BMRB Entry 25509

Title:
1H, 13C, 15N chemical shift assignments for APOBEC3G NTD variant, sNTD
Deposition date:
2015-02-28
Original release date:
2015-05-05
Authors:
Kouno, Takahide; Luengas, Elizabeth; Shigematu, Megumi; Shandilya, Shivender; Zhang, JingYing; Chen, Luan; Hara, Mayuko; Schiffer, Celia; Harris, Reuben; Matsuo, Hiroshi
Citation:

Citation: Kono, Takahide; Luengas, Elizabeth; Shigematu, Megumi; Shandilya, Shivender; Zhang, JingYing; Chen, Luan; Hara, Mayuko; Schiffer, Celia; Harris, Reuben; Matsuo, Hiroshi. "Structure of the Vif-binding domain of the antiviral enzyme APOBEC3G"  Nat. Struct. Mol. Biol. ., .-..

Assembly members:

Assembly members:
sNTD, polymer, 180 residues, 21316.219 Da.
ZINC ION, non-polymer, 65.409 Da.

Natural source:

Natural source:   Common Name: not available   Taxonomy ID: not available   Superkingdom: not available   Kingdom: not available   Genus/species: not available not available

Experimental source:

Experimental source:   Production method: recombinant technology   Host organism: Escherichia coli   Vector: pCold-GST

Data sets:
Data typeCount
13C chemical shifts317
15N chemical shifts147
1H chemical shifts289

Additional metadata:

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

Assembly:

Entity Assembly IDEntity NameEntity ID
1entity1
2ZINC ION2

Entities:

Entity 1, entity 180 residues - 21316.219 Da.

1   METASPPROASPTHRPHESERTYRASNPHE
2   ASNASNARGPROILELEUSERARGARGASN
3   THRVALTRPLEUCYSTYRGLUVALLYSTHR
4   LYSGLYPROSERARGPROPROLEUASPALA
5   LYSILEPHEARGGLYGLNVALTYRSERGLU
6   ASPLYSTYRHISPROGLUMETARGPHELEU
7   SERLEUVALSERLYSTRPLYSLEUHISARG
8   ASPGLNGLUTYRGLUVALTHRTRPTYRILE
9   SERTRPSERPROCYSTHRLYSCYSALAARG
10   ASPMETALATHRPHELEUGLNGLUASNTHR
11   HISVALTHRLEUTHRILEPHEVALALAARG
12   LEUTYRTYRALATRPASPPROASPTYRGLN
13   GLUALALEUARGSERLEUALAGLNALAGLY
14   ALATHRILELYSILEMETASNTYRASPGLU
15   PHEGLNHISCYSTRPSERLYSPHEVALTYR
16   SERGLNGLYALAPROPHEGLNPROTRPASP
17   GLYLEUASPGLUHISSERGLNALALEUSER
18   GLYARGLEUGLYGLUILELEUARGHISSER

Entity 2, ZINC ION - 65.409 Da.

1   ZN

Samples:

sample_1: entity, [U-100% 15N; U-85% 2H], 0.15-0.20 mM; sodium phosphate 10 mM; sodium chloride 100 mM; Tween 20 0.005%; TCEP 0.5 mM; sodium azide 0.01%; Choline o-sulfate, [U-98% 2H], 0.5 M; H2O 95%; D2O 5%

sample_2: entity, [U-100% 13C; U-100% 15N; U-85% 2H], 0.15-0.20 mM; sodium phosphate 10 mM; sodium chloride 100 mM; Tween 20 0.005%; TCEP 0.5 mM; sodium azide 0.01%; Choline o-sulfate, [U-98% 2H], 0.5 M; H2O 95%; D2O 5%

sample_3: entity, [U-100% 13C; U-100% 15N; U-60% 2H], 0.05-0.10 mM; sodium phosphate 10 mM; sodium chloride 100 mM; Tween 20 0.005%; TCEP 0.5 mM; sodium azide 0.01%; Choline o-sulfate, [U-98% 2H], 0.5 M; H2O 95%; D2O 5%

sample_4: entity, [U-80% 2H; 100% 15N-Arg], 0.05-0.10 mM; sodium phosphate 10 mM; sodium chloride 100 mM; Tween 20 0.005%; TCEP 0.5 mM; sodium azide 0.01%; Choline o-sulfate, [U-98% 2H], 0.5 M; H2O 95%; D2O 5%

sample_5: entity, [U-80% 2H; 100% 15N-Ile], 0.05-0.10 mM; sodium phosphate 10 mM; sodium chloride 100 mM; Tween 20 0.005%; TCEP 0.5 mM; sodium azide 0.01%; Choline o-sulfate, [U-98% 2H], 0.5 M; H2O 95%; D2O 5%

