BMRB Entry 30388

Title:
Solution NMR structure of cysteine-rich calcium bound domains of very low density lipoprotein receptor
Deposition date:
2017-12-21
Original release date:
2018-07-10
Authors:
Banerjee, K.; Gruschus, J.; Tjandra, N.; Yakovlev, S.; Medved, L.
Citation:

Citation: Banerjee, Koyeli; Yakovlev, Sergiy; Gruschus, James; Medved, Leonid; Tjandra, Nico. "Nuclear Magnetic Resonance Solution Structure of the Recombinant Fragment Containing Three Fibrin-Binding Cysteine-Rich Domains of the Very Low Density Lipoprotein Receptor"  Biochemistry 57, 4395-4403 (2018).
PubMed: 29965730

Assembly members:

Assembly members:
entity_1, polymer, 121 residues, 13175.093 Da.
entity_CA, non-polymer, 40.078 Da.

Natural source:

Natural source:   Common Name: Human   Taxonomy ID: 9606   Superkingdom: Eukaryota   Kingdom: Metazoa   Genus/species: Homo sapiens

Experimental source:

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

Data sets:
Data typeCount
13C chemical shifts403
15N chemical shifts125
1H chemical shifts647

Additional metadata:

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

Assembly:

Entity Assembly IDEntity NameEntity ID
1entity_11
2entity_2, 12
3entity_2, 22
4entity_2, 32

Entities:

Entity 1, entity_1 121 residues - 13175.093 Da.

1   LYSTHRCYSALAGLUSERASPPHEVALCYS
2   ASNASNGLYGLNCYSVALPROSERARGTRP
3   LYSCYSASPGLYASPPROASPCYSGLUASP
4   GLYSERASPGLUSERPROGLUGLNCYSHIS
5   METARGTHRCYSARGILEHISGLUILESER
6   CYSGLYALAHISSERTHRGLNCYSILEPRO
7   VALSERTRPARGCYSASPGLYGLUASNASP
8   CYSASPSERGLYGLUASPGLUGLUASNCYS
9   GLYASNILETHRCYSSERPROASPGLUPHE
10   THRCYSSERSERGLYARGCYSILESERARG
11   ASNPHEVALCYSASNGLYGLNASPASPCYS
12   SERASPGLYSERASPGLULEUASPCYSALA
13   PRO

Entity 2, entity_2, 1 - Ca - 40.078 Da.

1   CA

Samples:

sample_1: VLDLR, [U-99% 15N], 350 uM

sample_2: VLDLR, [U-99% 13C; U-99% 15N], 250 uM

sample_3: VLDLR, [U-99% 13C; U-99% 15N], 250 uM

sample_conditions_1: ionic strength: 100 mM; pH: 6.2; pressure: 760 mmHg; temperature: 306.5 K

sample_conditions_2: ionic strength: 100 mM; pH: 6.2; pressure: 760 mmHg; temperature: 306.5 K

Experiments:

NameSampleSample stateSample conditions
2D 1H-15N HSQCsample_1isotropicsample_conditions_1
3D HNCACBsample_2isotropicsample_conditions_2
3D CBCA(CO)NHsample_2isotropicsample_conditions_2
3D HNCAsample_2isotropicsample_conditions_2
3D HNCOsample_2isotropicsample_conditions_2
3D 1H-15N NOESYsample_1isotropicsample_conditions_1
3D 1H-13C NOESYsample_3isotropicsample_conditions_2
2D 1H-15N HSQCsample_1isotropicsample_conditions_1

Software:

TOPSPIN, Bruker Biospin - collection

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

Analysis, CCPN - data analysis

X-PLOR NIH, Schwieters, Kuszewski, Tjandra and Clore - refinement

TALOS, Cornilescu, Delaglio and Bax - geometry optimization

NMR spectrometers:

  • Bruker Avance 600 MHz
  • Bruker Avance 800 MHz

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