BMRB Entry 16659

Name: Assignment and structural characterization of intrinsically disordered CDK inhibitor phosphoSic1 from yeast
Published: 2010-05-05

Chem Shift validation: AVS_full, LACS
BMRB Entry DOI: doi:10.13018/BMR16659

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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:

Assignment and structural characterization of intrinsically disordered CDK inhibitor phosphoSic1 from yeast

Deposition date:

2009-12-30

Original release date:

2010-05-05

Authors:

Mittag, Tanja; Choy, Wing-Yiu; Marsh, Joseph; Orlicky, Stephen; Grishaev, Alexander; Lin, Hong; Sicheri, Frank; Tyers, Mike; Forman-Kay, Julie

Citation:

Citation: Mittag, Tanja; Marsh, Joseph; Grishaev, Alexander; Orlicky, Stephen; Lin, Hong; Sicheri, Frank; Tyers, Mike; Forman-Kay, Julie. "Structure/function implications in a dynamic complex of the intrinsically disordered Sic1 with the Cdc4 subunit of an SCF ubiquitin ligase." Structure (Cambridge, MA, U. S.) 18, 494-506 (2010).
PubMed: 20399186

Assembly members:

Assembly members:
pSic1, polymer, 92 residues, 10195 Da.
pSic1_G-1X, polymer, 92 residues, Formula weight is not available
pSic1_N21X, polymer, 92 residues, Formula weight is not available
pSic1_S38X, polymer, 92 residues, Formula weight is not available
pSic1_N64X, polymer, 92 residues, Formula weight is not available
pSic1_P83X, polymer, 92 residues, Formula weight is not available
pSic1_T90X, polymer, 92 residues, Formula weight is not available

Natural source:

Natural source: Common Name: baker's yeast Taxonomy ID: 4932 Superkingdom: Eukaryota Kingdom: Fungi Genus/species: Saccharomyces cerevisiae

Experimental source:

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

Entity Sequences (FASTA):

Entity Sequences (FASTA):
pSic1: GSMTPSXPPRSRGTRYLAQP SGNTSSSALMQGQKXPQKPS QNLVPVXPSTTKSFKNAPLL APPNSNMGMTXPFNGLTXPQ RXPFPKSSVKRT
pSic1_G-1X: XSMTPSXPPRSRGTRYLAQP SGNTSSSALMQGQKXPQKPS QNLVPVXPSTTKSFKNAPLL APPNSNMGMTXPFNGLTXPQ RXPFPKSSVKRT
pSic1_N21X: GSMTPSXPPRSRGTRYLAQP SGXTSSSALMQGQKXPQKPS QNLVPVXPSTTKSFKNAPLL APPNSNMGMTXPFNGLTXPQ RXPFPKSSVKRT
pSic1_S38X: GSMTPSXPPRSRGTRYLAQP SGNTSSSALMQGQKXPQKPX QNLVPVXPSTTKSFKNAPLL APPNSNMGMTXPFNGLTXPQ RXPFPKSSVKRT
pSic1_N64X: GSMTPSXPPRSRGTRYLAQP SGNTSSSALMQGQKXPQKPS QNLVPVXPSTTKSFKNAPLL APPNSXMGMTXPFNGLTXPQ RXPFPKSSVKRT
pSic1_P83X: GSMTPSXPPRSRGTRYLAQP SGNTSSSALMQGQKXPQKPS QNLVPVXPSTTKSFKNAPLL APPNSNMGMTXPFNGLTXPQ RXPFXKSSVKRT
pSic1_T90X: GSMTPSXPPRSRGTRYLAQP SGNTSSSALMQGQKXPQKPS QNLVPVXPSTTKSFKNAPLL APPNSNMGMTXPFNGLTXPQ RXPFPKSSVKRX

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
13C chemical shifts	171
15N chemical shifts	75
1H chemical shifts	75
heteronuclear NOE values	74
residual dipolar couplings	63
T1 relaxation values	74
T2 relaxation values	74

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	pSic1	1

Entities:

Entity 1, pSic1 92 residues - 10195 Da.

The first two residues represent a non-native artifact from cleavage of an affinity tag and are therefore numbered -1 and 0. Residue M1 is the actual beginning of the native Sic1 sequence. The construct used represents the first 90 residues of Sic1, the so-called targeting region. Residues 5, 33 and 45 are phosphoThr, 69,76 and 80 phosphoSer.

