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- PDB-6dgd: PriA helicase bound to dsDNA of a DNA replication fork -

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Basic information

Entry
Database: PDB / ID: 6dgd
TitlePriA helicase bound to dsDNA of a DNA replication fork
Components
  • DNA (5'-D(P*AP*GP*CP*AP*CP*GP*CP*CP*GP*AP*CP*T)-3')
  • DNA (5'-D(P*GP*AP*GP*CP*AP*CP*GP*CP*CP*GP*AP*CP*T)-3')
  • DNA (5'-D(P*GP*TP*CP*GP*GP*CP*GP*TP*GP*CP*TP*C)-3')
  • Primosomal protein N'
KeywordsDNA BINDING PROTEIN/DNA / DNA replication restart / PriA helicase / DNA replication fork binding / dsDNA / leading arm / DNA BINDING PROTEIN / DNA BINDING PROTEIN-DNA complex
Function / homology
Function and homology information


primosome complex / DNA replication, synthesis of primer / DNA unwinding involved in DNA replication / DNA helicase activity / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / hydrolase activity / DNA binding / zinc ion binding / ATP binding
Similarity search - Function
Primosomal protein N' / PriA DNA helicase, Cys-rich region (CRR) domain / Primosomal protein N', 3' DNA-binding domain / Primosomal protein N, C-terminal domain / Primosomal protein N', 3' DNA-binding domain superfamily / 3'DNA-binding domain (3'BD) / Primosomal protein N C-terminal domain / PriA DNA helicase Cys-rich region (CRR) domain / DEAD/DEAH box helicase / DEAD/DEAH box helicase domain ...Primosomal protein N' / PriA DNA helicase, Cys-rich region (CRR) domain / Primosomal protein N', 3' DNA-binding domain / Primosomal protein N, C-terminal domain / Primosomal protein N', 3' DNA-binding domain superfamily / 3'DNA-binding domain (3'BD) / Primosomal protein N C-terminal domain / PriA DNA helicase Cys-rich region (CRR) domain / DEAD/DEAH box helicase / DEAD/DEAH box helicase domain / helicase superfamily c-terminal domain / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
DNA / DNA (> 10) / Primosomal protein N'
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.823 Å
AuthorsSatyshur, K.A. / Windgassen, T.A. / Keck, J.L.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01 GM098885 United States
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2018
Title: Structure-specific DNA replication-fork recognition directs helicase and replication restart activities of the PriA helicase.
Authors: Windgassen, T.A. / Leroux, M. / Satyshur, K.A. / Sandler, S.J. / Keck, J.L.
History
DepositionMay 17, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 5, 2018Provider: repository / Type: Initial release
Revision 1.1Sep 19, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Oct 10, 2018Group: Data collection / Database references / Structure summary
Category: citation / entity
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _entity.formula_weight
Revision 1.3Jan 1, 2020Group: Author supporting evidence / Structure summary / Category: entity / pdbx_audit_support
Item: _entity.formula_weight / _pdbx_audit_support.funding_organization
Revision 1.4Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_radiation_wavelength.wavelength

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Primosomal protein N'
B: Primosomal protein N'
W: DNA (5'-D(P*AP*GP*CP*AP*CP*GP*CP*CP*GP*AP*CP*T)-3')
X: DNA (5'-D(P*GP*TP*CP*GP*GP*CP*GP*TP*GP*CP*TP*C)-3')
Y: DNA (5'-D(P*GP*AP*GP*CP*AP*CP*GP*CP*CP*GP*AP*CP*T)-3')
Z: DNA (5'-D(P*GP*TP*CP*GP*GP*CP*GP*TP*GP*CP*TP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)183,64423
Polymers182,1346
Non-polymers1,51017
Water362
1
A: Primosomal protein N'
W: DNA (5'-D(P*AP*GP*CP*AP*CP*GP*CP*CP*GP*AP*CP*T)-3')
X: DNA (5'-D(P*GP*TP*CP*GP*GP*CP*GP*TP*GP*CP*TP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,80213
Polymers90,9023
Non-polymers89910
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Primosomal protein N'
Y: DNA (5'-D(P*GP*AP*GP*CP*AP*CP*GP*CP*CP*GP*AP*CP*T)-3')
Z: DNA (5'-D(P*GP*TP*CP*GP*GP*CP*GP*TP*GP*CP*TP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,84310
Polymers91,2323
Non-polymers6117
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)100.560, 106.760, 256.830
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Primosomal protein N' / ATP-dependent helicase PriA


Mass: 83599.625 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Gene: priA, B1727_25905, CPT10_21250, SAMEA3304003_04572 / Plasmid: pET28-K.pneumoniae PriA / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2
References: UniProt: A0A1W2ITH4, Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement

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DNA chain , 3 types, 4 molecules WXZY

#2: DNA chain DNA (5'-D(P*AP*GP*CP*AP*CP*GP*CP*CP*GP*AP*CP*T)-3')


Mass: 3632.382 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (5'-D(P*GP*TP*CP*GP*GP*CP*GP*TP*GP*CP*TP*C)-3')


