BMRB Entry 34290

Name: Hybrid structure of the pRN1 helix bundle domain in complex with DNA and 2 ATP molecules
Published: 2018-12-19

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PDB ID: 6gvt
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full, LACS
BMRB Entry DOI: doi:10.13018/BMR34290
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Nicholas Rego and David Koes
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Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

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

Deposition date: 2018-06-21 Original release date: 2018-12-19

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:

assigned_chemical_shifts
- assigned_chemical_shifts_1

Data type	Count
13C chemical shifts	376
15N chemical shifts	104
1H chemical shifts	850

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Entity Assembly ID	Entity Name	Entity ID
1	entity_1	1
2	entity_2	2
3	ATP, 1	3
4	ATP, 2	3
5	MG, 1	4
6	MG, 2	4

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:

Name	Sample	Sample state	Sample conditions
3D HNCA	sample_4	isotropic	sample_conditions_1
3D HN(CO)CA	sample_4	isotropic	sample_conditions_1
3D HNCACB	sample_4	isotropic	sample_conditions_1
3D CBCA(CO)NH	sample_4	isotropic	sample_conditions_1
3D HNCO	sample_4	isotropic	sample_conditions_1
3D C(CO)NH	sample_4	isotropic	sample_conditions_1
3D H(CCO)NH	sample_4	isotropic	sample_conditions_1
3D 1H-15N NOESY	sample_4	isotropic	sample_conditions_1
3D 1H-13C NOESY aliphatic	sample_4	isotropic	sample_conditions_1
3D 1H-13C NOESY aromatic	sample_4	isotropic	sample_conditions_1
3D 1H-13C NOESY aromatic	sample_5	isotropic	sample_conditions_1
3D 1H-15N NOESY	sample_6	isotropic	sample_conditions_2
2D 1H-1H NOESY	sample_9	isotropic	sample_conditions_1
2D 1H-1H TOCSY	sample_9	isotropic	sample_conditions_1
2D 1H-1H NOESY	sample_7	isotropic	sample_conditions_2
2D 1H-1H TOCSY	sample_6	isotropic	sample_conditions_2
2D 1H-13C HSQC aromatic	sample_5	isotropic	sample_conditions_1
2D 1H-13C HSQC aliphatic	sample_5	isotropic	sample_conditions_1
2D-F1fF2f-NOESY	sample_5	isotropic	sample_conditions_1
2D-F2f-NOESY	sample_5	isotropic	sample_conditions_1
3D-13C-aliphatic-HfilteredHedited-NOESY	sample_5	isotropic	sample_conditions_1
3D-13C-aliphatic-HfilteredHedited-NOESY	sample_5	isotropic	sample_conditions_1
3D-13C-aromatic-HfilteredHedited-NOESY	sample_10	isotropic	sample_conditions_2
3D-13C-aromatic-HfilteredHedited-NOESY	sample_10	isotropic	sample_conditions_2
2D-imino-NOESY	sample_7	isotropic	sample_conditions_3
2D-natural-abundance-Chsqc	sample_7	isotropic	sample_conditions_1
DARR	sample_8	isotropic	sample_conditions_4
NCX(R)	sample_8	isotropic	sample_conditions_4
NCX(W)	sample_8	isotropic	sample_conditions_4
CHHP	sample_8	isotropic	sample_conditions_4
NHHP	sample_8	isotropic	sample_conditions_4
31P CPMAS	sample_8	isotropic	sample_conditions_4
31P-31P-DARR	sample_8	isotropic	sample_conditions_4
31P CPMAS	sample_8	isotropic	sample_conditions_4
2D 1H-15N HSQC	sample_4	isotropic	sample_conditions_1
2D 1H-15N HSQC	sample_4	isotropic	sample_conditions_2

Download simulated HSQC data in one of the following formats:
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SPARKY: Backbone or all simulated shifts

Biological Magnetic Resonance Data Bank

BMRB Entry 34290

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

Additional metadata:

Assembly:

Entities:

Samples:

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Software:

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