BMRB Entry 18717

Name: Structure of C-terminal domain of Ska1
Published: 2012-10-22

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PDB ID: 2lyc
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full, LACS, SPARTA
BMRB Entry DOI: doi:10.13018/BMR18717
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Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

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Title: Structure of C-terminal domain of Ska1 PubMed: 23085020

Deposition date: 2012-09-14 Original release date: 2012-10-22

Authors: Boeszoermenyi, Andras; Schmidt, Jens; Markus, Michelle; Oberer, Monika; Cheeseman, Iain; Wagner, Gerhard; Arthanari, Haribabu

Citation: Schmidt, Jens; Arthanari, Haribabu; Boeszoermenyi, Andras; Dashkevich, Natalia; Wilson-Kubalek, Elizabeth; Monnier, Nilah; Markus, Michelle; Oberer, Monika; Milligan, Ron; Bathe, Mark; Wagner, Gerhard; Grishchuk, Ekaterina; Cheeseman, Iain. "The kinetochore-bound Ska1 complex tracks depolymerizing microtubules and binds to curved protofilaments." Dev. Cell 23, 968-980 (2012).

Assembly members:
Ska1-MTBD, polymer, 130 residues, 15576.451 Da.

Natural source: Common Name: Nematodes Taxonomy ID: 6239 Superkingdom: Eukaryota Kingdom: Metazoa Genus/species: Caenorhabditis elegans

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

Entity Sequences (FASTA):
Ska1-MTBD: MNDIRIVPQITDEEFKTIPK YQLGRLTLEMMNEIVSKMDD FLMKKSKILGKTNKQLTRSD REVLDNWRELEMKARKRLPT TLFFIETDIRPMLQDRLRPS FAKAIPCLRHIRRIREERCG PLTFYYPGSS

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
13C chemical shifts	1072
15N chemical shifts	236
1H chemical shifts	1532

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	Ska1-MTBD	1

Entities:

Entity 1, Ska1-MTBD 130 residues - 15576.451 Da.

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

Samples:

sample_3: Ska1-MTBD, [U-100% 15N ILV-Methyl 13C], 0.800 mM; potassium phosphate 20 mM; NaCl 150 mM; DTT 1.5 mM; H2O 55 mM; sodium azide 0.0001 mM; D2O 100%

sample_1: Ska1-MTBD, [U-100% 13C; U-100% 15N], 0.800 mM; potassium phosphate 20 mM; NaCl 150 mM; DTT 1.5 mM; H2O 55 mM; sodium azide 0.00001 mM; H2O 95%; D2O 5%

sample_2: Ska1-MTBD, [U-100% 15N; ILV-Methyl 13C], 0.800 mM; potassium phosphate 20 mM; NaCl 150 mM; DTT 1.5 mM; H2O 55 mM; sodium azide 0.00001 mM; H2O 95%; D2O 5%

sample_conditions_1: ionic strength: 0.150 M; pH: 6.5; pressure: 1 atm; temperature: 298 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-15N HSQC	sample_1	isotropic	sample_conditions_1
2D 1H-13C HSQC	sample_1	isotropic	sample_conditions_1
3D HNCO	sample_1	isotropic	sample_conditions_1
3D HNCA	sample_1	isotropic	sample_conditions_1
3D HNCACB	sample_1	isotropic	sample_conditions_1
3D HN(CO)CA	sample_1	isotropic	sample_conditions_1
3D HCACO	sample_1	isotropic	sample_conditions_1
3D 1H-15N NOESY	sample_1	isotropic	sample_conditions_1
3D time shared 13C-15N NOESY	sample_2	isotropic	sample_conditions_1
4D HMQC-NOESY-HMQC	sample_3	isotropic	sample_conditions_1
2D-HBCBCGCDHD	sample_1	isotropic	sample_conditions_1
2D-HBCBCGCDCEHE	sample_1	isotropic	sample_conditions_1
3D C(CO)NH	sample_1	isotropic	sample_conditions_1
3D H(CCO)NH	sample_1	isotropic	sample_conditions_1
3D HCCH-TOCSY	sample_1	isotropic	sample_conditions_1

Software:

CYANA v3.0, Guntert, Mumenthaler and Wuthrich - refinement

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

CcpNMR, CCPN - chemical shift assignment

ProcheckNMR, Laskowski and MacArthur - validation

NMR spectrometers:

Varian INOVA 500 MHz
Varian INOVA 600 MHz
Bruker Avance 750 MHz
Bruker Avance 900 MHz

PDB	2LYC
EMBL	CAA21578
REF	NP_492739
SP	Q9XWS0

Biological Magnetic Resonance Data Bank