BMRB Entry 17770

Name: Sequence specific backbone resonance assignment of Vitamin D receptor ligand binding domain (VDRLBD) complexed with 1,25(OH)2 D3 and LXXLL motif (DRIP205)
Published: 2012-01-05

Chem Shift validation: AVS_full, LACS
BMRB Entry DOI: doi:10.13018/BMR17770

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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:

Sequence specific backbone resonance assignment of Vitamin D receptor ligand binding domain (VDRLBD) complexed with 1,25(OH)2 D3 and LXXLL motif (DRIP205)

Deposition date:

2011-07-07

Original release date:

2012-01-05

Authors:

Singarapu, Kiran; Zhu, Jinge; Westler, William; Deluca, Hector; Markley, John

Citation:

Citation: Singarapu, Kiran; Zhu, Jinge; Tonelli, Marco; Rao, Hongyu; Assadi-Porter, Fariba; Westler, William; DeLuca, Hector; Markley, John. "Ligand-specific structural changes in the vitamin d receptor in solution" Biochemistry 50, 11025-11033 (2011).
PubMed: 22112050

Assembly members:

Assembly members:
VDRLBD, polymer, 262 residues, Formula weight is not available
3EV, non-polymer, 416.636 Da.

Natural source:

Natural source: Common Name: Rat Taxonomy ID: 10116 Superkingdom: Eukaryota Kingdom: Metazoa Genus/species: Rattus norvegicus

Experimental source:

Experimental source: Production method: recombinant technology Host organism: Escherichia coli Vector: pET29b

Entity Sequences (FASTA):

Entity Sequences (FASTA):
VDRLBD: MLKDSLRPKLSEEQQHIIAI LLDAHHKTYDPTYADFRDFR PPVRVDGSTGSVTLDLSPLS MLPHLADLVSYSIQKVIGFA KMIPGFRDLTSDDQIVLLKS SAIEVIMLRSNQSFTMDDMS WDCGSQDYKYDVTDVSKAGH TLELIEPLIKFQVGLKKLNL HEEEHVLLMAICIVSPDRPG VQDAKLVEAIQDRLSNTLQT YIRCRHPPPGSHQLYAKMIQ KLADLRSLNEEHSKQYRSLS FQPENSMKLTPLVLEVFGNE IS

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
13C chemical shifts	717
15N chemical shifts	235
1H chemical shifts	235

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
Hide all

Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	VDRLBD	1
2	3EV	2

Entities:

Entity 1, VDRLBD 262 residues - Formula weight is not available

1

MET

LEU

LYS

ASP

SER

LEU

ARG

PRO

LYS

LEU

2

SER

GLU

GLN

HIS

ILE

ALA

ILE

3

LEU

ASP

ALA

HIS

LYS

THR

TYR

ASP

4

PRO

THR

TYR

ALA

ASP

PHE

ARG

ASP

PHE

ARG

5

PRO

VAL

ARG

VAL

ASP

GLY

SER

THR

GLY

6

SER

VAL

THR

LEU

ASP

LEU

SER

PRO

LEU

SER

7

MET

LEU

PRO

HIS

LEU

ALA

ASP

LEU

VAL

SER

8

TYR

SER

ILE

GLN

LYS

VAL

ILE

GLY

PHE

ALA

9

LYS

MET

ILE

PRO

GLY

PHE

ARG

ASP

LEU

THR

10

SER

ASP

GLN

ILE

VAL

LEU

LYS

SER

11

SER

ALA

ILE

GLU

VAL

ILE

MET

LEU

ARG

SER

12

ASN

GLN

SER

PHE

THR

MET

ASP

MET

SER

13

TRP

ASP

CYS

GLY

SER

GLN

ASP

TYR

LYS

TYR

14

ASP

VAL

THR

ASP

VAL

SER

LYS

ALA

GLY

HIS

15

THR

LEU

GLU

LEU

ILE

GLU

PRO

LEU

ILE

LYS

16

PHE

GLN

VAL

GLY

LEU

LYS

LEU

ASN

LEU

17

HIS

GLU

HIS

VAL

LEU

MET

ALA

18

ILE

CYS

ILE

VAL

SER

PRO

ASP

ARG

PRO

GLY

19

VAL

GLN

ASP

ALA

LYS

LEU

VAL

GLU

ALA

ILE

20

GLN

ASP

ARG

LEU

SER

ASN

THR

LEU

GLN

THR

21

TYR

ILE

ARG

CYS

ARG

HIS

PRO

GLY

22

SER

HIS

GLN

LEU

TYR

ALA

LYS

MET

ILE

GLN

23

LYS

LEU

ALA

ASP

LEU

ARG

SER

LEU

ASN

GLU

24

GLU

HIS

SER

LYS

GLN

TYR

ARG

SER

LEU

SER

25

PHE

GLN

PRO

GLU

ASN

SER

MET

LYS

LEU

THR

26

PRO

LEU

VAL

LEU

GLU

VAL

PHE

GLY

ASN

GLU

27

ILE

SER

Entity 2, 3EV - C27 H44 O3 - 416.636 Da.

1

3EV

Samples:

sample_1: VDRLBD, [U-100% 13C; U-100% 15N; U-100% 2H], 0.5 mM; H2O 95%; D2O 5%

sample_conditions_1: ionic strength: 50 mM; pH: 7.4; pressure: 1 atm; temperature: 273 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-15N HSQC-TROSY	sample_1	isotropic	sample_conditions_1
3D HNCA-TROSY	sample_1	isotropic	sample_conditions_1
3D HN(CO)CA-TROSY	sample_1	isotropic	sample_conditions_1
3D HN(CA)CB-TROSY	sample_1	isotropic	sample_conditions_1
3D 1H-15N NOESY-TROSY	sample_1	isotropic	sample_conditions_1
3D HNCO-TROSY	sample_1	isotropic	sample_conditions_1

Software:

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

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

TALOS, Cornilescu, Delaglio and Bax - data analysis

VNMRJ, Varian - collection

XEASY, Bartels et al. - data analysis

NMR spectrometers:

Varian INOVA 900 MHz