BMRB Entry 17479

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PDB ID:
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_anomalous, AVS_full, LACS
BMRB Entry DOI: doi:10.13018/BMR17479
MolProbity Validation Chart

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Title:
Structure of the human Shwachman-Bodian-Diamond syndrome (SBDS) protein
Deposition date:
2011-02-21
Original release date:
2011-05-05
Authors:
Hilcenko, Christine; Freund, Stefan; Warren, Alan
Citation:

Citation: Finch, Andrew; Hilcenko, Christine; Basse, Nicolas; Drynan, Lesley; Goyenechea, Beatriz; Menne, Tobias; Gonzalez Fernandez, Africa; Simpson, Paul; Arends, Clive; Donadieu, Mark; Bellanne-Chantelot, Jean; Costanzo, Christine; Boone, Michael; McKenzie, Charles; Freund, Andrew; Warren, Stefan. "Uncoupling of GTP hydrolysis from eIF6 release on the ribosome causes Shwachman-Diamond syndrome."  Genes Dev. 25, 917-929 (2011).
PubMed: 21536732

Assembly members:

Assembly members:
human_SBDS, polymer, 252 residues, 28813.812 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   Vector: pSBDS

Entity Sequences (FASTA):

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

Data sets:
Data typeCount
13C chemical shifts953
15N chemical shifts248
1H chemical shifts1642

Additional metadata:

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

Assembly:

Entity Assembly IDEntity NameEntity ID
1human_SBDS1

Entities:

Entity 1, human_SBDS 252 residues - 28813.812 Da.

1   GLYSERMETSERILEPHETHRPROTHRASN
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: potassium phosphate 25 mM; sodium chloride 150 mM; DTT 1 mM; sodium azide 0.05%; human_SBDS 0.48 mM; H2O 90%; D2O 10%

sample_2: potassium phosphate 25 mM; sodium chloride 150 mM; DTT 1 mM; sodium azide 0.05%; human_SBDS 0.5 mM; H2O 90%; D2O 10%

sample_3: potassium phosphate 25 mM; sodium chloride 150 mM; DTT 1 mM; sodium azide 0.05%; human_SBDS 0.3 mM; H2O 90%; D2O 10%

sample_4: potassium phosphate 25 mM; sodium chloride 150 mM; DTT 1 mM; sodium azide 0.05%; human_SBDS 0.4 mM; H2O 90%; D2O 10%

sample_5: potassium phosphate 25 mM; sodium chloride 150 mM; DTT 1 mM; sodium azide 0.05%; human_SBDS 0.35 mM; H2O 90%; D2O 10%

sample_6: potassium phosphate 25 mM; sodium chloride 150 mM; DTT 1 mM; sodium azide 0.05%; human_SBDS 0.4 mM; H2O 90%; D2O 10%

sample_conditions_1: ionic strength: 0.163 M; pH: 6.5; pressure: 1 atm; temperature: 298 K

sample_conditions_2: ionic strength: 0.163 M; pH: 6.5; pressure: 1 atm; temperature: 298 K

sample_conditions_3: ionic strength: 0.163 M; pH: 6.5; pressure: 1 atm; temperature: 298 K

sample_conditions_4: ionic strength: 0.163 M; pH: 6.5; pressure: 1 atm; temperature: 298 K

sample_conditions_5: ionic strength: 0.163 M; pH: 6.5; pressure: 1 atm; temperature: 298 K

sample_conditions_6: ionic strength: 0.163 M; pH: 6.5; pressure: 1 atm; temperature: 298 K

Experiments:

NameSampleSample stateSample conditions
3D HNCAsample_2isotropicsample_conditions_2
3D HNCOsample_2isotropicsample_conditions_2
3D HN(CO)CAsample_2isotropicsample_conditions_2
3D HBHA(CO)NHsample_2isotropicsample_conditions_2
3D HNCACBsample_2isotropicsample_conditions_2
3D HNCACOsample_2isotropicsample_conditions_2
3D HNCAsample_5isotropicsample_conditions_5
3D HNCOsample_5isotropicsample_conditions_5
3D HN(CO)CAsample_5isotropicsample_conditions_5
3D HBHA(CO)NHsample_5isotropicsample_conditions_5
3D HNCACBsample_5isotropicsample_conditions_5
3D HNCACOsample_5isotropicsample_conditions_5
2D 1H-15N HSQCsample_3isotropicsample_conditions_3
3D 1H-15N NOESYsample_1isotropicsample_conditions_1
3D 1H-13C NOESYsample_6isotropicsample_conditions_6
2D 1H-13C HSQCsample_6isotropicsample_conditions_6
3D HCCH-TOCSYsample_6isotropicsample_conditions_6
3D HCCH-COSYsample_6isotropicsample_conditions_6
3D HN(CAN)NHsample_2isotropicsample_conditions_2
3D (H)CC(CO)NHsample_2isotropicsample_conditions_2
3D H(CCCO)NHsample_2isotropicsample_conditions_2

Software:

SPARKY v3, Goddard - chemical shift assignment, peak picking

TOPSPIN v2.1, Bruker Biospin - processing

CNS, Brunger, Adams, Clore, Gros, Nilges and Read - structure calculation

NMR spectrometers:

  • Bruker Avance 700 MHz
  • Bruker DRX 900 MHz

Related Database Links:

BMRB 16119
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