BMRB Entry 35007

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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/BMR35007
MolProbity Validation Chart

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NMR-STAR v3 text file.
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Title:
Hydrid structure of the helix bundle domain of pRN1 primase in complex with DNA, ATP and dGTP
Deposition date:
2025-07-02
Original release date:
2026-03-18
Authors:
Wu, P.; Damberger, F.; Zehnder, J.; Schroder, N.; Lipps, G.; Wiegand, T.; Allain, F.H.
Citation:

Citation: Wu, P.; Damberger, F.; Zehnder, J.; Schroder, N.; Lipps, G.; Wiegand, T.; Allain, F.H.. "Molecular Basis for Primer Synthesis Initiation by DNA Primase"  .

Assembly members:

Assembly members:
entity_1, polymer, 118 residues, 13855.133 Da.
entity_2, polymer, 9 residues, 2706.785 Da.
entity_DGT, non-polymer, 507.181 Da.
entity_ATP, non-polymer, 507.181 Da.
entity_MG, non-polymer, 24.305 Da.

Natural source:

Natural source:   Common Name: Saccharolobus islandicus   Taxonomy ID: 43080   Superkingdom: Archaea   Kingdom: Thermoproteati   Genus/species: Saccharolobus islandicus

Experimental source:

Experimental source:   Production method: recombinant technology   Host organism: Escherichia coli BL21(DE3)

Entity Sequences (FASTA):

Entity Sequences (FASTA):
entity_1: GHMTVVEFEELRKELVKRDS GKPVEKIKEEICTKSPPKLI KEIICENKTYADVNIDRSRG DWHVILYLMKHGVTDPDKIL ELLPRDSKAKENEKWNTQKY FVITLSKAWSVVKKYLEA
entity_2: CTGTGCTCA

Data sets:
Data typeCount
13C chemical shifts562
15N chemical shifts124
1H chemical shifts995

Additional metadata:

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

Assembly:

Entity Assembly IDEntity NameEntity ID
1unit_11
2unit_22
3unit_33
4unit_44
5unit_55
6unit_65

Entities:

Entity 1, unit_1 118 residues - 13855.133 Da.

1   GLYHISMETTHRVALVALGLUPHEGLUGLU
2   LEUARGLYSGLULEUVALLYSARGASPSER
3   GLYLYSPROVALGLULYSILELYSGLUGLU
4   ILECYSTHRLYSSERPROPROLYSLEUILE
5   LYSGLUILEILECYSGLUASNLYSTHRTYR
6   ALAASPVALASNILEASPARGSERARGGLY
7   ASPTRPHISVALILELEUTYRLEUMETLYS
8   HISGLYVALTHRASPPROASPLYSILELEU
9   GLULEULEUPROARGASPSERLYSALALYS
10   GLUASNGLULYSTRPASNTHRGLNLYSTYR
11   PHEVALILETHRLEUSERLYSALATRPSER
12   VALVALLYSLYSTYRLEUGLUALA

Entity 2, unit_2 9 residues - 2706.785 Da.

1   DCDTDGDTDGDCDTDCDA

Entity 3, unit_3 - C10 H16 N5 O13 P3 - 507.181 Da.

1   DGT

Entity 4, unit_4 - C10 H16 N5 O13 P3 - 507.181 Da.

1   ATP

Entity 5, unit_5 - Mg - 24.305 Da.

1   MG

Samples:

sample_1: DNA 0.96 mM; HBD, [U-99% 13C; U-99% 15N], 0.8 mM; AppCp 2.4 mM; dGppCp 2.4 mM; Mg2+ 10 mM

sample_2: DNA 1 mM; HBD, [U-99% 13C; U-99% 15N], 1 mM; AppCp 1.2 mM; dGppCp 1.2 mM; Mg2+ 10 mM

sample_3: DNA 10.8 mM; HBD, [U-99% 13C; U-99% 15N], 0.8 mM; AppCp 1.6 mM; dGppCp 1.6 mM; Mg2+ 10 mM

sample_4: DNA 1.1 mM; HBD, [U-99% 13C; U-99% 15N], 1 mM; AppCp 1.2 mM; dGppCp 1.2 mM; Mg2+ 10 mM

