BMRB Entry 18951

Name: NMR solution structure of a MYB-like DNA binding domain of KNL-2 from C. Elegans
Published: 2014-03-31

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PDB ID: 2m3a
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_anomalous, AVS_full, SPARTA
BMRB Entry DOI: doi:10.13018/BMR18951
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Nicholas Rego and David Koes
3Dmol.js: molecular visualization with WebGL
Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

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Title:

NMR solution structure of a MYB-like DNA binding domain of KNL-2 from C. Elegans

Deposition date:

2013-01-15

Original release date:

2014-03-31

Authors:

Osborne, Michael; Borden, Katherine

Citation:

Citation: De Rop, Valerie; Dorn, Jonas; Osborne, Michael; Boisvert, Jacques; Ryan, Joel; Padeganeh, Abbas; Moevus, Corentin; Borden, Katherine; Maddox, Amy; Maddox, Paul. "Centromere epigenome stability is mediated by structural recognition by the Centromere Licensing Complex" Science ., .-..

Assembly members:

Assembly members:
KNL2, polymer, 134 residues, 15216.123 Da.

Natural source:

Natural source: Common Name: Caenorhabditis elegans Taxonomy ID: 6239 Superkingdom: Eukaryota Kingdom: Metazoa Genus/species: Caenorhabditis elegans

Experimental source:

Experimental source: Production method: recombinant technology Host organism: Escherichia coli Vector: pGEX-6P1

Entity Sequences (FASTA):

Entity Sequences (FASTA):
KNL2: GPLGSVAKKITWRKQDLDRL KRVIALKKPSASDADWTEVL RLLAKEGVVEPEVVRQIAIT RLKWVEPGPLGSVAKKITWR KQDLDRLKRVIALKKPSASD ADWTEVLRLLAKEGVVEPEV VRQIAITRLKWVEP

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
13C chemical shifts	170
15N chemical shifts	47
1H chemical shifts	351

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	MYB-like DNA binding domain of KNL-2 from C. Elegans	1

Entities:

Entity 1, MYB-like DNA binding domain of KNL-2 from C. Elegans 134 residues - 15216.123 Da.

Residues 1-5 (GPLGS) are a cloning artefact

1

GLY

PRO

LEU

GLY

SER

VAL

ALA

LYS

ILE

2

THR

TRP

ARG

LYS

GLN

ASP

LEU

ASP

ARG

LEU

3

LYS

ARG

VAL

ILE

ALA

LEU

LYS

PRO

SER

4

ALA

SER

ASP

ALA

ASP

TRP

THR

GLU

VAL

LEU

5

ARG

LEU

ALA

LYS

GLU

GLY

VAL

GLU

6

PRO

GLU

VAL

ARG

GLN

ILE

ALA

ILE

THR

7

ARG

LEU

LYS

TRP

VAL

GLU

PRO

GLY

PRO

LEU

8

GLY

SER

VAL

ALA

LYS

ILE

THR

TRP

ARG

9

LYS

GLN

ASP

LEU

ASP

ARG

LEU

LYS

ARG

VAL

10

ILE

ALA

LEU

LYS

PRO

SER

ALA

SER

ASP

11

ALA

ASP

TRP

THR

GLU

VAL

LEU

ARG

LEU

12

ALA

LYS

GLU

GLY

VAL

GLU

PRO

GLU

VAL

13

VAL

ARG

GLN

ILE

ALA

ILE

THR

ARG

LEU

LYS

14

TRP

VAL

GLU

PRO

Samples:

sample_1: KNL2, [U-99% 13C; U-99% 15N], 0.2 mM; sodium phosphate 20 mM; sodium chloride 100 mM; DTT 2 mM; sodium azide 0.02%; Magnesium Sulphate 5 mM

sample_2: KNL2, [U-99% 13C; U-99% 15N], 0.2 mM; sodium phosphate 20 mM; sodium chloride 100 mM; DTT 2 mM; sodium azide 0.02%; Magnesium Sulphate 5 mM

sample_conditions_1: pH: 6.5; pressure: 1 atm; temperature: 273 K

Experiments:

Name	Sample	Sample state	Sample conditions
3D 1H-13C NOESY aliphatic	sample_1	isotropic	sample_conditions_1
3D 1H-15N NOESY	sample_1	isotropic	sample_conditions_1
3D 1H-13C NOESY aromatic	sample_1	isotropic	sample_conditions_1
3D 1H-13C NOESY aliphatic	sample_2	isotropic	sample_conditions_1
3D 1H-13C NOESY aromatic	sample_2	isotropic	sample_conditions_1

Software:

CYANA v3,0, Guntert, Mumenthaler and Wuthrich - automated structure calculation

NMRView, Johnson, One Moon Scientific - data analysis

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

NMR spectrometers:

Varian INOVA 600 MHz