BMRB Entry 52365

Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR52365

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Title:
Chemical shifts, T1, T1rho, heteronuclear NOEs, RDCs of ubiquitin folding intermediate F'
Deposition date:
2024-03-26
Original release date:
2024-03-29
Authors:
Adhada, Sri Teja; Sarma, Siddhartha
Citation:

Citation: Adhada, Sri Teja; Sarma, Siddhartha. "Slow Conformational Exchange between Partially Folded and Near-Native States of Ubiquitin: Evidence for a Multistate Folding Model"  Biochemistry 63, 2565-2579 (2024).
PubMed: 39351677

Assembly members:

Assembly members:
entity_1, polymer, 77 residues, Formula weight is not available

Natural source:

Natural source:   Common Name: Japanese rice   Taxonomy ID: 39947   Superkingdom: Eukaryota   Kingdom: Viridiplantae   Genus/species: Oryza sativa

Experimental source:

Experimental source:   Production method: recombinant technology   Host organism: Escherichia coli   Vector: pET21a(+)

Entity Sequences (FASTA):

Entity Sequences (FASTA):
entity_1: MMQIFVKTLTGKTITLEVES SDTIDNVKAKIQDKEGIPPD QQRLIFAGKQLEDGRTLADY NIQKESTLHLVLRLRGG

Data typeCount
13C chemical shifts328
15N chemical shifts82
1H chemical shifts539
T1 relaxation values148
T1rho relaxation values148
heteronuclear NOE values145

Additional metadata:

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

Assembly:

Entity Assembly IDEntity NameEntity ID
1Ubiquitin from Rice1

Entities:

Entity 1, Ubiquitin from Rice 77 residues - Formula weight is not available

1   METMETGLNILEPHEVALLYSTHRLEUTHR
2   GLYLYSTHRILETHRLEUGLUVALGLUSER
3   SERASPTHRILEASPASNVALLYSALALYS
4   ILEGLNASPLYSGLUGLYILEPROPROASP
5   GLNGLNARGLEUILEPHEALAGLYLYSGLN
6   LEUGLUASPGLYARGTHRLEUALAASPTYR
7   ASNILEGLNLYSGLUSERTHRLEUHISLEU
8   VALLEUARGLEUARGGLYGLY

Samples:

sample_1: Ubiquitin from Rice (Oryza sativa) 1 ± 0.1 mM

sample_2: Ubiquitin from Rice (Oryza sativa), [U-15N], 1 ± 0.1 mM

sample_3: Ubiquitin from Rice (Oryza sativa), [U-13C; U-15N], 1 ± 0.1 mM

sample_conditions_1: ionic strength: 20 mM; pH: 2; pressure: 1 atm; temperature: 298 K

Experiments:

NameSampleSample stateSample conditions
2D 1H-15N HSQCsample_2isotropicsample_conditions_1
2D 1H-13C HSQCsample_3isotropicsample_conditions_1
T1/R1 relaxationsample_2isotropicsample_conditions_1
T1rho/R1rho relaxationsample_2isotropicsample_conditions_1
1H-15N heteronoesample_2isotropicsample_conditions_1
3D CBCA(CO)NHsample_3isotropicsample_conditions_1
3D HNCOsample_3isotropicsample_conditions_1
3D HNCACBsample_3isotropicsample_conditions_1
3D HN(CA)COsample_3isotropicsample_conditions_1
3D H(CCO)NHsample_3isotropicsample_conditions_1
3D C(CO)NHsample_3isotropicsample_conditions_1
3D 15N-separated NOESYsample_3isotropicsample_conditions_1
3D 13C-separated NOESYsample_3isotropicsample_conditions_1
2D 1H-15N IPAP HSQCsample_3anisotropicsample_conditions_1
2D 1H-15N IPAP HSQCsample_3isotropicsample_conditions_1
1D 1H DOSYsample_3isotropicsample_conditions_1
3D 1H-15N TOCSYsample_2isotropicsample_conditions_1
T1/R1 relaxationsample_3isotropicsample_conditions_1
T1rho/R1rho relaxationsample_3isotropicsample_conditions_1
1H-15N heteronoesample_3isotropicsample_conditions_1
3D HNCO LRAsample_3isotropicsample_conditions_1
3D HNHAsample_2isotropicsample_conditions_1

Software:

CcpNMR v2.5.2 - chemical shift assignment, peak picking

NMRPipe v10.9 - data analysis, processing

CYANA v3.98.15 - structure solution

X-PLOR NIH v3.4 - refinement

VNMRj v4.2 - collection

TOPSPIN v4.0.9 - collection

PINT - data analysis

NMR spectrometers:

  • Bruker Avance 700 MHz
  • Agilent DirectDrive 600 MHz

Related Database Links:

UNP P0CH34

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