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: 6gvq
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full, LACS
BMRB Entry DOI: doi:10.13018/BMR34290
MolProbity Validation Chart

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Nicholas Rego and David Koes
3Dmol.js: molecular visualization with WebGL
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

Deposition date:

2018-06-21

Original release date:

2018-12-19

Authors:

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

Citation:

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).
PubMed: 30595448

Assembly members:

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:

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

Experimental source:

Experimental source: Production method: chemical synthesis

Entity Sequences (FASTA):

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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Assembly:

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

Entities:

Entity 1, entity_1 9 residues - 2706.785 Da.

1

DC

DT

DG

DT

DG

DC

DT

DC

DA

Entity 2, entity_2 115 residues - 13528.738 Da.

1

THR

VAL

GLU

PHE

GLU

LEU

ARG

LYS

2

GLU

LEU

VAL

LYS

ARG

ASP

SER

GLY

LYS

PRO

3

VAL

GLU

LYS

ILE

LYS

GLU

ILE

CYS

THR

4

LYS

SER

PRO

LYS

LEU

ILE

LYS

GLU

ILE

5

ILE

CYS

GLU

ASN

LYS

THR

TYR

ALA

ASP

VAL

6

ASN

ILE

ASP

ARG

SER

ARG

GLY

ASP

TRP

HIS

7

VAL

ILE

LEU

TYR

LEU

MET

LYS

HIS

GLY

VAL

8

THR

ASP

PRO

ASP

LYS

ILE

LEU

GLU

LEU

9

PRO

ARG

ASP

SER

LYS

ALA

LYS

GLU

ASN

GLU

10

LYS

TRP

ASN

THR

GLN

LYS

TYR

PHE

VAL

ILE

11

THR

LEU

SER

LYS

ALA

TRP

SER

VAL

LYS

12

LYS

TYR

LEU

GLU

ALA

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:

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

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

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