BMRBj - BMREntryMaster

Found 1 Document (0.895 seconds)

BMRB: 30696

6V88

Solution NMR structure of Dictyostelium discoideum Skp1A (truncated) dimer

Authors

Kim, H.W., Eletsky, A., West, C.M.

Assembly

SCF ubiquitin ligase complex protein SKP1a

Entity

1. SCF ubiquitin ligase complex protein SKP1a (polymer), 116 monomers, 12983.76 × 2 Da Detail

SLVKLESSDE KVFEIEKEIA CMSVTIKNMI EDIGESDSPI PLPNVTSTIL EKVLDYCRHH HQHPGGSGLD DIPPYDRDFC KVDQPTLFEL ILAANYLDIK PLLDVTCKTV ANMIRG

Total weight

25967.52 Da

Max. entity weight

12983.76 Da

Source organism

Dictyostelium discoideum

Exptl. method

solution NMR

Refine. method

simulated annealing

Data set

assigned_chemical_shifts, spectral_peak_list

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 99.4 %, Completeness (bb): 99.3 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	99.4 % (1335 of 1343)	99.1 % (691 of 697)	99.8 % (531 of 532)	99.1 % (113 of 114)
Backbone	99.3 % (675 of 680)	98.7 % (226 of 229)	99.7 % (342 of 343)	99.1 % (107 of 108)
Sidechain	99.6 % (771 of 774)	99.4 % (465 of 468)	100.0 % (300 of 300)	100.0 % (6 of 6)
Aromatic	100.0 % (70 of 70)	100.0 % (35 of 35)	100.0 % (35 of 35)
Methyl	100.0 % (144 of 144)	100.0 % (72 of 72)	100.0 % (72 of 72)

1. entity 1

SLVKLESSDE KVFEIEKEIA CMSVTIKNMI EDIGESDSPI PLPNVTSTIL EKVLDYCRHH HQHPGGSGLD DIPPYDRDFC KVDQPTLFEL ILAANYLDIK PLLDVTCKTV ANMIRG

Show sample condition

Sample

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 308 K, pH 6.0, Details 0.5 mM [U-90% 13C; U-90% 15N] DDSkp1, 50 mM MES, 50 mM NaCl, 5 mM DTT, 0.05 % sodium azide, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
1	DDSkp1	[U-90% 13C; U-90% 15N]	0.5 mM
2	MES	natural abundance	50 mM
3	NaCl	natural abundance	50 mM
4	DTT	natural abundance	5 mM
5	sodium azide	natural abundance	0.05 %

Protein Blocks Logo

Calculated from 20 models in PDB: 6V88, Strand ID: A, B Detail

Release date

2020-02-03

Citation

Skp1 Dimerization Conceals Its F-Box Protein Binding Site
Kim, H.W., Eletsky, A., Gonzalez, K.J., van der Wel, H., Strauch, E.M., Prestegard, J.H., West, C.M.
Biochemistry (2020), 59, 1527-1536, PubMed 32227851 , DOI 10.1021/acs.biochem.0c00094 , Abstract

Related entities 1. SCF ubiquitin ligase complex protein SKP1a, : 1 : 243 entities Detail

Interaction partners 1. SCF ubiquitin ligase complex protein SKP1a, : 1 interactors Detail

More details for 1 interactors identified by 1 citations

Experiments performed 14 experiments Detail

1 2D [15N, 1H]-HSQC

Instrument

Bruker AVANCE NEO - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 308 K, pH 6.0, Details 0.5 mM [U-90% 13C; U-90% 15N] DDSkp1, 50 mM MES, 50 mM NaCl, 5 mM DTT, 0.05 % sodium azide, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
1	DDSkp1	[U-90% 13C; U-90% 15N]	0.5 mM
2	MES	natural abundance	50 mM
3	NaCl	natural abundance	50 mM
4	DTT	natural abundance	5 mM
5	sodium azide	natural abundance	0.05 %

2 2D [13C, 1H] CT-HSQC aliphatic

Instrument

Bruker AVANCE NEO - 800 MHz

Sample

#	Name	Isotope labeling	Concentration
1	DDSkp1	[U-90% 13C; U-90% 15N]	0.5 mM
2	MES	natural abundance	50 mM
3	NaCl	natural abundance	50 mM
4	DTT	natural abundance	5 mM
5	sodium azide	natural abundance	0.05 %

