BMRB Entry 18717

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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/BMR18717
MolProbity Validation Chart

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Title:
Structure of C-terminal domain of Ska1
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:

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).
PubMed: 23085020

Assembly members:

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

Natural source:

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

Experimental source:

Experimental source:   Production method: recombinant technology   Host organism: Escherichia coli   Vector: pET3aTr

Entity Sequences (FASTA):

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

Data sets:
Data typeCount
13C chemical shifts1072
15N chemical shifts236
1H chemical shifts1532

Additional metadata:

  • Assembly
  • Samples and Experiments
  • Software
  • Spectrometers
  • Hide all

Assembly:

Entity Assembly IDEntity NameEntity ID
1Ska1-MTBD1

Entities:

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

1   METASNASPILEARGILEVALPROGLNILE
2   THRASPGLUGLUPHELYSTHRILEPROLYS
3   TYRGLNLEUGLYARGLEUTHRLEUGLUMET
4   METASNGLUILEVALSERLYSMETASPASP
5   PHELEUMETLYSLYSSERLYSILELEUGLY
6   LYSTHRASNLYSGLNLEUTHRARGSERASP
7   ARGGLUVALLEUASPASNTRPARGGLULEU
8   GLUMETLYSALAARGLYSARGLEUPROTHR
9   THRLEUPHEPHEILEGLUTHRASPILEARG
10   PROMETLEUGLNASPARGLEUARGPROSER
11   PHEALALYSALAILEPROCYSLEUARGHIS
12   ILEARGARGILEARGGLUGLUARGCYSGLY
13   PROLEUTHRPHETYRTYRPROGLYSERSER

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:

NameSampleSample stateSample conditions
2D 1H-15N HSQCsample_1isotropicsample_conditions_1
2D 1H-13C HSQCsample_1isotropicsample_conditions_1
3D HNCOsample_1isotropicsample_conditions_1
3D HNCAsample_1isotropicsample_conditions_1
3D HNCACBsample_1isotropicsample_conditions_1
3D HN(CO)CAsample_1isotropicsample_conditions_1
3D HCACOsample_1isotropicsample_conditions_1
3D 1H-15N NOESYsample_1isotropicsample_conditions_1
3D time shared 13C-15N NOESYsample_2isotropicsample_conditions_1
4D HMQC-NOESY-HMQCsample_3isotropicsample_conditions_1
2D-HBCBCGCDHDsample_1isotropicsample_conditions_1
2D-HBCBCGCDCEHEsample_1isotropicsample_conditions_1
3D C(CO)NHsample_1isotropicsample_conditions_1
3D H(CCO)NHsample_1isotropicsample_conditions_1
3D HCCH-TOCSYsample_1isotropicsample_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

Related Database Links:

PDB
EMBL CAA21578
REF NP_492739
SP Q9XWS0
AlphaFold Q9XWS0

Download HSQC peak lists in one of the following formats:
CSV: Backbone or all simulated peaks
SPARKY: Backbone or all simulated peaks