BMRB Entry 5349

Name: PBX Homeodomain-DNA complex
Published: 2003-01-06

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PDB ID: 1lfu
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_anomalous, AVS_full, LACS
BMRB Entry DOI: doi:10.13018/BMR5349
MolProbity Validation Chart

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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:

PBX Homeodomain-DNA complex

Deposition date:

2002-04-19

Original release date:

2003-01-06

Authors:

Sprules, Tara; Green, Nancy; Featherstone, Mark; Gehring, Kalle

Citation:

Citation: Sprules, Tara; Green, Nancy; Featherstone, Mark; Gehring, Kalle. "Lock and Key Binding of the HOX YPWM Peptide to the PBX Homeodomain" J. Biol. Chem. 278, 1053-1058 (2003).

Assembly members:

Assembly members:
PBX homeodomain, polymer, 82 residues, Formula weight is not available
DNA, polymer, 28 residues, Formula weight is not available

Natural source:

Natural source: Common Name: Mouse Taxonomy ID: 10090 Superkingdom: Eukaryota Kingdom: Metazoa Genus/species: Mus musculus

Experimental source:

Experimental source: Production method: recombinant technology Host organism: Escherichia coli Vector: pET11a

Entity Sequences (FASTA):

Entity Sequences (FASTA):
PBX homeodomain: MARRKRRNFNKQATEILNEY FYSHLSNPYPSEEAKEELAK KSGITVSQVSNWFGNKRIRY KKNIGKFQEEANIYAAKTAV TA
DNA: GCGCATGATTGCCCGGGCAA TCATGCGC

Data sets:

assigned_chemical_shifts
- PBX_chemical_shifts
- DNA_chemical_shifts

Data type	Count
13C chemical shifts	317
1H chemical shifts	778
15N chemical shifts	89

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	Extended PBX Homeodomain	1
2	14mer DNA duplex	2

Entities:

Entity 1, Extended PBX Homeodomain 82 residues - Formula weight is not available

1

MET

ALA

ARG

LYS

ARG

ASN

PHE

ASN

2

LYS

GLN

ALA

THR

GLU

ILE

LEU

ASN

GLU

TYR

3

PHE

TYR

SER

HIS

LEU

SER

ASN

PRO

TYR

PRO

4

SER

GLU

ALA

LYS

GLU

LEU

ALA

LYS

5

LYS

SER

GLY

ILE

THR

VAL

SER

GLN

VAL

SER

6

ASN

TRP

PHE

GLY

ASN

LYS

ARG

ILE

ARG

TYR

7

LYS

ASN

ILE

GLY

LYS

PHE

GLN

GLU

8

ALA

ASN

ILE

TYR

ALA

LYS

THR

ALA

VAL

9

THR

ALA

Entity 2, 14mer DNA duplex 28 residues - Formula weight is not available

1

DG

DC

DG

DC

DA

DT

DG

DA

DT

2

DG

DC

DG

DC

DA

3

DT

DC

DA

DT

DG

DC

DG

DC

Samples:

sample_1: PBX homeodomain, [U-15N], 1.5 mM; DNA 1.5 mM; DSS 0.2 mM; sodium phosphate 10 mM

sample_2: PBX homeodomain, [U-15N; U-13C], 1.9 mM; DNA 1.9 mM; DSS 0.2 mM; sodium phosphate 10 mM

sample_3: PBX homeodomain 1.4 mM; DNA 1.4 mM; DSS 0.2 mM; sodium phosphate 10 mM

standard_conditions: pH: 7.0; temperature: 303 K

Experiments:

Name	Sample	Sample state	Sample conditions
15N HSQC-NOESY	not available	not available	standard_conditions
13C HSQC-NOESY	not available	not available	standard_conditions
HNHA	not available	not available	standard_conditions
2D NOESY	not available	not available	standard_conditions
CBCACONH	not available	not available	standard_conditions
13C HSQC	not available	not available	standard_conditions
13C-filtered NOESY	not available	not available	standard_conditions

Software:

No software information available

NMR spectrometers:

Bruker DRX 500 MHz
Varian INOVA 750 MHz

BMRB	4357 4358 4359
PDB	1B72 1LFU 1PUF
DBJ	BAA96135 BAA96136 BAB83538 BAF84104 BAG10741
GB	AAA21832 AAA36484 AAA36764 AAA60031 AAB71191
PIR	B33061
REF	NP_001094151 NP_001128334 NP_001179697 NP_001191890 NP_001191892
SP	P40424 P41778
TPG	DAA32038
AlphaFold	P40424 P41778