sample_5: DNA 1 mM; HBD 1 mM; AppCp 2 mM; dGppCp 2 mM; Mg2+ 10 mM

sample_6: DNA 1 mM; HBD 1 mM; AppCp 1.2 mM; dGppCp 1.2 mM; Mg2+ 10 mM

sample_7: DNA 0.254 mM; dGppCp 0.924 mM; Mg2+ 10 mM; pRN1 primase H145A, [U-100% 15N; U-80% 2H], 0.231 mM; AppNHp 0.924 mM

sample_8: DNA 4 mM; HBD 4 mM; AppCp 4 mM; dGppCp 4 mM; Mg2+ 10 mM

sample_9: DNA 2.5 mM; AppCp 4.6 mM; dGppCp 4.6 mM; Mg2+ 10 mM; pRN1 primase H145A, [U-100% 13C; U-100% 15N], 2.3 mM

sample_10: DNA 0.254 mM; dGppCp 0.924 mM; Mg2+ 10 mM; AppNHp 0.924 mM; pRN1 primase, [U-15N; U-2H], 0.231 mM

sample_conditions_1: ionic strength: 100 mM; pH: 7.0; pressure: 1 atm; temperature: 298 K

sample_conditions_2: ionic strength: 75 mM; pH: 7.0; pressure: 1 atm; temperature: 298 K

sample_conditions_3: ionic strength: 50 mM; pH: 7.0; pressure: 1 atm; temperature: 298 K

sample_conditions_4: ionic strength: 120 mM; pH: 7.0; pressure: 1 atm; temperature: 298 K

sample_conditions_5: ionic strength: 50 mM; pH: 7.0; pressure: 1 atm; temperature: 278 K

Experiments:

NameSampleSample stateSample conditions
3D HNCAsample_1isotropicsample_conditions_1
3D HN(CA)COsample_1isotropicsample_conditions_1
3D HN(CO)CAsample_1isotropicsample_conditions_1
3D HNCACBsample_1isotropicsample_conditions_1
3D CBCA(CO)NHsample_1isotropicsample_conditions_1
3D HNCOsample_1isotropicsample_conditions_1
3D C(CO)NHsample_1isotropicsample_conditions_1
3D H(CCO)NHsample_1isotropicsample_conditions_1
3D 1H-15N NOESYsample_1isotropicsample_conditions_1
3D 1H-13C NOESY aliphaticsample_4isotropicsample_conditions_2
3D 1H-13C NOESY aliphaticsample_3isotropicsample_conditions_1
3D 1H-13C NOESY aromaticsample_3isotropicsample_conditions_1
3D 1H-13C NOESY aromaticsample_4isotropicsample_conditions_2
2D 1H-13C HSQC aromaticsample_3isotropicsample_conditions_1
2D 1H-13C HSQC aliphaticsample_3isotropicsample_conditions_1
2D-F1fF2f-NOESYsample_2isotropicsample_conditions_2
2D-F2f-NOESYsample_2isotropicsample_conditions_2
3D-13C-aliphatic-HfilteredHedited-NOESYsample_3isotropicsample_conditions_1
3D-13C-aromatic-HfilteredHedited-NOESYsample_3isotropicsample_conditions_1
2D-imino-NOESYsample_5isotropicsample_conditions_2
2D-natural-abundance-Nhsqcsample_8isotropicsample_conditions_4
2D-natural-abundance-Chsqc-aliphaticsample_6isotropicsample_conditions_2
2D-natural-abundance-Chsqc-aromaticsample_6isotropicsample_conditions_2
2D 1H-15N HSQCsample_1isotropicsample_conditions_1
2D 1H-15N HSQCsample_3isotropicsample_conditions_1
CHHPsample_9isotropicsample_conditions_5
NHHPsample_9isotropicsample_conditions_5
hPHsample_7isotropicsample_conditions_5
hPHsample_10isotropicsample_conditions_5

Software:

CYANA v3.98.15, Guntert, Mumenthaler and Wuthrich - structure calculation

NMRFAM-SPARKY v1.470, Goddard - chemical shift assignment, data analysis

CANDID, Herrmann, Guntert and Wuthrich - peak picking

Amber v20, Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollman - refinement

TopSpin v4.0.7, Bruker Biospin - collection, processing

NMR spectrometers:

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