Mass: 3670.377 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: DNA chain DNA (5'-D(P*GP*AP*GP*CP*AP*CP*GP*CP*CP*GP*AP*CP*T)-3')


Mass: 3961.588 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 3 types, 19 molecules

#5: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#6: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: SO4
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 4

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Sample preparation

Crystal
IDDensity Matthews (Å3/Da)Density % sol (%)
13.7867.5
2
3
4
Crystal grow
Temperature (K)Crystal-IDMethodpHDetails
2931vapor diffusion, hanging drop5.685 mM sodium citrate-NaOH pH 5.60, 0.25 M ammonium suflate, 0.75 M lithium sulfate, and 4 % glycerol
2932vapor diffusion, hanging drop5.685 mM sodium citrate-NaOH pH 5.60, 0.25 M ammonium suflate, 0.8 M lithium sulfate, 4 % glycerol, 5 mM spermidine tetrahydrochloride, 20 mM praseodymium III acetate hydrate
2933vapor diffusion, hanging drop5.685 mM sodium citrate-NaOH pH 5.60, 0.25 M ammonium suflate, 0.75 M lithium sulfate, 4 % glycerol, 5 mM spermidine tetrahydrochloride, and 0.1-0.2 mM adenosine diphosphate
2934vapor diffusion, hanging drop5.685 mM sodium citrate-NaOH pH 5.60, 0.25 M ammonium suflate, 0.75 M lithium sulfate, 4 % glycerol, 5 mM spermidine tetrahydrochloride, and 0.1-0.2 mM potassium chloride

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21002
31003
41004
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONAPS 21-ID-D11.1271295
SYNCHROTRONAPS 21-ID-D21.1271295
SYNCHROTRONAPS 21-ID-D31.1271997
SYNCHROTRONAPS 21-ID-D41.1271997
Detector
TypeIDDetectorDate
DECTRIS EIGER X 9M1PIXELNov 26, 2016
DECTRIS EIGER X 9M2PIXELNov 26, 2016
DECTRIS EIGER X 9M3PIXELJun 25, 2016
DECTRIS EIGER X 9M4PIXELJun 25, 2016
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray2
3SINGLE WAVELENGTHMx-ray3
4SINGLE WAVELENGTHMx-ray4
Radiation wavelength
IDWavelength (Å)Relative weight
11.12712951
21.12719971
31
41
Reflection

Entry-ID: 6DGD / CC1/2: 0.999

Resolution (Å)Num. obs% possible obs (%)Redundancy (%)Rmerge(I) obsRrim(I) allDiffraction-IDNet I/σ(I)
2.823-49.3436696898.637.90.21540.2183111.93
2.83-49.4966262794.114.50.107213.64
2.81-49.876692498.513.40.097316.87
3-49.325544998.813.3413.53
Reflection shell
Resolution (Å)Redundancy (%)Mean I/σ(I) obsNum. unique obsCC1/2Rrim(I) allDiffraction-ID% possible all
2.823-2.92424.60.7562760.5783.78186.57
2.83-2.9114.50.6744480.5834.102291.2
2.81-2.8910.70.739960.4583.237380.6
3-3.0810.70.6334480.2664.283484.4

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4NL4 removing the winged helix domain

4nl4


Resolution: 2.823→49.343 Å / SU ML: 0.45 / Cross valid method: FREE R-VALUE / Phase error: 36.26
RfactorNum. reflection% reflection
Rfree0.2899 1999 -
Rwork0.2475 --
obs-66476 98.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.823→49.343 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10577 1000 69 2 11648
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01312108
X-RAY DIFFRACTIONf_angle_d1.13416655
X-RAY DIFFRACTIONf_dihedral_angle_d13.6366908
X-RAY DIFFRACTIONf_chiral_restr0.0651897
X-RAY DIFFRACTIONf_plane_restr0.0071983
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.823-2.8920.50161740.45045884X-RAY DIFFRACTION89.06
2.8937-2.97190.44881360.39074588X-RAY DIFFRACTION100
2.9719-3.05930.39131520.34874607X-RAY DIFFRACTION100
3.0593-3.15810.3671350.32564598X-RAY DIFFRACTION100
3.1581-3.27090.38661400.30374586X-RAY DIFFRACTION100
3.2709-3.40180.32851480.28054610X-RAY DIFFRACTION100
3.4018-3.55660.3031420.27064639X-RAY DIFFRACTION100
3.5566-3.74410.31041370.26334624X-RAY DIFFRACTION100
3.7441-3.97860.30751540.25284641X-RAY DIFFRACTION100
3.9786-4.28560.27871520.22744656X-RAY DIFFRACTION100
4.2856-4.71660.28021400.21044662X-RAY DIFFRACTION100
4.7166-5.39830.25121390.23474686X-RAY DIFFRACTION100
5.3983-6.79850.29731470.26964759X-RAY DIFFRACTION100
6.7985-49.3430.2641520.20254932X-RAY DIFFRACTION100

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