3 2D [13C, 1H] CT-HSQC aromatic

Instrument

Bruker AVANCE NEO - 800 MHz

Sample

#	Name	Isotope labeling	Concentration
1	DDSkp1	[U-90% 13C; U-90% 15N]	0.5 mM
2	MES	natural abundance	50 mM
3	NaCl	natural abundance	50 mM
4	DTT	natural abundance	5 mM
5	sodium azide	natural abundance	0.05 %

4 3D 13C/15N-edited [1H,1H] NOESY

Instrument

Bruker AVANCE NEO - 800 MHz

Sample

#	Name	Isotope labeling	Concentration
1	DDSkp1	[U-90% 13C; U-90% 15N]	0.5 mM
2	MES	natural abundance	50 mM
3	NaCl	natural abundance	50 mM
4	DTT	natural abundance	5 mM
5	sodium azide	natural abundance	0.05 %

5 3D TROSY-HNCACB

Instrument

Bruker AVANCE NEO - 800 MHz

Sample

#	Name	Isotope labeling	Concentration
1	DDSkp1	[U-90% 13C; U-90% 15N]	0.5 mM
2	MES	natural abundance	50 mM
3	NaCl	natural abundance	50 mM
4	DTT	natural abundance	5 mM
5	sodium azide	natural abundance	0.05 %

6 3D (H)CCH-COSY aromatic

Instrument

Bruker AVANCE NEO - 800 MHz

Sample

#	Name	Isotope labeling	Concentration
1	DDSkp1	[U-90% 13C; U-90% 15N]	0.5 mM
2	MES	natural abundance	50 mM
3	NaCl	natural abundance	50 mM
4	DTT	natural abundance	5 mM
5	sodium azide	natural abundance	0.05 %

7 3D (H)CCH-COSY aliphatic

Instrument

Bruker AVANCE NEO - 800 MHz

Sample

#	Name	Isotope labeling	Concentration
1	DDSkp1	[U-90% 13C; U-90% 15N]	0.5 mM
2	MES	natural abundance	50 mM
3	NaCl	natural abundance	50 mM
4	DTT	natural abundance	5 mM
5	sodium azide	natural abundance	0.05 %

8 3D (H)CCH-TOCSY aliphatic

Instrument

Bruker AVANCE NEO - 800 MHz

Sample

#	Name	Isotope labeling	Concentration
1	DDSkp1	[U-90% 13C; U-90% 15N]	0.5 mM
2	MES	natural abundance	50 mM
3	NaCl	natural abundance	50 mM
4	DTT	natural abundance	5 mM
5	sodium azide	natural abundance	0.05 %

9 3D 13C/15N-filtered 13C/15N-edited [1H,1H] NOESY

Instrument

Agilent VNMRS - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
1	DDSkp1	[U-90% 13C; U-90% 15N]	0.5 mM
2	MES	natural abundance	50 mM
3	NaCl	natural abundance	50 mM
4	DTT	natural abundance	5 mM
5	sodium azide	natural abundance	0.05 %

10 2D long-range [15N, 1H]-HSQC

Instrument

Agilent VNMRS - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
1	DDSkp1	[U-90% 13C; U-90% 15N]	0.5 mM
2	MES	natural abundance	50 mM
3	NaCl	natural abundance	50 mM
4	DTT	natural abundance	5 mM
5	sodium azide	natural abundance	0.05 %

11 3D HNCO

Instrument

Agilent VNMRS - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
1	DDSkp1	[U-90% 13C; U-90% 15N]	0.5 mM
2	MES	natural abundance	50 mM
3	NaCl	natural abundance	50 mM
4	DTT	natural abundance	5 mM
5	sodium azide	natural abundance	0.05 %

12 3D HBHA(CO)NH

Instrument

Agilent VNMRS - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
1	DDSkp1	[U-90% 13C; U-90% 15N]	0.5 mM
2	MES	natural abundance	50 mM
3	NaCl	natural abundance	50 mM
4	DTT	natural abundance	5 mM
5	sodium azide	natural abundance	0.05 %

