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- PDB-6rb4: Crystal structure of the Pri1 subunit of human primase -

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Basic information

Entry
Database: PDB / ID: 6rb4
TitleCrystal structure of the Pri1 subunit of human primase
ComponentsDNA primase small subunit
KeywordsREPLICATION / Primase / DNA-dependent RNA polymerase / ATP / priming
Function / homology
Function and homology information


DNA primase AEP / ribonucleotide binding / DNA replication initiation / Telomere C-strand synthesis initiation / Inhibition of replication initiation of damaged DNA by RB1/E2F1 / alpha DNA polymerase:primase complex / Polymerase switching / Processive synthesis on the lagging strand / : / primosome complex ...DNA primase AEP / ribonucleotide binding / DNA replication initiation / Telomere C-strand synthesis initiation / Inhibition of replication initiation of damaged DNA by RB1/E2F1 / alpha DNA polymerase:primase complex / Polymerase switching / Processive synthesis on the lagging strand / : / primosome complex / Removal of the Flap Intermediate / DNA replication, synthesis of primer / Polymerase switching on the C-strand of the telomere / Activation of the pre-replicative complex / DNA replication initiation / Defective pyroptosis / magnesium ion binding / zinc ion binding / nucleoplasm / membrane
Similarity search - Function
DNA primase, PRIM domain / DNA primase, PRIM domain / DNA primase, small subunit, eukaryotic/archaeal / DNA primase, small subunit / DNA primase small subunit / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
DNA primase small subunit
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsKilkenny, M.L. / Pellegrini, L.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Wellcome TrustRG74868 United Kingdom
CitationJournal: Acs Chem.Biol. / Year: 2019
Title: Structural Basis for Inhibition of Human Primase by Arabinofuranosyl Nucleoside Analogues Fludarabine and Vidarabine.
Authors: Holzer, S. / Rzechorzek, N.J. / Short, I.R. / Jenkyn-Bedford, M. / Pellegrini, L. / Kilkenny, M.L.
History
DepositionApr 9, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 11, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 2, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DNA primase small subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,0346
Polymers48,7211
Non-polymers3145
Water8,377465
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area760 Å2
ΔGint11 kcal/mol
Surface area18530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.659, 78.659, 148.335
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein DNA primase small subunit / DNA primase 49 kDa subunit / p49


Mass: 48720.516 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PRIM1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta2
References: UniProt: P49642, Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 465 / 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: 1

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Sample preparation

CrystalDensity Matthews: 2.35 Å3/Da / Density % sol: 47.76 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop
Details: 100mM Bis Tris propane pH 6.5, 24 % PEG 3350, 150 mM NaF

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.98011 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 13, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98011 Å / Relative weight: 1
ReflectionResolution: 1.5→44.5 Å / Num. obs: 75113 / % possible obs: 99.89 % / Redundancy: 2 % / CC1/2: 1 / Rrim(I) all: 0.02722 / Net I/σ(I): 15.76
Reflection shellResolution: 1.5→1.554 Å / Redundancy: 2 % / Rmerge(I) obs: 0.5433 / Mean I/σ(I) obs: 1.49 / Num. unique obs: 7355 / CC1/2: 0.655 / % possible all: 99.35

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
XDSdata reduction
Cootmodel building
PHENIXrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4BPU

4bpu


Resolution: 1.5→44.498 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.96
RfactorNum. reflection% reflection
Rfree0.2148 3785 5.04 %
Rwork0.1929 --
obs0.1941 75090 99.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.5→44.498 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3260 0 17 465 3742
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.013485
X-RAY DIFFRACTIONf_angle_d0.8444717
X-RAY DIFFRACTIONf_dihedral_angle_d12.9622111
X-RAY DIFFRACTIONf_chiral_restr0.055492
X-RAY DIFFRACTIONf_plane_restr0.007608
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.5190.41781520.37172558X-RAY DIFFRACTION98
1.519-1.5390.37241310.36482592X-RAY DIFFRACTION100
1.539-1.56010.39591200.32852604X-RAY DIFFRACTION100
1.5601-1.58240.32621180.31262617X-RAY DIFFRACTION100
1.5824-1.6060.29421510.28842606X-RAY DIFFRACTION100
1.606-1.63110.35261430.28412598X-RAY DIFFRACTION100
1.6311-1.65780.27491370.27212596X-RAY DIFFRACTION100
1.6578-1.68640.28051340.27112624X-RAY DIFFRACTION100
1.6864-1.71710.32111350.2592611X-RAY DIFFRACTION100
1.7171-1.75010.28511550.25942611X-RAY DIFFRACTION100
1.7501-1.78580.24881230.24672623X-RAY DIFFRACTION100
1.7858-1.82460.29751430.23842603X-RAY DIFFRACTION100
1.8246-1.86710.25341390.24522632X-RAY DIFFRACTION100
1.8671-1.91380.29791370.23332620X-RAY DIFFRACTION100
1.9138-1.96550.25971500.23262612X-RAY DIFFRACTION100
1.9655-2.02340.25671360.21512624X-RAY DIFFRACTION100
2.0234-2.08870.2361350.20152622X-RAY DIFFRACTION100
2.0887-2.16330.23831380.1992642X-RAY DIFFRACTION100
2.1633-2.24990.24571270.19722658X-RAY DIFFRACTION100
2.2499-2.35230.20471430.18382629X-RAY DIFFRACTION100
2.3523-2.47630.20031390.18342679X-RAY DIFFRACTION100
2.4763-2.63150.20471660.17722617X-RAY DIFFRACTION100
2.6315-2.83460.2171430.17692669X-RAY DIFFRACTION100
2.8346-3.11980.20291440.17452686X-RAY DIFFRACTION100
3.1198-3.57110.19831520.16732718X-RAY DIFFRACTION100
3.5711-4.49850.16151450.14452740X-RAY DIFFRACTION100
4.4985-44.51750.15751490.17812914X-RAY DIFFRACTION100

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