BMRB Entry 34984

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PDB ID:
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR34984
MolProbity Validation Chart

NMR-STAR file interactive viewer.
NMR-STAR v3 text file.
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Title:
Solution NMR structure of Arkadia 2 RING domain
Deposition date:
2025-02-28
Original release date:
2026-03-23
Authors:
Marousis, K.; Giannari, D.; Seliami, A.; Politi, M.; Birkou, M.; Bentrop, D.; Episkopou, V.; Spyroulias, G.
Citation:

Citation: Marousis, K.; Politi, M.; Giannari, D.; Seliami, A.; Birkou, M.; Bentrop, D.; Episkopou, V.; Spyroulias, G.. "Mechanistic insights into the Auto-ubiquitiniation of ARKADIA 2C RING domain"  .

Assembly members:

Assembly members:
entity_1, polymer, 68 residues, 7740.865 Da.
entity_ZN, non-polymer, 65.409 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 BL21(DE3)   Vector: pGex-47-1

Entity Sequences (FASTA):

Entity Sequences (FASTA):
entity_1: KGKKDEGEESDTDEKCTICL SMLEDGEDVRRLPCMHLFHQ LCVDQWLAMSKKCPICRVDI ETQLGADS

Data sets:
Data typeCount
13C chemical shifts273
15N chemical shifts63
1H chemical shifts430

Additional metadata:

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

Assembly:

Entity Assembly IDEntity NameEntity ID
1unit_11
2unit_22
3unit_32

Entities:

Entity 1, unit_1 68 residues - 7740.865 Da.

1   LYSGLYLYSLYSASPGLUGLYGLUGLUSER
2   ASPTHRASPGLULYSCYSTHRILECYSLEU
3   SERMETLEUGLUASPGLYGLUASPVALARG
4   ARGLEUPROCYSMETHISLEUPHEHISGLN
5   LEUCYSVALASPGLNTRPLEUALAMETSER
6   LYSLYSCYSPROILECYSARGVALASPILE
7   GLUTHRGLNLEUGLYALAASPSER

Entity 2, unit_2 - Zn - 65.409 Da.

1   ZN

Samples:

sample_1: ARKADIA 2 E3 Ub ligase, RING Domain, [U-99% 15N], 0.7 mM; potassium phosphate 50 mM; DSS 2 mM

sample_2: ARKADIA 2 E3 Ub ligase, RING Domain, [U-99% 13C; U-99% 15N], 0.7 mM; potassium phosphate 50 mM; DSS 2 mM

sample_3: ARKADIA 2 E3 Ub ligase, RING Domain 0.7 mM; potassium phosphate 50 mM; DSS 2 mM

sample_conditions_1: ionic strength: 50 mM; pH: 7; pressure: 1 atm; temperature: 298 K

Experiments:

NameSampleSample stateSample conditions
2D 1H-13C HSQC aliphaticsample_2isotropicsample_conditions_1
2D 1H-15N HSQCsample_1isotropicsample_conditions_1
2D 1H-1H NOESYsample_3isotropicsample_conditions_1
3D 1H-13C NOESY aliphaticsample_2isotropicsample_conditions_1
3D 1H-13C NOESY aromaticsample_2isotropicsample_conditions_1
3D 1H-15N NOESYsample_1isotropicsample_conditions_1
1D 1Hsample_3isotropicsample_conditions_1
3D HNHAsample_2isotropicsample_conditions_1
3D HBHA(CO)NHsample_2isotropicsample_conditions_1
3D HNCACBsample_2isotropicsample_conditions_1
3D CBCA(CO)NHsample_2isotropicsample_conditions_1
3D HN(CA)COsample_2isotropicsample_conditions_1
3D HNCOsample_2isotropicsample_conditions_1
3D HN(CO)CAsample_2isotropicsample_conditions_1
3D HNCAsample_2isotropicsample_conditions_1
3D HCCH-TOCSYsample_2isotropicsample_conditions_1
2D 1H-13C HSQC aromaticsample_2isotropicsample_conditions_1
2D 1H-15N Trosy HSQCsample_1isotropicsample_conditions_1

Software:

CARA v1.8.4, Keller and Wuthrich - chemical shift assignment

XEASY, Bartels et al. - peak picking

DYANA, Guntert, Braun and Wuthrich - structure calculation

Amber v5.0, Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollman - refinement

NMR spectrometers:

  • Bruker AVANCE 600 MHz
  • Bruker AVANCE III HD 700 MHz

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