BMRB Entry 18671

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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/BMR18671
MolProbity Validation Chart

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Title:
Solution structure of the complex between the Sgt2 homodimerization domain and the Get5 UBL domain
Deposition date:
2012-08-19
Original release date:
2012-11-20
Authors:
Chartron, Justin; VanderVelde, David; Clemons, William
Citation:

Citation: Chartron, Justin; VanderVelde, David; Clemons, William. "Structures of the Sgt2/SGTA dimerization domain with the Get5/UBL4A UBL domain reveal an interaction that forms a conserved dynamic interface."  Cell Rep. 2, 1620-1632 (2012).
PubMed: 23142665

Assembly members:

Assembly members:
Get5, polymer, 81 residues, 9170.889 Da.
Sgt2, polymer, 74 residues, 7889.790 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   Vector: pET33b

Entity Sequences (FASTA):

Entity Sequences (FASTA):
Get5: MVHLTLKKIQAPKFSIEHDF SPSDTILQIKQHLISEEKAS HISEIKLLLKGKVLHDNLFL SDLKVTPANSTITVMIKPNL E
Sgt2: SVDSASKEEIAALIVNYFSS IVEKKEISEDGADSLNVAMD CISEAFGFEREAVSGILGKS EFKGQHLADILNSA

Data sets:
Data typeCount
13C chemical shifts522
15N chemical shifts136
1H chemical shifts948

Additional metadata:

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

Entity Assembly IDEntity NameEntity ID
1Get51
2Sgt2_12
3Sgt2_22

Entities:

Entity 1, Get5 81 residues - 9170.889 Da.

1   METVALHISLEUTHRLEULYSLYSILEGLN
2   ALAPROLYSPHESERILEGLUHISASPPHE
3   SERPROSERASPTHRILELEUGLNILELYS
4   GLNHISLEUILESERGLUGLULYSALASER
5   HISILESERGLUILELYSLEULEULEULYS
6   GLYLYSVALLEUHISASPASNLEUPHELEU
7   SERASPLEULYSVALTHRPROALAASNSER
8   THRILETHRVALMETILELYSPROASNLEU
9   GLU

Entity 2, Sgt2_1 74 residues - 7889.790 Da.

1   SERVALASPSERALASERLYSGLUGLUILE
2   ALAALALEUILEVALASNTYRPHESERSER
3   ILEVALGLULYSLYSGLUILESERGLUASP
4   GLYALAASPSERLEUASNVALALAMETASP
5   CYSILESERGLUALAPHEGLYPHEGLUARG
6   GLUALAVALSERGLYILELEUGLYLYSSER
7   GLUPHELYSGLYGLNHISLEUALAASPILE
8   LEUASNSERALA

Samples:

sample_1: Get5 1 mM; Sgt2, [U-100% 13C; U-100% 15N], 2 mM; Bis-Tris 10 mM; L-arginine 50 mM; L-glutamic acid 50 mM; sodium azide 0.02%; H2O 90%; D2O 10%

sample_2: Get5 1 mM; Sgt2, [U-100% 13C; U-100% 15N], 2 mM; Bis-Tris 10 mM; L-arginine 50 mM; L-glutamic acid 50 mM; sodium azide 0.02%; polyacrylamide 3.5%; H2O 90%; D2O 10%

sample_3: Get5, [U-100% 13C; U-100% 15N], 1 mM; Sgt2 2 mM; Bis-Tris 10 mM; L-arginine 50 mM; L-glutamic acid 50 mM; sodium azide 0.02%; H2O 90%; D2O 10%

sample_4: Get5, [U-100% 13C; U-100% 15N], 1 mM; Sgt2 2 mM; Bis-Tris 10 mM; L-arginine 50 mM; L-glutamic acid 50 mM; sodium azide 0.02%; polyacrylamide 3.5%; H2O 90%; D2O 10%

sample_conditions_1: ionic strength: 0 mM; pH: 6.1; pressure: 1 atm; temperature: 310 K

Experiments:

NameSampleSample stateSample conditions
2D 1H-15N HSQCsample_1isotropicsample_conditions_1
3D 1H-15N NOESYsample_1isotropicsample_conditions_1
3D 1H-15N TOCSYsample_1isotropicsample_conditions_1
2D 1H-13C HSQC aliphaticsample_1isotropicsample_conditions_1
2D 1H-13C HSQC aromaticsample_1isotropicsample_conditions_1
2D 1H-15N HSQCsample_3isotropicsample_conditions_1
3D HNCACBsample_3isotropicsample_conditions_1
3D HNCOsample_3isotropicsample_conditions_1
3D (H)CCH-TOCSYsample_3isotropicsample_conditions_1
3D HCCH-TOCSYsample_3isotropicsample_conditions_1
3D 1H-15N NOESYsample_3isotropicsample_conditions_1
3D 1H-13C NOESY aliphaticsample_3isotropicsample_conditions_1
2D 1H-15N HSQCsample_2anisotropicsample_conditions_1
2D 1H-15N HSQCsample_4anisotropicsample_conditions_1

Software:

VNMRJ, Varian - collection

Analysis, CCPN - chemical shift assignment

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

TALOS+, Cornilescu, Delaglio and Bax - data analysis

ARIA v2.3, Linge, O'Donoghue and Nilges - refinement, structure solution

HADDOCK v2.1, Alexandre Bonvin - refinement, structure solution

TOPSPIN, Bruker Biospin - collection

PALES, Zweckstetter and Bax - data analysis

NMR spectrometers:

  • Varian INOVA 600 MHz
  • Bruker Avance 800 MHz

Related Database Links:

BMRB 18342 18669 18341 18670
PDB
DBJ GAA26218 GAA26330
EMBL CAA88151 CAA99130 CAY86179 CAA99195 CAY86295
GB AHY77206 AJP41438 AJT70857 AJT71348 AJT71834 AAC49487 AHY77314 EDN63877 EDV10615 EDZ69384
REF NP_014530 NP_014649
SP Q12285 Q12118
TPG DAA10672 DAA10789
AlphaFold Q12285 Q12118

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