1

GLY

SER

MET

THR

PRO

SER

TPO

PRO

ARG

2

SER

ARG

GLY

THR

ARG

TYR

LEU

ALA

GLN

PRO

3

SER

GLY

ASN

THR

SER

ALA

LEU

MET

4

GLN

GLY

GLN

LYS

TPO

PRO

GLN

LYS

PRO

SER

5

GLN

ASN

LEU

VAL

PRO

VAL

TPO

PRO

SER

THR

6

THR

LYS

SER

PHE

LYS

ASN

ALA

PRO

LEU

7

ALA

PRO

ASN

SER

ASN

MET

GLY

MET

THR

8

SEP

PRO

PHE

ASN

GLY

LEU

THR

SEP

PRO

GLN

9

ARG

SEP

PRO

PHE

PRO

LYS

SER

VAL

LYS

10

ARG

THR

Samples:

sample_1: pSic1, [U-13C; U-15N], 0.5 mM; potassium phosphate 50 mM; sodium chloride 150 mM; sodium azide 0.02%; EDTA 1 mM; DSS 1 mM; H2O 90%; D2O 10%

sample_2: pSic1, [U-15N], 0.5 mM; potassium phosphate 50 mM; sodium chloride 150 mM; sodium azide 0.02%; EDTA 1 mM; DSS 1 mM; H2O 90%; D2O 10%

sample_3: pSic1, [U-15N], 0.5 mM; potassium phosphate 50 mM; sodium chloride 150 mM; sodium azide 0.02%; EDTA 1 mM; DSS 1 mM; PEG(C12E5)/hexanol 0.08 v/v; H2O 90%; D2O 10%

sample_4: pSic1_G-1X, [U-15N], 0.5 mM; potassium phosphate 50 mM; sodium chloride 150 mM; sodium azide 0.02%; EDTA 1 mM; DSS 1 mM; H2O 90%; D2O 10%

sample_5: pSic1_N21X, [U-15N], 0.5 mM; potassium phosphate 50 mM; sodium chloride 150 mM; sodium azide 0.02%; EDTA 1 mM; DSS 1 mM; H2O 90%; D2O 10%

sample_6: pSic1_S38X, [U-15N], 0.5 mM; potassium phosphate 50 mM; sodium chloride 150 mM; sodium azide 0.02%; EDTA 1 mM; DSS 1 mM; H2O 90%; D2O 10%

sample_7: pSic1_N64X, [U-15N], 0.5 mM; potassium phosphate 50 mM; sodium chloride 150 mM; sodium azide 0.02%; EDTA 1 mM; DSS 1 mM; H2O 90%; D2O 10%

sample_8: pSic1_P83X, [U-15N], 0.5 mM; potassium phosphate 50 mM; sodium chloride 150 mM; sodium azide 0.02%; EDTA 1 mM; DSS 1 mM; H2O 90%; D2O 10%

sample_9: pSic1_T90X, [U-15N], 0.5 mM; potassium phosphate 50 mM; sodium chloride 150 mM; sodium azide 0.02%; EDTA 1 mM; DSS 1 mM; H2O 90%; D2O 10%

sample_conditions_1: ionic strength: 0.2 M; pH: 7.0; pressure: 1 atm; temperature: 278 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-15N HSQC	sample_2	isotropic	sample_conditions_1
3D CBCA(CO)NH	sample_1	isotropic	sample_conditions_1
3D HNCACB	sample_1	isotropic	sample_conditions_1
3D C(CO)NH	sample_1	isotropic	sample_conditions_1
3D HNCO	sample_1	isotropic	sample_conditions_1
pseudo3D 15N T1	sample_2	isotropic	sample_conditions_1
pseudo3D 15N T1rho	sample_2	isotropic	sample_conditions_1
pseudo3D 1H-15N hetNOE	sample_2	isotropic	sample_conditions_1
2D 1H-15N IPAP	sample_3	anisotropic	sample_conditions_1
pseudo3D NH R2 for PRE	sample_4	isotropic	sample_conditions_1
pseudo3D NH R2 for PRE	sample_5	isotropic	sample_conditions_1
pseudo3D NH R2 for PRE	sample_6	isotropic	sample_conditions_1
pseudo3D NH R2 for PRE	sample_7	isotropic	sample_conditions_1
pseudo3D NH R2 for PRE	sample_8	isotropic	sample_conditions_1
pseudo3D NH R2 for PRE	sample_9	isotropic	sample_conditions_1

Software:

ENSEMBLE, Marsh, Choy, Forman-Kay - ensemble generation

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

NMRView, Johnson, One Moon Scientific - chemical shift assignment

FuDA, Kristensen and Hansen - peak integration, RDC analysis

NMR spectrometers:

Varian INOVA 500 MHz
Varian INOVA 800 MHz