BMRB

Biological Magnetic Resonance Data Bank


A Repository for Data from NMR Spectroscopy on Proteins, Peptides, Nucleic Acids, and other Biomolecules
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BMRB Entry 30590

Title: Structure of WHB in complex with Ubiquitin Variant   PubMed: 31350353

Deposition date: 2019-03-19 Original release date: 2019-08-07

Authors: Edmond, R.; Grace, C.

Citation: Watson, E.; Grace, C.; Zhang, W.; Miller, D.; Davidson, I.; Prabu, J.; Yu, S.; Bolhuis, D.; Kulko, E.; Vollrath, R.; Haselbach, D.; Stark, H.; Peters, J.; Brown, N.; Sidhu, S.; Schulman, B.. "Protein engineering of a ubiquitin-variant inhibitor of APC/C identifies a cryptic K48 ubiquitin chain binding site."  Proc. Natl. Acad. Sci. USA ., .-. (2019).

Assembly members:
entity_1, polymer, 75 residues, 8550.763 Da.
entity_2, polymer, 75 residues, 8552.692 Da.
entity_3, polymer, 90 residues, 10259.662 Da.

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

Experimental source:   Production method: recombinant technology   Host organism: Escherichia coli-Pichia pastoris shuttle vector pPpARG4

Entity Sequences (FASTA):
entity_1: GMQIFVDTVQWKTITLEVEP SDTIENVKAKIQDKEGIPPD QQRLIFAGKQLEDGRTLSDY NIQKESALILLLTLR
entity_2: GMQIFVDTVQWKTITLEVEP SDTIENVKAKIQDKEGIPPD QQRLDFAGKQLEDGRTLSDY NIQKESALILLLTLR
entity_3: GSESDSGMASQADQKEEELL LFWTYIQAMLTNLESLSLDR IYNMLRMFVVTGPALAEIDL QELQGYLQKKVRDQQLVYSA GVYRLPKNCS

Data sets:
Data typeCount
13C chemical shifts758
15N chemical shifts221
1H chemical shifts1316

Additional metadata:

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

Assembly:

Entity Assembly IDEntity NameEntity ID
1entity_11
2entity_22
3entity_33

Entities:

Entity 1, entity_1 75 residues - 8550.763 Da.

1   GLYMETGLNILEPHEVALASPTHRVALGLN
2   TRPLYSTHRILETHRLEUGLUVALGLUPRO
3   SERASPTHRILEGLUASNVALLYSALALYS
4   ILEGLNASPLYSGLUGLYILEPROPROASP
5   GLNGLNARGLEUILEPHEALAGLYLYSGLN
6   LEUGLUASPGLYARGTHRLEUSERASPTYR
7   ASNILEGLNLYSGLUSERALALEUILELEU
8   LEULEUTHRLEUARG

Entity 2, entity_2 75 residues - 8552.692 Da.

1   GLYMETGLNILEPHEVALASPTHRVALGLN
2   TRPLYSTHRILETHRLEUGLUVALGLUPRO
3   SERASPTHRILEGLUASNVALLYSALALYS
4   ILEGLNASPLYSGLUGLYILEPROPROASP
5   GLNGLNARGLEUASPPHEALAGLYLYSGLN
6   LEUGLUASPGLYARGTHRLEUSERASPTYR
7   ASNILEGLNLYSGLUSERALALEUILELEU
8   LEULEUTHRLEUARG

Entity 3, entity_3 90 residues - 10259.662 Da.

1   GLYSERGLUSERASPSERGLYMETALASER
2   GLNALAASPGLNLYSGLUGLUGLULEULEU
3   LEUPHETRPTHRTYRILEGLNALAMETLEU
4   THRASNLEUGLUSERLEUSERLEUASPARG
5   ILETYRASNMETLEUARGMETPHEVALVAL
6   THRGLYPROALALEUALAGLUILEASPLEU
7   GLNGLULEUGLNGLYTYRLEUGLNLYSLYS
8   VALARGASPGLNGLNLEUVALTYRSERALA
9   GLYVALTYRARGLEUPROLYSASNCYSSER

Samples:

sample_1: entity_1, [U-99% 13C; U-99% 15N], 0.5 mM; entity_2, [U-99% 13C; U-99% 15N], 0.5 mM; entity_3, [U-99% 13C; U-99% 15N], 0.5 mM; Ubiquitin Variant 0.6 mM; NaCl 100 mM

sample_conditions_1: ionic strength: 100 mM; pH: 7; pressure: 1 atm; temperature: 308 K

Experiments:

NameSampleSample stateSample conditions
2D 1H-15N HSQCsample_1isotropicsample_conditions_1
2D 1H-13C HSQC aliphaticsample_1isotropicsample_conditions_1
2D 1H-13C HSQC aromaticsample_1isotropicsample_conditions_1
3D CBCA(CO)NHsample_1isotropicsample_conditions_1
3D HNCACBsample_1isotropicsample_conditions_1
3D HCCH-TOCSYsample_1isotropicsample_conditions_1
3D HNCAsample_1isotropicsample_conditions_1
3D 1H-15N NOESYsample_1isotropicsample_conditions_1
3D 1H-13C NOESY aliphaticsample_1isotropicsample_conditions_1
3D 1H-13C NOESY aromaticsample_1isotropicsample_conditions_1
3D 1H-13C filtered NOESYsample_1isotropicsample_conditions_1
3D HBHA(CO)NHsample_1isotropicsample_conditions_1
2D 1H-15N HSQCsample_1isotropicsample_conditions_1
2D 1H-13C HSQC aliphaticsample_1isotropicsample_conditions_1
2D 1H-13C HSQC aromaticsample_1isotropicsample_conditions_1
3D HNCACBsample_1isotropicsample_conditions_1
3D HNCAsample_1isotropicsample_conditions_1
3D HBHA(CO)NHsample_1isotropicsample_conditions_1
3D 1H-15N NOESYsample_1isotropicsample_conditions_1
3D 1H-13C NOESY aliphaticsample_1isotropicsample_conditions_1
3D 1H-13C NOESY aromaticsample_1isotropicsample_conditions_1
3D H(CCO)NHsample_1isotropicsample_conditions_1
3D 1H-13C filtered NOESYsample_1isotropicsample_conditions_1

Software:

TopSpin, Bruker Biospin - processing

CARA, Keller and Wuthrich - chemical shift assignment, peak picking

CYANA, Guntert, Mumenthaler and Wuthrich - refinement, structure calculation

CNS - refinement

NMR spectrometers:

  • Bruker AVANCE III 600 MHz
  • Bruker AVANCE III 700 MHz
  • Bruker AVANCE III 800 MHz

Download simulated HSQC data in one of the following formats:
CSV: Backbone or all simulated shifts
SPARKY: Backbone or all simulated shifts