BMRB Entry 16119

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PDB ID:
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_anomalous, AVS_full, LACS, SPARTA
BMRB Entry DOI: doi:10.13018/BMR16119
MolProbity Validation Chart

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NMR-STAR v3 text file.
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Title:
Structure of the human Shwachman-Bodian-Diamond syndrome protein, SBDS
Deposition date:
2009-01-14
Original release date:
2010-01-11
Authors:
de Oliveira, Juliana; Sforca, Mauricio; Blumenschein, Tharin; Guimaraes, Beatriz; Zanchin, Nilson; Zeri, Ana Carolina
Citation:

Citation: de Oliveira, Juliana Ferreira; Sforca, Mauricio; Blumenschein, Tharin; Goldfeder, Mauricio; Guimaraes, Beatriz; Oliveira, Carla Columbano; Zanchin, Nilson; Zeri, Ana-Carolina. "Structure, Dynamics, and RNA Interaction Analysis of the Human SBDS Protein."  J. Mol. Biol. 396, 1053-1069 (2010).
PubMed: 20053358

Assembly members:

Assembly members:
SBDS, polymer, 252 residues, Formula weight is not available

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   Vector: pET-TEV

Entity Sequences (FASTA):

Entity Sequences (FASTA):
SBDS: GHMSIFTPTNQIRLTNVAVV RMKRAGKRFEIACYKNKVVG WRSGVEKDLDEVLQTHSVFV NVSKGQVAKKEDLISAFGTD DQTEICKQILTKGEVQVSDK ERHTQLEQMFRDIATIVADK CVNPETKRPYTVILIERAMK DIHYSVKTNKSTKQQALEVI KQLKEKMKIERAHMRLRFIL PVNEGKKLKEKLKPLIKVIE SEDYGQQLEIVCLIDPGCFR EIDELIKKETKGKGSLEVLN LKDVEEGDEKFE

Data sets:
Data typeCount
13C chemical shifts979
15N chemical shifts216
1H chemical shifts1303

Additional metadata:

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

Assembly:

Entity Assembly IDEntity NameEntity ID
1SBDS1

Entities:

Entity 1, SBDS 252 residues - Formula weight is not available

1   GLYHISMETSERILEPHETHRPROTHRASN
2   GLNILEARGLEUTHRASNVALALAVALVAL
3   ARGMETLYSARGALAGLYLYSARGPHEGLU
4   ILEALACYSTYRLYSASNLYSVALVALGLY
5   TRPARGSERGLYVALGLULYSASPLEUASP
6   GLUVALLEUGLNTHRHISSERVALPHEVAL
7   ASNVALSERLYSGLYGLNVALALALYSLYS
8   GLUASPLEUILESERALAPHEGLYTHRASP
9   ASPGLNTHRGLUILECYSLYSGLNILELEU
10   THRLYSGLYGLUVALGLNVALSERASPLYS
11   GLUARGHISTHRGLNLEUGLUGLNMETPHE
12   ARGASPILEALATHRILEVALALAASPLYS
13   CYSVALASNPROGLUTHRLYSARGPROTYR
14   THRVALILELEUILEGLUARGALAMETLYS
15   ASPILEHISTYRSERVALLYSTHRASNLYS
16   SERTHRLYSGLNGLNALALEUGLUVALILE
17   LYSGLNLEULYSGLULYSMETLYSILEGLU
18   ARGALAHISMETARGLEUARGPHEILELEU
19   PROVALASNGLUGLYLYSLYSLEULYSGLU
20   LYSLEULYSPROLEUILELYSVALILEGLU
21   SERGLUASPTYRGLYGLNGLNLEUGLUILE
22   VALCYSLEUILEASPPROGLYCYSPHEARG
23   GLUILEASPGLULEUILELYSLYSGLUTHR
24   LYSGLYLYSGLYSERLEUGLUVALLEUASN
25   LEULYSASPVALGLUGLUGLYASPGLULYS
26   PHEGLU

Samples:

sample_1: SBDS, [U-100% 13C; U-100% 15N; U-80% 2H], 0.5 mM; DTT, no, 1.0 mM; sodium phosphate, no, 50 mM; sodium chloride, no, 20 mM; sodium azide, no, 0.05%; H2O 90%; D2O 10%

sample_2: SBDS, [U-99% 13C; U-99% 15N], 0.5 mM; DTT, no, 1.0 mM; sodium phosphate, no, 50 mM; sodium chloride, no, 20 mM; sodium azide, no, 0.05%; H2O 90%; D2O 10%

sample_3: SBDS, [U-99% 13C; U-99% 15N], 0.5 mM; DTT, no, 1.0 mM; sodium phosphate, no, 50 mM; sodium chloride, no, 20 mM; sodium azide, no, 0.05%; D2O 100%

sample_conditions_1: ionic strength: 0.071 M; pH: 7.2; pressure: 1 atm; temperature: 293 K

Experiments:

NameSampleSample stateSample conditions
3D HNCACBsample_1isotropicsample_conditions_1
3D CBCA(CO)NHsample_1isotropicsample_conditions_1
3D HNCAsample_1isotropicsample_conditions_1
3D HN(CO)CAsample_1isotropicsample_conditions_1
3D HNCOsample_1isotropicsample_conditions_1
3D 1H-15N NOESYsample_2isotropicsample_conditions_1
3D HCCH-TOCSYsample_3isotropicsample_conditions_1
3D 1H-13C NOESYsample_3isotropicsample_conditions_1
3D 1H-15N TOCSYsample_2isotropicsample_conditions_1
2D 1H-15N HSQC_T1sample_2isotropicsample_conditions_1
2D 1H-15N HSQC_T1sample_2isotropicsample_conditions_1
2D 1H-15N HSQC_T2sample_2isotropicsample_conditions_1
2D 1H-15N HSQC_T2sample_2isotropicsample_conditions_1
2D 1H-15N HSQC_NOEsample_2isotropicsample_conditions_1
2D 1H-15N HSQC_NOEsample_2isotropicsample_conditions_1

Software:

NMRPipe, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - processing

NMRView v5, Johnson, One Moon Scientific - chemical shift assignment, peak picking

CYANA, Guntert, Mumenthaler and Wuthrich - geometry optimization, structure solution

DYANA, Guntert, Braun and Wuthrich - geometry optimization, structure solution

DISCOVER, Accelrys Software Inc. - refinement

InsightII, Accelrys Software Inc. - data analysis

ProcheckNMR, Laskowski and MacArthur - data analysis

NMR spectrometers:

  • Varian INOVA 600 MHz
  • Bruker Avance 800 MHz

Related Database Links:

BMRB 17479
PDB
DBJ BAA91905 BAB23803 BAB29487 BAB31612 BAE40670
EMBL CAH91068
GB AAH03849 AAH65700 AAH86335 AAI04586 AAN77490
REF NP_001008290 NP_001029611 NP_001125618 NP_001231322 NP_057122
SP P70122 Q3SWZ6 Q5RAZ2 Q5RK30 Q9Y3A5
TPG DAA15388
AlphaFold P70122 Q3SWZ6 Q5RAZ2 Q5RK30 Q9Y3A5

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