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- PDB-4bpw: Crystal structure of human primase bound to UTP -

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Basic information

Entry
Database: PDB / ID: 4bpw
TitleCrystal structure of human primase bound to UTP
Components
  • DNA PRIMASE LARGE SUBUNITPrimase
  • DNA PRIMASE SMALL SUBUNITPrimase
KeywordsTRANSFERASE / DNA-DEPENDENT RNA POLYMERASE / DNA REPLICATION
Function / homology
Function and homology information


DNA primase AEP / positive regulation of DNA primase activity / ribonucleotide binding / DNA replication initiation / DNA/RNA hybrid binding / Telomere C-strand synthesis initiation / Inhibition of replication initiation of damaged DNA by RB1/E2F1 / Polymerase switching / Processive synthesis on the lagging strand / alpha DNA polymerase:primase complex ...DNA primase AEP / positive regulation of DNA primase activity / ribonucleotide binding / DNA replication initiation / DNA/RNA hybrid binding / Telomere C-strand synthesis initiation / Inhibition of replication initiation of damaged DNA by RB1/E2F1 / Polymerase switching / Processive synthesis on the lagging strand / alpha DNA polymerase:primase complex / Removal of the Flap Intermediate / DNA primase activity / Polymerase switching on the C-strand of the telomere / DNA replication, synthesis of primer / DNA replication initiation / Activation of the pre-replicative complex / Defective pyroptosis / 4 iron, 4 sulfur cluster binding / magnesium ion binding / DNA binding / zinc ion binding / nucleoplasm / membrane / metal ion binding
Similarity search - Function
Transcription Elongation Factor S-II; Chain A - #80 / DNA primase, PRIM domain / DNA primase, PRIM domain / DNA primase, small subunit, eukaryotic/archaeal / DNA primase, large subunit, eukaryotic / DNA primase, small subunit / DNA primase small subunit / DNA primase large subunit, eukaryotic/archaeal / Eukaryotic and archaeal DNA primase, large subunit / Transcription Elongation Factor S-II; Chain A ...Transcription Elongation Factor S-II; Chain A - #80 / DNA primase, PRIM domain / DNA primase, PRIM domain / DNA primase, small subunit, eukaryotic/archaeal / DNA primase, large subunit, eukaryotic / DNA primase, small subunit / DNA primase small subunit / DNA primase large subunit, eukaryotic/archaeal / Eukaryotic and archaeal DNA primase, large subunit / Transcription Elongation Factor S-II; Chain A / Alpha-Beta Complex / Up-down Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
URIDINE 5'-TRIPHOSPHATE / DNA primase small subunit / DNA primase large subunit
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 3.003 Å
AuthorsKilkenny, M.L. / Perera, R.L. / Pellegrini, L.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2013
Title: Structures of Human Primase Reveal Design of Nucleotide Elongation Site and Mode of Pol Alpha Tethering
Authors: Kilkenny, M.L. / Longo, M.A. / Perera, R.L. / Pellegrini, L.
History
DepositionMay 28, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 25, 2013Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2013Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DNA PRIMASE SMALL SUBUNIT
B: DNA PRIMASE LARGE SUBUNIT
C: DNA PRIMASE SMALL SUBUNIT
D: DNA PRIMASE LARGE SUBUNIT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)160,97712
Polymers159,7804
Non-polymers1,1968
Water0
1
A: DNA PRIMASE SMALL SUBUNIT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,7065
Polymers50,1081
Non-polymers5984
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
C: DNA PRIMASE SMALL SUBUNIT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,7065
Polymers50,1081
Non-polymers5984
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
B: DNA PRIMASE LARGE SUBUNIT


Theoretical massNumber of molelcules
Total (without water)29,7821
Polymers29,7821
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: DNA PRIMASE LARGE SUBUNIT


Theoretical massNumber of molelcules
Total (without water)29,7821
Polymers29,7821
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)116.394, 69.438, 127.087
Angle α, β, γ (deg.)90.00, 104.90, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
22
/ NCS ensembles :
ID
1
2

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Components

#1: Protein DNA PRIMASE SMALL SUBUNIT / Primase / PRIMASE / DNA PRIMASE 49 KDA SUBUNIT / P49


Mass: 50108.023 Da / Num. of mol.: 2 / Fragment: PRIS / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): ROSETTA2
References: UniProt: P49642, Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases
#2: Protein DNA PRIMASE LARGE SUBUNIT / Primase / PRIMASE / DNA PRIMASE 58 KDA SUBUNIT / P58


