BMRB Entry 36420

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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/BMR36420
MolProbity Validation Chart

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NMR-STAR v3 text file.
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Title:
Multi-state structure determination and dynamics analysis elucidate a new ubiquitin-recognition mechanism of yeast ubiquitin C-terminal hydrolase.
Deposition date:
2021-04-15
Original release date:
2025-11-01
Authors:
Okada, M.; Tateishi, Y.; Nojiri, E.; Mikawa, T.; Rajesh, S.; Ogasawa, H.; Ueda, T.; Yagi, H.; Kohno, T.; Kigawa, T.; Shimada, I.; Guentert, P.; Yutaka, I.; Ikeya, T.
Citation:

Citation: Okada, M.; Tateishi, Y.; Nojiri, E.; Mikawa, T.; Rajesh, S.; Yagi, H.; Ogasawa, H.; Ueda, T.; Shimada, I.; Kohno, T.; Kigawa, T.; Guentert, P.; Yutaka, I.; Ikeya, T.. "Multi-state structure determination and dynamics analysis elucidate a new ubiquitin-recognition mechanism of yeast ubiquitin C-terminal hydrolase."  .

Assembly members:

Assembly members:
Ubiquitin carboxyl-terminal hydrolase YUH1, polymer, 236 residues, 26405.23 Da.

Natural source:

Natural source:   Common Name: baker's yeast   Taxonomy ID: 4932   Superkingdom: Eukaryota   Kingdom: Fungi   Genus/species: Saccharomyces cerevisiae

Experimental source:

Experimental source:   Production method: recombinant technology   Host organism: Escherichia coli BL21(DE3)   Vector: pET24a

Entity Sequences (FASTA):

Entity Sequences (FASTA):
Ubiquitin carboxyl-terminal hydrolase YUH1: MSGENRAVVPIESNPEVFTN FAHKLGLKNEWAYFDIYSLT EPELLAFLPRPVKAIVLLFP INEDRKSSTSQQITSSYDVI WFKQSVKNACGLYAILHSLS NNQSLLEPGSDLDNFLKSQS DTSSSKNRFDDVTTDQFVLN VIKENVQTFSTGQSEAPEAT ADTNLHYITYVEENGGIFEL DGRNLSGPLYLGKSDPTATD LIEQELVRVRVASYMENANE EDVLNFAMLGLGPNWE

Data typeCount
13C chemical shifts932
15N chemical shifts249
1H chemical shifts1553
chemical shift perturbation values754

Additional metadata:

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

Assembly:

Entity Assembly IDEntity NameEntity ID
1entity_11

Entities:

Entity 1, entity_1 236 residues - 26405.23 Da.

1   METSERGLYGLUASNARGALAVALVALPRO
2   ILEGLUSERASNPROGLUVALPHETHRASN
3   PHEALAHISLYSLEUGLYLEULYSASNGLU
4   TRPALATYRPHEASPILETYRSERLEUTHR
5   GLUPROGLULEULEUALAPHELEUPROARG
6   PROVALLYSALAILEVALLEULEUPHEPRO
7   ILEASNGLUASPARGLYSSERSERTHRSER
8   GLNGLNILETHRSERSERTYRASPVALILE
9   TRPPHELYSGLNSERVALLYSASNALACYS
10   GLYLEUTYRALAILELEUHISSERLEUSER
11   ASNASNGLNSERLEULEUGLUPROGLYSER
12   ASPLEUASPASNPHELEULYSSERGLNSER
13   ASPTHRSERSERSERLYSASNARGPHEASP
14   ASPVALTHRTHRASPGLNPHEVALLEUASN
15   VALILELYSGLUASNVALGLNTHRPHESER
16   THRGLYGLNSERGLUALAPROGLUALATHR
17   ALAASPTHRASNLEUHISTYRILETHRTYR
18   VALGLUGLUASNGLYGLYILEPHEGLULEU
19   ASPGLYARGASNLEUSERGLYPROLEUTYR
20   LEUGLYLYSSERASPPROTHRALATHRASP
21   LEUILEGLUGLNGLULEUVALARGVALARG
22   VALALASERTYRMETGLUASNALAASNGLU
23   GLUASPVALLEUASNPHEALAMETLEUGLY
24   LEUGLYPROASNTRPGLU

Samples:

sample_1: ubiquitin hydrolase, [U-100% 13C; U-100% 15N; U-50% 2H], 2 mM; H2O 90%; D2O, [U-2H], 10%

sample_2: ubiquitin hydrolase, [U-100% 15N], 2 mM; H2O 90%; D2O, [U-2H], 10%

sample_3: ubiquitin hydrolase, Ile/Leu/Val-methyl-selectively 1H/13C-labeled and Phe/Tyr/Trp-aromatic ring-selectively 1H-labeled, 2 mM; H2O 90%; D2O, [U-2H], 10%

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

Experiments:

NameSampleSample stateSample conditions
3D HNCAsample_1isotropicsample_conditions_1
3D HN(CO)CAsample_1isotropicsample_conditions_1
3D CBCA(CO)NHsample_1isotropicsample_conditions_1
3D CBCANHsample_1isotropicsample_conditions_1
3D HBHA(CO)NHsample_1isotropicsample_conditions_1
3D HSQC-NOESY-HSQCsample_1isotropicsample_conditions_1
3D 1H-15N NOESYsample_1anisotropicsample_conditions_1
3D 1H-13C NOESYsample_1isotropicsample_conditions_1
3D HCCH-TOCSYsample_1isotropicsample_conditions_1
3D C(CO)NHsample_1isotropicsample_conditions_1
3D H(CCO)NHsample_1isotropicsample_conditions_1
3D H(CCO)NHsample_3isotropicsample_conditions_1
3D C(CO)NHsample_3isotropicsample_conditions_1
3D CCNHsample_3isotropicsample_conditions_1
3D 1H-13C NOESYsample_3isotropicsample_conditions_1
2D 1H-1H TOCSYsample_3isotropicsample_conditions_1
3D 1H-15N NOESYsample_3isotropicsample_conditions_1
3D TROSY-HNCOsample_3isotropicsample_conditions_1
heteronuclear 1H-15N NOEsample_2isotropicsample_conditions_1
T2 relaxationsample_2isotropicsample_conditions_1
T1 relaxationsample_2isotropicsample_conditions_1
T2 relaxationsample_2isotropicsample_conditions_1
T1 relaxationsample_2isotropicsample_conditions_1
heteronuclear 1H-15N NOEsample_2isotropicsample_conditions_1
2D 1H-15N HSQCsample_2isotropicsample_conditions_1
2D 1H-15N IPAP HSQCsample_2anisotropicsample_conditions_1
2D 1H-13C HSQCsample_1isotropicsample_conditions_1

Software:

CYANA v3.99.0, Guntert, Mumenthaler and Wuthrich - structure calculation

Azara v2.8.1, Boucher - processing

CcpNmr Analysis v2.5.0, CCPN - chemical shift assignment

TopSpin v3.5, Bruker Biospin - collection

OPAL v1.4, Luginbuhl, Guntert, Billeter and Wuthrich - refinement

CcpNmr Analysis v2.5.0, CCPN - peak picking

NMR spectrometers:

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

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