13 3D CBCA(CO)NH

Instrument

Agilent VNMRS - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
1	DDSkp1	[U-90% 13C; U-90% 15N]	0.5 mM
2	MES	natural abundance	50 mM
3	NaCl	natural abundance	50 mM
4	DTT	natural abundance	5 mM
5	sodium azide	natural abundance	0.05 %

14 3D (HCA)CONH

Instrument

Agilent VNMRS - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
1	DDSkp1	[U-90% 13C; U-90% 15N]	0.5 mM
2	MES	natural abundance	50 mM
3	NaCl	natural abundance	50 mM
4	DTT	natural abundance	5 mM
5	sodium azide	natural abundance	0.05 %

Chemical shift validation 3 contents Detail

Properties

Input source #1: Assigned chemical shifts - Assigned chemical shifts	bmr30696_3.str
Diamagnetism of the molecular assembly	True (excluding Oxygen atoms)
Whether the assembly has a disulfide bond	None
Whether the assembly has a other bond	None
Whether the assembly contains a cyclic polymer	None
Overall data processing status	Warning

Disulfide bonds

None

Other bonds (neither disulfide, covalent nor hydrogen bonds, e.g. Zinc–sulphur bond)

None

Non-standard residues

None

Content subtype: bmr30696_3.str

#	Content subtype	Saveframe	Status	# of rows	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chemical_shifts_1	Warning	1506		100.0 (chain: 1, length: 116)
1	Chemical shift references	chem_shift_reference_1	OK	3		No information

Assigned chemical shifts

Saveframe: assigned_chemical_shifts_1

Status: Warning

Sequence coverage of experimental data

Entity_assembly_ID: 1, Chain length: 116, Sequence coverage: 100.0%

--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100
SLVKLESSDEKVFEIEKEIACMSVTIKNMIEDIGESDSPIPLPNVTSTILEKVLDYCRHHHQHPGGSGLDDIPPYDRDFCKVDQPTLFELILAANYLDIK
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
SLVKLESSDEKVFEIEKEIACMSVTIKNMIEDIGESDSPIPLPNVTSTILEKVLDYCRHHHQHPGGSGLDDIPPYDRDFCKVDQPTLFELILAANYLDIK

-------110------
PLLDVTCKTVANMIRG
||||||||||||||||
PLLDVTCKTVANMIRG

Total number of assignments
- ¹H chemical shifts: 851
- ¹³C chemical shifts: 531
- ¹⁵N chemical shifts: 124

Completeness of assignments

Entity_assemble_ID: 1

Excluded Atom_ID in statistics

Comp_index_ID	Comp_ID	Atom_ID	CS value (ppm)
7	SER	HG	5.641
23	SER	HG	7.031
57	CYS	HG	2.884
59	HIS	ND1	179.556
59	HIS	NE2	188.261
60	HIS	ND1	183.073
60	HIS	NE2	179.6
61	HIS	ND1	198.72
61	HIS	NE2	178.696
63	HIS	ND1	176.481
63	HIS	NE2	186.003
106	THR	HG1	4.075
107	CYS	HG	2.531

All atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	697	696	99.9
¹³C chemical shifts	532	531	99.8
¹⁵N chemical shifts	117	116	99.1

Backbone atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	229	228	99.6
¹³C chemical shifts	232	231	99.6
¹⁵N chemical shifts	108	107	99.1

Side chain atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	468	468	100.0
¹³C chemical shifts	300	300	100.0
¹⁵N chemical shifts	9	9	100.0

Methyl group atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	75	75	100.0
¹³C chemical shifts	75	75	100.0

Aromatic group atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	35	35	100.0
¹³C chemical shifts	35	35	100.0

Redox state of CYS
Peptide bond of PRO
Tautomeric state of HIS
Rotameric state of ILE , LEU, and VAL
Histogram of normalized assigned chemical shifts
Random coil index and derived parameters (S² and NMR RMSD)
- Chain_ID: 1

Keywords PROTEIN BINDING, Ubiquitin ligase E3 SCF complex Skp1

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Found 1 Document (0.895 seconds)

BMRB: 30696

Sample

Related entities 1. SCF ubiquitin ligase complex protein SKP1a, : 1 : 243 entities Detail

Interaction partners 1. SCF ubiquitin ligase complex protein SKP1a, : 1 interactors Detail

Experiments performed 14 experiments Detail

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Chemical shift validation 3 contents Detail