Mass: 29782.174 Da / Num. of mol.: 2 / Fragment: PRIL, RESIDUES 1-253
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): ROSETTA2
References: UniProt: P49643, Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-UTP / URIDINE 5'-TRIPHOSPHATE / Uridine triphosphate


Mass: 484.141 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H15N2O15P3 / Comment: UTP*YM

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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: 3.5 Å3/Da / Density % sol: 65 % / Description: NONE
Crystal growDetails: 100MM TRIS-HCL/BICINE PH 8.5, 20% GLYCEROL, 10% PEG4000 AND 20MM EACH OF AN ALCOHOL MIX COMPRISING 1,6-HEXANEDIOL, 1-BUTANOL, 1,2-PROPANEDIOL, 2-PROPANOL, 1,4-BUTANEDIOL AND 1,3-PROPANEDIOL.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795
DetectorType: ADSC CCD / Detector: CCD / Date: Sep 17, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 3→48.87 Å / Num. obs: 39304 / % possible obs: 99.3 % / Observed criterion σ(I): 0 / Redundancy: 4.8 % / Biso Wilson estimate: 105.46 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 18.5
Reflection shellResolution: 3→3.13 Å / Redundancy: 4.8 % / Rmerge(I) obs: 1.5 / Mean I/σ(I) obs: 1.2 / % possible all: 98.6

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
Aimlessdata scaling
RefinementMethod to determine structure: OTHER
Starting model: NONE

Resolution: 3.003→46.784 Å / SU ML: 0.5 / σ(F): 1.27 / Phase error: 32.12 / Stereochemistry target values: ML
Details: THE STRUCTURE WAS REFINED IN PHENIX WITH RIDING HYDROGENS. THE HYDROGENS HAVE BEEN INCLUDED IN THE ENTRY.
RfactorNum. reflection% reflection
Rfree0.2534 3832 5.1 %
Rwork0.2152 --
obs0.2172 39252 98.28 %
Solvent computationShrinkage radii: 1.1 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 94.6 Å2
Refinement stepCycle: LAST / Resolution: 3.003→46.784 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9784 0 64 0 9848
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00410087
X-RAY DIFFRACTIONf_angle_d0.92413608
X-RAY DIFFRACTIONf_dihedral_angle_d12.6293848
X-RAY DIFFRACTIONf_chiral_restr0.0371460
X-RAY DIFFRACTIONf_plane_restr0.0041719
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.0026-3.04060.46621250.45472468X-RAY DIFFRACTION92
3.0406-3.08060.43711130.42932731X-RAY DIFFRACTION98
3.0806-3.12280.42761460.3832618X-RAY DIFFRACTION99
3.1228-3.16740.41571550.36632692X-RAY DIFFRACTION99
3.1674-3.21470.4331260.34922668X-RAY DIFFRACTION99
3.2147-3.26490.37751190.33252662X-RAY DIFFRACTION99
3.2649-3.31840.38721570.32082689X-RAY DIFFRACTION99
3.3184-3.37560.35721490.29962638X-RAY DIFFRACTION99
3.3756-3.4370.33681400.29072671X-RAY DIFFRACTION99
3.437-3.50310.32041300.28212683X-RAY DIFFRACTION99
3.5031-3.57460.31310.25742657X-RAY DIFFRACTION99
3.5746-3.65220.28691400.24572747X-RAY DIFFRACTION99
3.6522-3.73720.27091510.22492637X-RAY DIFFRACTION99
3.7372-3.83060.27451640.22532652X-RAY DIFFRACTION99
3.8306-3.93410.2551730.21832622X-RAY DIFFRACTION99
3.9341-4.04980.28441450.21532679X-RAY DIFFRACTION99
4.0498-4.18050.23521410.19892697X-RAY DIFFRACTION99
4.1805-4.32980.2351570.19272689X-RAY DIFFRACTION99
4.3298-4.5030.22651390.17942685X-RAY DIFFRACTION99
4.503-4.70770.21161100.17692695X-RAY DIFFRACTION99
4.7077-4.95570.23171380.18032683X-RAY DIFFRACTION99
4.9557-5.26580.23861460.18852651X-RAY DIFFRACTION99
5.2658-5.67170.24891510.19822682X-RAY DIFFRACTION99
5.6717-6.24130.25141630.21212641X-RAY DIFFRACTION98
6.2413-7.14170.25111280.21392638X-RAY DIFFRACTION98
7.1417-8.98730.19011460.18632614X-RAY DIFFRACTION97
8.9873-46.78950.221490.18042439X-RAY DIFFRACTION91

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