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BMRB Entry 19522

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PDB ID:
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full, LACS, SPARTA
BMRB Entry DOI: doi:10.13018/BMR19522
MolProbity Validation Chart

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Title: Solution Structure of the Complex Between BCL-xL and the p53 Core Domain determined with PRE restraints

Deposition date: 2013-09-25 Original release date: 2015-07-24

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

Citation: Viacava Follis, Ariele; Ou, Li; Llambi, Fabien; Green, Douglas; Kriwacki, Richard. "The DNA Binding Domain is a Promiscuous Interaction Hub that Mediates the Nuclear and Cytoplasmic Functions of p53"  Nat. Struct. Biol. ., .-..

Assembly members:
BCL-xL, polymer, 212 residues, 16553.609 Da.
p53, polymer, 214 residues, 22016.141 Da.
ZINC ION, non-polymer, 65.409 Da.

Natural source:   Common Name: not available   Taxonomy ID: not available   Superkingdom: not available   Kingdom: not available   Genus/species: not available not available

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

Entity Sequences (FASTA):
BCL-xL: GHSMSQSNRELVVDFLSYKL SQKGYSWSQFSDVEENRTEA PEGTESEMETPSAINGNPSW HLADSPAVNGATGHSSSLDA REVIPMAAVKQALREAGDEF ELRYRRAFSDLTSQLHITPG TAYQSFEQVVNELFRDGVNW GRIVAFFSFGGALCVESVDK EMQVLVSRIAAWMATYLNDH LEPWIQENGGWDTFVELYGN NAAAESRKGQER
p53: GHSTYQGSYGFRLGFLHSGT AKSVTCTYSPALNKMFCQLA KTCPVQLWVDSTPPPGTRVR AMAIYKQSQHMTEVVRRCPH HERCSDSDGLAPPQHLIRVE GNLRVEYLDDRNTFRHSVVV PYEPPEVGSDCTTIHYNYMC NSSCMGGMNRRPILTIITLE DSSGNLLGRNSFEVRVCACP GRDRRTEEENLRKKGEPHHE LPPGSTKRALSNNT

Data sets:
Data typeCount
13C chemical shifts646
15N chemical shifts209
1H chemical shifts399

Additional metadata:

  • Assembly
  • Samples and Experiments
  • Software
  • Spectrometers
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Assembly:

Entity Assembly IDEntity NameEntity ID
1BCL-xL1
2p532
3ZINC ION3

Entities:

Entity 1, BCL-xL 212 residues - 16553.609 Da.

The three N terminal residues constitute the leftover portion of a cleaved 6XHis affinity tag. The construct bears a deletion of the C terminal 22 aminoacids for solubility reasons

1   GLYHISSERMETSERGLNSERASNARGGLU
2   LEUVALVALASPPHELEUSERTYRLYSLEU
3   SERGLNLYSGLYTYRSERTRPSERGLNPHE
4   SERASPVALGLUGLUASNARGTHRGLUALA
5   PROGLUGLYTHRGLUSERGLUMETGLUTHR
6   PROSERALAILEASNGLYASNPROSERTRP
7   HISLEUALAASPSERPROALAVALASNGLY
8   ALATHRGLYHISSERSERSERLEUASPALA
9   ARGGLUVALILEPROMETALAALAVALLYS
10   GLNALALEUARGGLUALAGLYASPGLUPHE
11   GLULEUARGTYRARGARGALAPHESERASP
12   LEUTHRSERGLNLEUHISILETHRPROGLY
13   THRALATYRGLNSERPHEGLUGLNVALVAL
14   ASNGLULEUPHEARGASPGLYVALASNTRP
15   GLYARGILEVALALAPHEPHESERPHEGLY
16   GLYALALEUCYSVALGLUSERVALASPLYS
17   GLUMETGLNVALLEUVALSERARGILEALA
18   ALATRPMETALATHRTYRLEUASNASPHIS
19   LEUGLUPROTRPILEGLNGLUASNGLYGLY
20   TRPASPTHRPHEVALGLULEUTYRGLYASN
21   ASNALAALAALAGLUSERARGLYSGLYGLN
22   GLUARG

Entity 2, p53 214 residues - 22016.141 Da.

1   GLYHISSERTHRTYRGLNGLYSERTYRGLY
2   PHEARGLEUGLYPHELEUHISSERGLYTHR
3   ALALYSSERVALTHRCYSTHRTYRSERPRO
4   ALALEUASNLYSMETPHECYSGLNLEUALA
5   LYSTHRCYSPROVALGLNLEUTRPVALASP
6   SERTHRPROPROPROGLYTHRARGVALARG
7   ALAMETALAILETYRLYSGLNSERGLNHIS
8   METTHRGLUVALVALARGARGCYSPROHIS
9   HISGLUARGCYSSERASPSERASPGLYLEU
10   ALAPROPROGLNHISLEUILEARGVALGLU
11   GLYASNLEUARGVALGLUTYRLEUASPASP
12   ARGASNTHRPHEARGHISSERVALVALVAL
13   PROTYRGLUPROPROGLUVALGLYSERASP
14   CYSTHRTHRILEHISTYRASNTYRMETCYS
15   ASNSERSERCYSMETGLYGLYMETASNARG
16   ARGPROILELEUTHRILEILETHRLEUGLU
17   ASPSERSERGLYASNLEULEUGLYARGASN
18   SERPHEGLUVALARGVALCYSALACYSPRO
19   GLYARGASPARGARGTHRGLUGLUGLUASN
20   LEUARGLYSLYSGLYGLUPROHISHISGLU
21   LEUPROPROGLYSERTHRLYSARGALALEU
22   SERASNASNTHR

Entity 3, ZINC ION - Zn - 65.409 Da.

