BMRB Entry 19299

Name: Analysis of target DNA binding sites through NMR structural analysis of the MLV IN CTD and homology modeling of the CCD domains.
Published: 2013-12-16

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PDB ID: 2m9u
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full, LACS
BMRB Entry DOI: doi:10.13018/BMR19299
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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:

Analysis of target DNA binding sites through NMR structural analysis of the MLV IN CTD and homology modeling of the CCD domains.

Deposition date:

2013-06-12

Original release date:

2013-12-16

Authors:

Aiyer, Sriram; Schneider, William; Chander, Ashwin; Roth, Monica; Montelione, Gaetano; Genomics Consortium, Northeast Structural; Rossi, Paolo

Citation:

Citation: Aiyer, Sriram; Schneider, William; Chander, Ashwin; Montelione, Gaetano; Roth, Monica; Rossi, Paolo. "Analysis of target DNA binding sites through NMR structural analysis of the MLV IN CTD and homology modeling of the CCD domains." .

Assembly members:

Assembly members:
OR41A-15.1, polymer, 91 residues, 10239.74 Da.

Natural source:

Natural source: Common Name: Murine leukemia virus Taxonomy ID: 11786 Superkingdom: Viruses Kingdom: not available Genus/species: Gammaretrovirus Murine leukemia virus

Experimental source:

Experimental source: Production method: recombinant technology Host organism: Escherichia coli Vector: pET15NESG

Entity Sequences (FASTA):

Entity Sequences (FASTA):
OR41A-15.1: MGHHHHHHSHMVGDTVWVRR HQTKNLEPRWKGPYTVLLTT PTALKVDGIAAWIHAAHVKA ADPGGGPSSRLTWRVQRSQN PLKIRLTREAP

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
13C chemical shifts	334
15N chemical shifts	74
1H chemical shifts	492

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	MLV CTD IN	1

Entities:

Entity 1, MLV CTD IN 91 residues - 10239.74 Da.

The sequence used to solve the structure is a construct (329-408 amino acids) of the the full length Moloney murine leukemia virus integrase protein (IN)(408 amino acids). The construct has a non-cleavable tag at the N terminus (M G H H H H H H S H M) that is used for purification.

1

MET

GLY

HIS

SER

HIS

2

MET

VAL

GLY

ASP

THR

VAL

TRP

VAL

ARG

3

HIS

GLN

THR

LYS

ASN

LEU

GLU

PRO

ARG

TRP

4

LYS

GLY

PRO

TYR

THR

VAL

LEU

THR

5

PRO

THR

ALA

LEU

LYS

VAL

ASP

GLY

ILE

ALA

6

ALA

TRP

ILE

HIS

ALA

HIS

VAL

LYS

ALA

7

ALA

ASP

PRO

GLY

PRO

SER

ARG

8

LEU

THR

TRP

ARG

VAL

GLN

ARG

SER

GLN

ASN

9

PRO

LEU

LYS

ILE

ARG

LEU

THR

ARG

GLU

ALA

10

PRO

Samples:

sample_1: MLV IN CTD, [U-100% 13C; U-100% 15N], 0.5 mM; NaCl 100 mM; potassium glutamate 50 mM; MES 20 mM; DSS 50 uM

sample_2: MLV IN CTD, [U-10% 13C; U-100% 15N], 0.5 mM; NaCl 100 mM; potassium glutamate 50 mM; MES 20 mM; DSS 50 uM

sample_conditions_2: ionic strength: 150 mM; pH: 6.5; pressure: 1 atm; temperature: 298 K

sample_conditions_1: ionic strength: 150 mM; pH: 6.5; 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_1	isotropic	sample_conditions_1
3D HNCO	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 HBHA(CO)NH	sample_1	isotropic	sample_conditions_1
3D HCCH-TOCSY	sample_1	isotropic	sample_conditions_1
3D 13C-edited_NOESY	sample_1	isotropic	sample_conditions_1
3D 1H-15N NOESY	sample_1	isotropic	sample_conditions_1
3D 13C-edited_NOESY	sample_1	isotropic	sample_conditions_1
2D 1H-15N HSQC	sample_2	isotropic	sample_conditions_2
2D 1H-13C HSQC	sample_2	isotropic	sample_conditions_2

Software:

AutoAssign v2.2.1, Zimmerman, Moseley, Kulikowski and Montelione - chemical shift assignment

AutoStruct v2.2.1, Huang, Tejero, Powers and Montelione - chemical shift assignment, structure solution

CYANA v2.1, Guntert, Mumenthaler and Wuthrich - geometry optimization, structure solution

CNS v2.0.6, Brunger, Adams, Clore, Gros, Nilges and Read - geometry optimization, refinement

SPARKY v2.1, Goddard - peak picking

NMR spectrometers:

Bruker Avance 800 MHz