BMRB Entry 18793

Name: Solution structure of BCL-xL in complex with PUMA BH3 peptide
Published: 2013-01-22

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PDB ID: 2m04
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full, SPARTA
BMRB Entry DOI: doi:10.13018/BMR18793
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Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

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Title: Solution structure of BCL-xL in complex with PUMA BH3 peptide PubMed: 23340338

Deposition date: 2012-10-19 Original release date: 2013-01-22

Authors: Viacava Follis, Ariele; Royappa, Grace; Kriwacki, Richard

Citation: Follis, Ariele Viacava; Chipuk, Jerry; Fisher, John; Yun, Mi-Kyung; Grace, Christy; Nourse, Amanda; Baran, Katherine; Ou, Li; Min, Lie; White, Stephen; Green, Douglas; Kriwacki, Richard. "PUMA binding induces partial unfolding within BCL-xL to disrupt p53 binding and promote apoptosis." Nat. Chem. Biol. 9, 163-168 (2013).

Assembly members:
BCL-xL_comp, polymer, 180 residues, 19845.008 Da.
PUMA_BH3, polymer, 25 residues, 3053.351 Da.

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):
BCL-xL_comp: MSAMSQSNRELVVDFLSYKL SQKGYSWSQFSDVEENRTEA PEGTESEAVKQALREAGDEF ELRYRRAFSDLTSQLHITPG TAYQSFEQVVNELFRDGVNW GRIVAFFSFGGALCVESVDK EMQVLVSRIAAWMATYLNDH LEPWIQENGGWDTFVELYGN NAAAESRKGQERLEHHHHHH
PUMA_BH3: EEQWAREIGAQLRRMADDLN AQYER

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
13C chemical shifts	541
15N chemical shifts	173
1H chemical shifts	481

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	BCL-xL_comp	1
2	PUMA_BH3	2

Entities:

Entity 1, BCL-xL_comp 180 residues - 19845.008 Da.

Wild-type Human protein with truncation of 22 C terminal residues and disordered loop between alpha helices 1 and 2

1	MET	SER	ALA	MET	SER	GLN	SER	ASN	ARG	GLU
2	LEU	VAL	VAL	ASP	PHE	LEU	SER	TYR	LYS	LEU
3	SER	GLN	LYS	GLY	TYR	SER	TRP	SER	GLN	PHE
4	SER	ASP	VAL	GLU	GLU	ASN	ARG	THR	GLU	ALA
5	PRO	GLU	GLY	THR	GLU	SER	GLU	ALA	VAL	LYS
6	GLN	ALA	LEU	ARG	GLU	ALA	GLY	ASP	GLU	PHE
7	GLU	LEU	ARG	TYR	ARG	ARG	ALA	PHE	SER	ASP
8	LEU	THR	SER	GLN	LEU	HIS	ILE	THR	PRO	GLY
9	THR	ALA	TYR	GLN	SER	PHE	GLU	GLN	VAL	VAL
10	ASN	GLU	LEU	PHE	ARG	ASP	GLY	VAL	ASN	TRP
11	GLY	ARG	ILE	VAL	ALA	PHE	PHE	SER	PHE	GLY
12	GLY	ALA	LEU	CYS	VAL	GLU	SER	VAL	ASP	LYS
13	GLU	MET	GLN	VAL	LEU	VAL	SER	ARG	ILE	ALA
14	ALA	TRP	MET	ALA	THR	TYR	LEU	ASN	ASP	HIS
15	LEU	GLU	PRO	TRP	ILE	GLN	GLU	ASN	GLY	GLY
16	TRP	ASP	THR	PHE	VAL	GLU	LEU	TYR	GLY	ASN
17	ASN	ALA	ALA	ALA	GLU	SER	ARG	LYS	GLY	GLN
18	GLU	ARG	LEU	GLU	HIS	HIS	HIS	HIS	HIS	HIS

Entity 2, PUMA_BH3 25 residues - 3053.351 Da.

1

GLU

GLN

TRP

ALA

ARG

GLU

ILE

GLY

ALA

2

GLN

LEU

ARG

MET

ALA

ASP

LEU

ASN

3

ALA

GLN

TYR

GLU

ARG

Samples:

sample_1: BCL-xL_comp, [U-100% 13C; U-100% 15N; U-95% 2H; Ile,Leu,Val C1H3], 0.9 mM; sodium phosphate 10 mM; sodium chloride 40 mM; NaN3 0.1%; H2O 92%; D2O 8%; PUMA BH3 0.9 mM

sample_2: BCL-xL, [U-100% 13C; U-100% 15N], 0.9 mM; sodium phosphate 10 mM; sodium chloride 40 mM; NaN3 0.1%; H2O 92%; D2O 8%; PUMA BH3 0.9 mM

sample_conditions_1: ionic strength: 50 mM; pH: 7.0; pressure: 1 atm; temperature: 273 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-15N HSQC	sample_1	isotropic	sample_conditions_1
2D 1H-15N HSQC	sample_2	isotropic	sample_conditions_1
2D 1H-1H TOCSY 14N edited	sample_1	isotropic	sample_conditions_1
2D 1H-1H NOESY 14N edited	sample_1	isotropic	sample_conditions_1
2D 1H-13C HSQC	sample_1	isotropic	sample_conditions_1
3D HNCA	sample_2	isotropic	sample_conditions_1
3D HNCACB	sample_2	isotropic	sample_conditions_1
3D HNCACB	sample_1	isotropic	sample_conditions_1
3D HNCO	sample_1	isotropic	sample_conditions_1
3D HN(CA)CO	sample_1	isotropic	sample_conditions_1
3D HCCH-TOCSY	sample_1	isotropic	sample_conditions_1
3D 1H-15N NOESY	sample_1	isotropic	sample_conditions_1
3D 1H-13C NOESY aliphatic	sample_1	isotropic	sample_conditions_1

Software:

TOPSPIN, Bruker Biospin - collection, processing

CARA, Keller and Wuthrich - chemical shift assignment, data analysis, peak picking

CYANA, Guntert, Mumenthaler and Wuthrich - chemical shift assignment, peak picking, structure solution

AMBER, Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollm - refinement

NMR spectrometers:

Bruker Avance 800 MHz
Bruker Avance 600 MHz

Biological Magnetic Resonance Data Bank