sample_6: entity, [U-80% 2H; 100% 15N-Leu], 0.05-0.10 mM; sodium phosphate 10 mM; sodium chloride 100 mM; Tween 20 0.005%; TCEP 0.5 mM; sodium azide 0.01%; Choline o-sulfate, [U-98% 2H], 0.5 M; H2O 95%; D2O 5%

sample_7: entity, [U-80% 2H; 100% 15N-Lys], 0.05-0.10 mM; sodium phosphate 10 mM; sodium chloride 100 mM; Tween 20 0.005%; TCEP 0.5 mM; sodium azide 0.01%; Choline o-sulfate, [U-98% 2H], 0.5 M; H2O 95%; D2O 5%

sample_8: entity, [U-80% 2H; 100% 15N-Phe], 0.05-0.10 mM; sodium phosphate 10 mM; sodium chloride 100 mM; Tween 20 0.005%; TCEP 0.5 mM; sodium azide 0.01%; Choline o-sulfate, [U-98% 2H], 0.5 M; H2O 95%; D2O 5%

sample_9: entity, [U-80% 2H; 100% 15N-Tyr], 0.05-0.10 mM; sodium phosphate 10 mM; sodium chloride 100 mM; Tween 20 0.005%; TCEP 0.5 mM; sodium azide 0.01%; Choline o-sulfate, [U-98% 2H], 0.5 M; H2O 95%; D2O 5%

sample_10: entity, [U-80% 2H; 100% 1H, 100% 13C-Ala], 0.05-0.10 mM; sodium phosphate 10 mM; sodium chloride 100 mM; Tween 20 0.005%; TCEP 0.5 mM; sodium azide 0.01%; Choline o-sulfate, [U-98% 2H], 0.5 M; H2O 95%; D2O 5%

sample_11: entity, [U-80% 2H; 100% 1H, 100% 13C-Arg], 0.05-0.10 mM; sodium phosphate 10 mM; sodium chloride 100 mM; Tween 20 0.005%; TCEP 0.5 mM; sodium azide 0.01%; Choline o-sulfate, [U-98% 2H], 0.5 M; D2O 100%

sample_12: entity, [U-80% 2H; 100% 1H, 100% 13C-Ile], 0.05-0.10 mM; sodium phosphate 10 mM; sodium chloride 100 mM; Tween 20 0.005%; TCEP 0.5 mM; sodium azide 0.01%; Choline o-sulfate, [U-98% 2H], 0.5 M; D2O 100%

sample_13: entity, [U-80% 2H; 100% 1H, 100% 13C-Leu], 0.05-0.10 mM; sodium phosphate 10 mM; sodium chloride 100 mM; Tween 20 0.005%; TCEP 0.5 mM; sodium azide 0.01%; Choline o-sulfate, [U-98% 2H], 0.5 M; D2O 100%

sample_14: entity, [U-80% 2H; 100% 1H, 100% 13C-Lys], 0.05-0.10 mM; sodium phosphate 10 mM; sodium chloride 100 mM; Tween 20 0.005%; TCEP 0.5 mM; sodium azide 0.01%; Choline o-sulfate, [U-98% 2H], 0.5 M; D2O 100%

sample_15: entity, [U-80% 2H; 100% 1H, 100% 13C-Met], 0.05-0.10 mM; sodium phosphate 10 mM; sodium chloride 100 mM; Tween 20 0.005%; TCEP 0.5 mM; sodium azide 0.01%; Choline o-sulfate, [U-98% 2H], 0.5 M; D2O 100%

sample_16: entity, [U-80% 2H; 100% 1H, 100% 13C-Phe], 0.05-0.10 mM; sodium phosphate 10 mM; sodium chloride 100 mM; Tween 20 0.005%; TCEP 0.5 mM; sodium azide 0.01%; Choline o-sulfate, [U-98% 2H], 0.5 M; D2O 100%

sample_17: entity, [U-80% 2H; 100% 1H, 100% 13C-Thr], 0.05-0.10 mM; sodium phosphate 10 mM; sodium chloride 100 mM; Tween 20 0.005%; TCEP 0.5 mM; sodium azide 0.01%; Choline o-sulfate, [U-98% 2H], 0.5 M; D2O 100%

sample_18: entity, [U-80% 2H; 100% 1H, 100% 13C-Tyr], 0.05-0.10 mM; sodium phosphate 10 mM; sodium chloride 100 mM; Tween 20 0.005%; TCEP 0.5 mM; sodium azide 0.01%; Choline o-sulfate, [U-98% 2H], 0.5 M; D2O 100%

sample_19: entity, [U-80% 2H; 100% 1H, 100% 13C-Val], 0.05-0.10 mM; sodium phosphate 10 mM; sodium chloride 100 mM; Tween 20 0.005%; TCEP 0.5 mM; sodium azide 0.01%; Choline o-sulfate, [U-98% 2H], 0.5 M; D2O 100%

