BMRB Entry 26731

Name: Structural and dynamics studies of Pax5 reveal asymmetry in stability and DNA binding by the Paired domain
Published: 2016-07-14

Chem Shift validation: AVS_full, LACS
BMRB Entry DOI: doi:10.13018/BMR26731

NMR-STAR file interactive viewer.
NMR-STAR v3 text file.
NMR-STAR v2.1 text file (deprecated)
XML gzip file.
RDF gzip file.
All files associated with the entry

Nicholas Rego and David Koes
3Dmol.js: molecular visualization with WebGL
Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

Select model:

I am color blind

Download raw data. Direct link to this display. Help

Title: Structural and dynamics studies of Pax5 reveal asymmetry in stability and DNA binding by the Paired domain PubMed: 27067111

Deposition date: 2016-01-14 Original release date: 2016-07-14

Authors: Perez-Borrajero, Cecilia; McIntosh, Lawrence

Citation: Perez-Borrajero, Cecilia; Okon, Mark; McIntosh, Lawrence. "Structural and Dynamics Studies of Pax5 Reveal Asymmetry in Stability and DNA Binding by the Paired Domain" J. Mol. Biol. 428, 2372-2391 (2016).

Assembly members:
Paired_domain_of_Pax5, polymer, 151 residues, Formula weight is not available
DNA_1, polymer, 25 residues, Formula weight is not available
DNA_2, polymer, 25 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):
Paired_domain_of_Pax5: GHMDLEKNYPTPRTSRTGHG GVNQLGGVFVNGRPLPDVVR QRIVELAHQGVRPCDISRQL RVSHGCVSKILGRYYETGSI KPGVIGGSKPKVATPKVVEK IAEYKRQNPTMFAWEIRDRL LAERVCDNDTVPSVSSINRI IRTKVQQPPNQ
DNA_1: CGGTGGTCACGCCTCAGTGC CCCAT
DNA_2: GCCACCAGTGCGGAGTCACG GGGTA

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
13C chemical shifts	424
15N chemical shifts	135
1H chemical shifts	135

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
Hide all

Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	Paired domain of Pax5	1
2	DNA_1	2
3	DNA_2	3

Entities:

Entity 1, Paired domain of Pax5 151 residues - Formula weight is not available

1

GLY

HIS

MET

ASP

LEU

GLU

LYS

ASN

TYR

PRO

2

THR

PRO

ARG

THR

SER

ARG

THR

GLY

HIS

GLY

3

GLY

VAL

ASN

GLN

LEU

GLY

VAL

PHE

VAL

4

ASN

GLY

ARG

PRO

LEU

PRO

ASP

VAL

ARG

5

GLN

ARG

ILE

VAL

GLU

LEU

ALA

HIS

GLN

GLY

6

VAL

ARG

PRO

CYS

ASP

ILE

SER

ARG

GLN

LEU

7

ARG

VAL

SER

HIS

GLY

CYS

VAL

SER

LYS

ILE

8

LEU

GLY

ARG

TYR

GLU

THR

GLY

SER

ILE

9

LYS

PRO

GLY

VAL

ILE

GLY

SER

LYS

PRO

10

LYS

VAL

ALA

THR

PRO

LYS

VAL

GLU

LYS

11

ILE

ALA

GLU

TYR

LYS

ARG

GLN

ASN

PRO

THR

12

MET

PHE

ALA

TRP

GLU

ILE

ARG

ASP

ARG

LEU

13

LEU

ALA

GLU

ARG

VAL

CYS

ASP

ASN

ASP

THR

14

VAL

PRO

SER

VAL

SER

ILE

ASN

ARG

ILE

15

ILE

ARG

THR

LYS

VAL

GLN

PRO

ASN

16

GLN

Entity 2, DNA_1 25 residues - Formula weight is not available

1

DC

DG

DT

DG

DT

DC

DA

DC

2

DG

DC

DT

DC

DA

DG

DT

DG

DC

3

DC

DA

DT

Entity 3, DNA_2 25 residues - Formula weight is not available

1

DG

DC

DA

DC

DA

DG

DT

DG

2

DC

DG

DA

DG

DT

DC

DA

DC

DG

3

DG

DT

DA

Samples:

sample_1: Paired domain of Pax5, [U-100% 13C; U-100% 15N; U-80% 2H], 0.35 mM; DNA_1 0.35 mM; DNA_2 0.35 mM; MES 20 mM; NaCl 20 mM; DTT 2 mM; EDTA 0.5 mM

sample_conditions_1: ionic strength: 0.02 M; pH: 6.5; pressure: 1 atm; temperature: 298.15 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-15N HSQC	sample_1	isotropic	sample_conditions_1
3D CBCA(CO)NH	sample_1	isotropic	sample_conditions_1
3D HNCACB	sample_1	isotropic	sample_conditions_1
3D HNCO	sample_1	isotropic	sample_conditions_1
3D HN(CO)CA	sample_1	isotropic	sample_conditions_1

Software:

SPARKY, Goddard - chemical shift assignment, data analysis

NMR spectrometers:

Bruker Avance 850 MHz

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