BMRB

Biological Magnetic Resonance Data Bank


A Repository for Data from NMR Spectroscopy on Proteins, Peptides, Nucleic Acids, and other Biomolecules
Member of WWPDB

BMRB Entry 25601

Title: Ensemble structure the closed state of Lys63-linked diubiquitin in the absence of a ligand   PubMed: 26090905

Authors: Liu, Zhu; Gong, Zhou

Citation: Liu, Zhu; Gong, Zhou; Yang, Ju; Jiang, Wen-Xue; Zhu, Wen-Kai; Guo, Da-Chuan; Zhang, Wei-Ping; Liu, Mai-Li; Tang, Chun. "Lys63-linked ubiquitin chain adopts multiple conformational states for specific target recognition"  eLIFE 4, e05767-e05767 (2015).

Assembly members:
entity_1, polymer, 76 residues, 8539.906 Da.
entity_2, polymer, 71 residues, 8035.261 Da.
entity_MTN, non-polymer, 264.385 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

Entity Sequences (FASTA):
entity_1: MQIFVKTLTGKTITLEVEPS DTIECVKAKIQDKEGIPPDQ QRLIFAGCQLEDGRTLSDYN IQKESTLHLVLRLRGG
entity_2: MQIFVKTLTGKTITLEVEPS DTIENVKAKIQDKEGIPPDQ QRLIFAGKQLEDGRTLSDYN IQKESTLHLVL

Data sets:
Data typeCount
15N chemical shifts135
1H chemical shifts135

Additional metadata:

  • Assembly
  • Samples and Experiments
  • Software
  • Spectrometers
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Assembly:

Entity Assembly IDEntity NameEntity ID
1entity_11
2entity_22
3S-[(1-OXYL-2,2,5,5-TETRAMETHYL-2,5-DIHYDRO-1H-PYRROL-3-YL)METHYL] METHANESULFONOTHIOATE_13
4S-[(1-OXYL-2,2,5,5-TETRAMETHYL-2,5-DIHYDRO-1H-PYRROL-3-YL)METHYL] METHANESULFONOTHIOATE_23

Entities:

Entity 1, entity_1 76 residues - 8539.906 Da.

N25 and K48 mutated to C, one at a time

1   METGLNILEPHEVALLYSTHRLEUTHRGLY
2   LYSTHRILETHRLEUGLUVALGLUPROSER
3   ASPTHRILEGLUCYSVALLYSALALYSILE
4   GLNASPLYSGLUGLYILEPROPROASPGLN
5   GLNARGLEUILEPHEALAGLYCYSGLNLEU
6   GLUASPGLYARGTHRLEUSERASPTYRASN
7   ILEGLNLYSGLUSERTHRLEUHISLEUVAL
8   LEUARGLEUARGGLYGLY

Entity 2, entity_2 71 residues - 8035.261 Da.

1   METGLNILEPHEVALLYSTHRLEUTHRGLY
2   LYSTHRILETHRLEUGLUVALGLUPROSER
3   ASPTHRILEGLUASNVALLYSALALYSILE
4   GLNASPLYSGLUGLYILEPROPROASPGLN
5   GLNARGLEUILEPHEALAGLYLYSGLNLEU
6   GLUASPGLYARGTHRLEUSERASPTYRASN
7   ILEGLNLYSGLUSERTHRLEUHISLEUVAL
8   LEU

Entity 3, S-[(1-OXYL-2,2,5,5-TETRAMETHYL-2,5-DIHYDRO-1H-PYRROL-3-YL)METHYL] METHANESULFONOTHIOATE_1 - C10 H18 N O3 S2 - 264.385 Da.

1   MTN

Samples:

sample_1: N25C_MTS protein, [U-100% 15N], 0.5 mM; D2O, [U-99% 2H], 10 % v/v; sodium chloride 100 mM; sodium acetate 10 mM

sample_2: K48C_MTS protein, [U-100% 15N], 0.5 mM; D2O, [U-99% 2H], 10 % v/v; sodium chloride 100 mM; sodium acetate 10 mM

sample_3: N25C_MTS mixture protein, [U-100% 15N], 1 mM; D2O, [U-99% 2H], 10 % v/v; sodium chloride 100 mM; sodium acetate 10 mM

sample_4: K48C_MTS mixture protein, [U-100% 15N], 1 mM; D2O, [U-99% 2H], 10 % v/v; sodium chloride 100 mM; sodium acetate 10 mM

sample_5: 15N_distal-14N_proximal, [U-100% 15N], 0.5 mM; D2O, [U-99% 2H], 10 % v/v; sodium chloride 100 mM; sodium acetate 10 mM

sample_6: 14N_distal-15N_proximal, [U-100% 15N], 0.5 mM; D2O, [U-99% 2H], 10 % v/v; sodium chloride 100 mM; sodium acetate 10 mM

sample_conditions_1: ionic strength: 100 mM; pH: 6.0; pressure: 1 atm; temperature: 303 K

sample_conditions_2: ionic strength: 100 mM; pH: 6.0; pressure: 1 atm; temperature: 303 K

sample_conditions_3: ionic strength: 100 mM; pH: 6.0; pressure: 1 atm; temperature: 303 K

sample_conditions_4: ionic strength: 100 mM; pH: 6.0; pressure: 1 atm; temperature: 303 K

sample_conditions_5: ionic strength: 100 mM; pH: 6.0; pressure: 1 atm; temperature: 303 K

sample_conditions_6: ionic strength: 100 mM; pH: 6.0; pressure: 1 atm; temperature: 303 K

Experiments:

NameSampleSample stateSample conditions
transverse relaxation rate measurementsample_1isotropicsample_conditions_1
transverse relaxation rate measurementsample_2isotropicsample_conditions_2
transverse relaxation rate measurementsample_3isotropicsample_conditions_3
transverse relaxation rate measurementsample_4isotropicsample_conditions_4
2D 1H-15N HSQCsample_5isotropicsample_conditions_5
2D 1H-15N HSQCsample_6isotropicsample_conditions_6

Software:

X-PLOR_NIH, Schwieters, Kuszewski, Tjandra and Clore - structure solution

NMR spectrometers:

  • Bruker Avance 600 MHz
  • Bruker Avance 850 MHz

Related Database Links: