BMRB

Biological Magnetic Resonance Data Bank


A Repository for Data from NMR Spectroscopy on Proteins, Peptides, Nucleic Acids, and other Biomolecules
Member of WWPDB

BMRB Entry 34290

Title: Hybrid structure of the pRN1 helix bundle domain in complex with DNA and 2 ATP molecules   PubMed: 30595448

Authors: Boudet, J.; Wiegand, T.; Meier, B.; Lipps, G.; Allain, F.

Citation: Boudet, J.; Devillier, J.; Wiegand, T.; Salmon, L.; Meier, B.; Lipps, G.; Allain, F.. "A Small Helical Bundle Prepares Primer Synthesis by Binding Two Nucleotides that Enhance Sequence-Specific Recognition of the DNA Template"  Cell 176, 154-166 (2019).

Assembly members:
entity_1, polymer, 9 residues, 2706.785 Da.
entity_2, polymer, 115 residues, 13528.738 Da.
entity_ATP, non-polymer, 507.181 Da.
entity_MG, non-polymer, 24.305 Da.

Natural source:   Common Name: Sulfolobus islandicus   Taxonomy ID: 43080   Superkingdom: Archaea   Kingdom: not available   Genus/species: Sulfolobus islandicus

Experimental source:   Production method: chemical synthesis

Entity Sequences (FASTA):
entity_1: CTGTGCTCA
entity_2: TVVEFEELRKELVKRDSGKP VEKIKEEICTKSPPKLIKEI ICENKTYADVNIDRSRGDWH VILYLMKHGVTDPDKILELL PRDSKAKENEKWNTQKYFVI TLSKAWSVVKKYLEA

Data sets:
Data typeCount
13C chemical shifts376
15N chemical shifts104
1H chemical shifts850

Additional metadata:

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

Assembly:

Entity Assembly IDEntity NameEntity ID
1entity_11
2entity_22
3ATP, 13
4ATP, 23
5MG, 14
6MG, 24

Entities:

Entity 1, entity_1 9 residues - 2706.785 Da.

1   DCDTDGDTDGDCDTDCDA

Entity 2, entity_2 115 residues - 13528.738 Da.

1   THRVALVALGLUPHEGLUGLULEUARGLYS
2   GLULEUVALLYSARGASPSERGLYLYSPRO
3   VALGLULYSILELYSGLUGLUILECYSTHR
4   LYSSERPROPROLYSLEUILELYSGLUILE
5   ILECYSGLUASNLYSTHRTYRALAASPVAL
6   ASNILEASPARGSERARGGLYASPTRPHIS
7   VALILELEUTYRLEUMETLYSHISGLYVAL
8   THRASPPROASPLYSILELEUGLULEULEU
9   PROARGASPSERLYSALALYSGLUASNGLU
10   LYSTRPASNTHRGLNLYSTYRPHEVALILE
11   THRLEUSERLYSALATRPSERVALVALLYS
12   LYSTYRLEUGLUALA

Entity 3, ATP, 1 - C10 H16 N5 O13 P3 - 507.181 Da.

1   ATP

Entity 4, MG, 1 - Mg - 24.305 Da.

1   MG

Samples:

sample_4: pRN1 helix bundle domain in complex with DNA and ATP, [U-99% 13C; U-99% 15N], 1.0 mM; DNA (5'-D(*CP*TP*GP*TP*GP*CP*TP*CP*A)-3') 1.0 mM; ADENOSINE-5'-TRIPHOSPHATE 4.0 mM; magnesium 10 mM

sample_5: pRN1 helix bundle domain in complex with DNA and ATP, [U-100% 13C], 0.7 mM; DNA (5'-D(*CP*TP*GP*TP*GP*CP*TP*CP*A)-3') 0.7 mM; ADENOSINE-5'-TRIPHOSPHATE 4.0 mM; magnesium 10.0 mM

sample_6: pRN1 helix bundle domain in complex with DNA and ATP, [U-99% 15N], 1.0 mM; DNA (5'-D(*CP*TP*GP*TP*GP*CP*TP*CP*A)-3') 1.0 mM; ADENOSINE-5'-TRIPHOSPHATE 4.0 mM; magnesium 10.0 mM

sample_7: DNA (5'-D(*CP*TP*GP*TP*GP*CP*TP*CP*A)-3') 1.0 mM; ADENOSINE-5'-TRIPHOSPHATE 4.0 mM; magnesium 10.0 mM; pRN1 the helix bundle domain in complex with DNA and ATP 1.0 mM

sample_8: DNA (5'-D(*CP*TP*GP*TP*GP*CP*TP*CP*A)-3') 4.0 mM; ADENOSINE-5'-TRIPHOSPHATE 10.0 mM; magnesium 10.0 mM; functional-pRN1-primase, [U-99% 13C; U-99% 15N], 4.0 mM

sample_9: pRN1 helix bundle domain in complex with DNA and ATP 1.0 mM; DNA (5'-D(*CP*TP*GP*TP*GP*CP*TP*CP*A)-3') 1.0 mM; ADENOSINE-5'-TRIPHOSPHATE 4.0 mM; magnesium 10.0 mM

sample_10: pRN1 helix bundle domain in complex with DNA and ATP, [U-100% 13C], 1.0 mM; DNA (5'-D(*CP*TP*GP*TP*GP*CP*TP*CP*A)-3') 1.0 mM; ADENOSINE-5'-TRIPHOSPHATE 4.0 mM; magnesium 10 mM

sample_conditions_1: ionic strength: 60 mM; pH: 7.0; pressure: 1 atm; temperature: 298 K

sample_conditions_2: ionic strength: 110 mM; pH: 5.0; pressure: 1 atm; temperature: 298 K

sample_conditions_3: ionic strength: 110 mM; pH: 5.0; pressure: 1 atm; temperature: 278 K

sample_conditions_4: ionic strength: 60 mM; pH: 7.0; pressure: 1 atm; temperature: 278 K

Experiments:

NameSampleSample stateSample conditions
3D HNCAsample_4isotropicsample_conditions_1
3D HN(CO)CAsample_4isotropicsample_conditions_1
3D HNCACBsample_4isotropicsample_conditions_1
3D CBCA(CO)NHsample_4isotropicsample_conditions_1
3D HNCOsample_4isotropicsample_conditions_1
3D C(CO)NHsample_4isotropicsample_conditions_1
3D H(CCO)NHsample_4isotropicsample_conditions_1
3D 1H-15N NOESYsample_4isotropicsample_conditions_1
3D 1H-13C NOESY aliphaticsample_4isotropicsample_conditions_1
3D 1H-13C NOESY aromaticsample_4isotropicsample_conditions_1
3D 1H-13C NOESY aromaticsample_5isotropicsample_conditions_1
3D 1H-15N NOESYsample_6isotropicsample_conditions_2
2D 1H-1H NOESYsample_9isotropicsample_conditions_1
2D 1H-1H TOCSYsample_9isotropicsample_conditions_1
2D 1H-1H NOESYsample_7isotropicsample_conditions_2
2D 1H-1H TOCSYsample_6isotropicsample_conditions_2
2D 1H-13C HSQC aromaticsample_5isotropicsample_conditions_1
2D 1H-13C HSQC aliphaticsample_5isotropicsample_conditions_1
2D-F1fF2f-NOESYsample_5isotropicsample_conditions_1
2D-F2f-NOESYsample_5isotropicsample_conditions_1
3D-13C-aliphatic-HfilteredHedited-NOESYsample_5isotropicsample_conditions_1
3D-13C-aliphatic-HfilteredHedited-NOESYsample_5isotropicsample_conditions_1
3D-13C-aromatic-HfilteredHedited-NOESYsample_10isotropicsample_conditions_2
3D-13C-aromatic-HfilteredHedited-NOESYsample_10isotropicsample_conditions_2
2D-imino-NOESYsample_7isotropicsample_conditions_3
2D-natural-abundance-Chsqcsample_7isotropicsample_conditions_1
DARRsample_8isotropicsample_conditions_4
NCX(R)sample_8isotropicsample_conditions_4
NCX(W)sample_8isotropicsample_conditions_4
CHHPsample_8isotropicsample_conditions_4
NHHPsample_8isotropicsample_conditions_4
31P CPMASsample_8isotropicsample_conditions_4
31P-31P-DARRsample_8isotropicsample_conditions_4
31P CPMASsample_8isotropicsample_conditions_4
2D 1H-15N HSQCsample_4isotropicsample_conditions_1
2D 1H-15N HSQCsample_4isotropicsample_conditions_2

Software:

CYANA, Guntert P. - structure calculation

SPARKY, Goddard - chemical shift assignment, data analysis

MARS, Jung and Zweckstetter - chemical shift assignment

CANDID, Herrmann, Guntert and Wuthrich - peak picking

AMBER, Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollman - refinement

TOPSPIN, Bruker Biospin - collection, processing

CcpNMR, CCPN - data analysis

NMR spectrometers:

  • Bruker AVANCE III HD 900 MHz
  • Bruker AVANCE III 700 MHz
  • Bruker AVANCE III 600 MHz
  • Bruker AVANCE III 850 MHz
  • Bruker AVANCE III 500 MHz

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