guntert, Mumenthaler and Wuthrich - peak picking, refinement

NMRView, Johnson, One Moon Scientific - data analysis

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

TALOS, Cornilescu, Delaglio and Bax - chemical shift calculation

NMR spectrometers:

Bruker DMX 500 MHz
Bruker DMX 600 MHz
Bruker DMX 800 MHz
Bruker DMX 900 MHz
Bruker DRX 750 MHz

Download simulated HSQC data in one of the following formats:
CSV: Backbone or all simulated shifts
SPARKY: Backbone or all simulated shifts