1   ZN

Samples:

p53_assignment: p53, [U-98% 13C; U-98% 15N; U-98% 2H], 0.6 mM; sodium phosphate 10 mM; sodium chloride 40 mM; DTT 5 mM; NaN3 0.01%; H2O 93%; D2O 7%

labeled_p53_BCL-xL: p53, [U-98% 13C; U-98% 15N; U-98% 2H], 0.6 mM; BCL-xL 0.65 mM; H2O 93%; D2O 7%

151MTSL_BCL-xL_ox: p53, [U-98% 15N; U-98% 2H], 0.1 mM; BCL-xL_C151MTSL 0.1 mM; H2O 93%; D2O 7%

151MTSL_BCL-xL_red: p53, [U-98% 15N; U-98% 2H], 0.1 mM; BCL-xL_C151MTSL 0.1 mM; DTT 10 mM; H2O 93%; D2O 7%

122MTSL_BCL-xL_ox: p53, [U-98% 15N; U-98% 2H], 0.1 mM; BCL-xL_C151S_S122C MTSL 0.1 mM; H2O 93%; D2O 7%

122MTSL_BCL-xL_red: p53, [U-98% 15N; U-98% 2H], 0.1 mM; BCL-xL_C151S_S122C MTSL 0.1 mM; DTT 10 mM; H2O 93%; D2O 7%

2MTSL_BCL-xL_ox: p53, [U-98% 15N; U-98% 2H], 0.1 mM; BCL-xL_C151S_S2C MTSL 0.1 mM; H2O 93%; D2O 7%

2MTSL_BCL-xL_red: p53, [U-98% 15N; U-98% 2H], 0.1 mM; BCL-xL_C151S_S2C MTSL 0.1 mM; DTT 10 mM; H2O 93%; D2O 7%

BCL-xL_Co_p53: BCL-xL, [U-98% 15N; U-98% 2H], 0.1 mM; Co_p53 0.1 mM; H2O 93%; D2O 7%

BCL-xL_Zn_p53: BCL-xL, [U-98% 15N; U-98% 2H], 0.1 mM; p53 0.1 mM; H2O 93%; D2O 7%

sample_conditions_1: ionic strength: 0.05 M; pH: 7.0; pressure: 1 atm; temperature: 298 K

Experiments:

NameSampleSample stateSample conditions
2D 1H-15N HSQCp53_assignmentisotropicsample_conditions_1
2D 1H-15N HSQClabeled_p53_BCL-xLisotropicsample_conditions_1
2D 1H-15N HSQC151MTSL_BCL-xL_oxisotropicsample_conditions_1
2D 1H-15N HSQC151MTSL_BCL-xL_redisotropicsample_conditions_1
2D 1H-15N HSQC122MTSL_BCL-xL_oxisotropicsample_conditions_1
2D 1H-15N HSQC122MTSL_BCL-xL_oxisotropicsample_conditions_1
2D 1H-15N HSQC2MTSL_BCL-xL_oxisotropicsample_conditions_1
2D 1H-15N HSQC2MTSL_BCL-xL_redisotropicsample_conditions_1
2D 1H-15N HSQCBCL-xL_Co_p53isotropicsample_conditions_1
2D 1H-15N HSQCBCL-xL_Zn_p53isotropicsample_conditions_1
3D 1H-15N NOESYlabeled_p53_BCL-xLisotropicsample_conditions_1
3D HNCAp53_assignmentisotropicsample_conditions_1
3D HNCACBp53_assignmentisotropicsample_conditions_1
3D HNCOp53_assignmentisotropicsample_conditions_1
3D HN(CO)CAp53_assignmentisotropicsample_conditions_1
2D 1H-13C HSQC aliphaticp53_assignmentisotropicsample_conditions_1
3D HCCH-TOCSYp53_assignmentisotropicsample_conditions_1
3D 1H-13C NOESY aliphaticp53_assignmentisotropicsample_conditions_1
2D 1H-13C HSQC aliphaticlabeled_p53_BCL-xLisotropicsample_conditions_1
2D CBCACOBCL-xL_Co_p53isotropicsample_conditions_1
2D CBCACOBCL-xL_Zn_p53isotropicsample_conditions_1
2D 1H-13C HSQC aliphaticBCL-xL_Co_p53isotropicsample_conditions_1
2D 1H-13C HSQC aliphaticBCL-xL_Zn_p53isotropicsample_conditions_1

Software:

TOPSPIN v2.1, Bruker Biospin - collection, processing

CARA, Keller, R.L.J. - chemical shift assignment, data analysis

HADDOCK, Bonvin, A. - refinement, structure solution

NMR spectrometers:

  • Bruker Avance 800 MHz
  • Bruker Avance 600 MHz

Related Database Links:

GB CAA80661 AAA51039 AAA82173 AAA82174 AAB17352 AAB17353 BAC16799
BMRB 19520 19521
PDB
DBJ BAB71819 BAB85856 BAE27189 BAE42906 BAE73044
EMBL CAA04597 CAA57886 CAA58557 CAA80661 CAI56777
REF NP_001003072 NP_001009226 NP_001009228 NP_001028842 NP_001028844
SP O77737 P53563 Q07817 Q64373
TPG DAA23121

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