sample_20: entity, [U-80% 2H; 100% 1H-Phe,Tyr,Ile], 0.05-0.10 mM; sodium phosphate 10 mM; sodium chloride 100 mM; Tween 20 0.005%; TCEP 0.5 mM; sodium azide 0.01%; Choline o-sulfate, [U-98% 2H], 0.5 M; D2O 100%

sample_21: entity, [U-80% 2H; 100% 1H-Phe,Tyr,Leu], 0.05-0.10 mM; sodium phosphate 10 mM; sodium chloride 100 mM; Tween 20 0.005%; TCEP 0.5 mM; sodium azide 0.01%; Choline o-sulfate, [U-98% 2H], 0.5 M; D2O 100%

sample_22: entity, [U-80% 2H; 100% 1H-Phe,Tyr,Val], 0.05-0.10 mM; sodium phosphate 10 mM; sodium chloride 100 mM; Tween 20 0.005%; TCEP 0.5 mM; sodium azide 0.01%; Choline o-sulfate, [U-98% 2H], 0.5 M; D2O 100%

sample_23: entity, [U-80% 2H; 100% 1H-Trp,Ile,Leu,Val], 0.05-0.10 mM; sodium phosphate 10 mM; sodium chloride 100 mM; Tween 20 0.005%; TCEP 0.5 mM; sodium azide 0.01%; Choline o-sulfate, [U-98% 2H], 0.5 M; D2O 100%

sample_24: entity 0.15-0.20 mM; sodium phosphate 10 mM; sodium chloride 100 mM; Tween 20 0.005%; TCEP 0.5 mM; sodium azide 0.01%; Choline o-sulfate, [U-98% 2H], 0.5 M; D2O 100%

condition_1: pH: 7.3; pressure: 1 atm; temperature: 298 K

Experiments:

NameSampleSample stateSample conditions
2D 1H-15N TROSYsample_1isotropiccondition_1
3D HNCA-TROSYsample_2isotropiccondition_1
3D HN(CO)CA-TROSYsample_2isotropiccondition_1
3D HNCO-TROSYsample_2isotropiccondition_1
3D HN(CA)CO-TROSYsample_2isotropiccondition_1
3D HNCACB-TROSYsample_2isotropiccondition_1
3D HN(CO)CACB-TROSYsample_2isotropiccondition_1
3D 15N-edited NOESYsample_3isotropiccondition_1
2D 1H-15N TROSYsample_4isotropiccondition_1
2D 1H-15N TROSYsample_5isotropiccondition_1
2D 1H-15N TROSYsample_6isotropiccondition_1
2D 1H-15N TROSYsample_7isotropiccondition_1
2D 1H-15N TROSYsample_8isotropiccondition_1
2D 1H-15N TROSYsample_9isotropiccondition_1
2D 1H-13C HSQCsample_10isotropiccondition_1
2D 1H-13C HSQCsample_11isotropiccondition_1
2D 1H-13C HSQCsample_12isotropiccondition_1
2D 1H-13C HSQCsample_13isotropiccondition_1
2D 1H-13C HSQCsample_14isotropiccondition_1
2D 1H-13C HSQCsample_15isotropiccondition_1
2D 1H-13C HSQCsample_16isotropiccondition_1
2D 1H-13C HSQCsample_17isotropiccondition_1
2D 1H-13C HSQCsample_18isotropiccondition_1
2D 1H-13C HSQCsample_19isotropiccondition_1
2D 1H-1H NOESYsample_10isotropiccondition_1
2D 1H-1H NOESYsample_11isotropiccondition_1
2D 1H-1H NOESYsample_12isotropiccondition_1
2D 1H-1H NOESYsample_13isotropiccondition_1
2D 1H-1H NOESYsample_14isotropiccondition_1
2D 1H-1H NOESYsample_15isotropiccondition_1
2D 1H-1H NOESYsample_16isotropiccondition_1
2D 1H-1H NOESYsample_17isotropiccondition_1
2D 1H-1H NOESYsample_18isotropiccondition_1
2D 1H-1H NOESYsample_19isotropiccondition_1
2D 1H-1H NOESYsample_20isotropiccondition_1
2D 1H-1H NOESYsample_21isotropiccondition_1
2D 1H-1H NOESYsample_22isotropiccondition_1
2D 1H-1H NOESYsample_23isotropiccondition_1
2D 1H-1H NOESYsample_24isotropiccondition_1
3D 1H-13C NOESYsample_3isotropiccondition_1

Software:

TOPSPIN, Bruker Biospin - collection

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

SPARKY, Goddard - data analysis

TALOS, Cornilescu, Delaglio and Bax - estimation of dihedral angles

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

Molmol, Koradi, Billeter and Wuthrich - drawing structures

MacPyMol, Schrodinger - drawing structures

ProcheckNMR, Laskowski and MacArthur - evaluation of structure quality

NMR spectrometers:

  • Bruker Avance 700 MHz
  • Bruker Avance 850 MHz
  • Bruker Avance 900 MHz

Related Database Links:

PDB

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