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- PDB-5f0q: Crystal structure of C-terminal domain of the human DNA primase l... -

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Basic information

Entry
Database: PDB / ID: 5f0q
TitleCrystal structure of C-terminal domain of the human DNA primase large subunit with bound DNA template/RNA primer
Components
  • DNA (5'-D(*GP*CP*CP*GP*CP*CP*AP*AP*CP*AP*TP*A)-3')
  • DNA primase large subunitPrimase
  • RNA (5'-R(P*GP*GP*CP*GP*GP*C)-3')
KeywordsTranferase/DNA/RNA / Tranferase-DNA-RNA complex / DNA primase / large subunit / iron-sulfur cluster / RNA / DNA / primer / template / triphosphate / initiation site
Function / homology
Function and homology information


positive regulation of DNA primase activity / DNA replication initiation / DNA/RNA hybrid binding / 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 / Removal of the Flap Intermediate / Polymerase switching on the C-strand of the telomere ...positive regulation of DNA primase activity / DNA replication initiation / DNA/RNA hybrid binding / 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 / Removal of the Flap Intermediate / Polymerase switching on the C-strand of the telomere / DNA replication, synthesis of primer / Activation of the pre-replicative complex / DNA replication initiation / Defective pyroptosis / 4 iron, 4 sulfur cluster binding / DNA binding / nucleoplasm / metal ion binding
Similarity search - Function
DNA primase, large subunit, eukaryotic / DNA primase large subunit, eukaryotic/archaeal / Eukaryotic and archaeal DNA primase, large subunit
Similarity search - Domain/homology
IRON/SULFUR CLUSTER / DNA / DNA (> 10) / RNA / DNA primase large subunit
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.21 Å
AuthorsTahirov, T.H. / Baranovskiy, A.G. / Babayeva, N.D.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM101167 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)CA036727 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM103403 United States
CitationJournal: J.Biol.Chem. / Year: 2016
Title: Mechanism of Concerted RNA-DNA Primer Synthesis by the Human Primosome.
Authors: Baranovskiy, A.G. / Babayeva, N.D. / Zhang, Y. / Gu, J. / Suwa, Y. / Pavlov, Y.I. / Tahirov, T.H.
History
DepositionNov 28, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 23, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 30, 2016Group: Database references
Revision 1.2Jun 1, 2016Group: Database references
Revision 1.3Sep 20, 2017Group: Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Nov 1, 2017Group: Author supporting evidence / Category: pdbx_struct_assembly_auth_evidence
Revision 1.5Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.6Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA primase large subunit
B: DNA primase large subunit
C: RNA (5'-R(P*GP*GP*CP*GP*GP*C)-3')
D: DNA (5'-D(*GP*CP*CP*GP*CP*CP*AP*AP*CP*AP*TP*A)-3')
E: RNA (5'-R(P*GP*GP*CP*GP*GP*C)-3')
F: DNA (5'-D(*GP*CP*CP*GP*CP*CP*AP*AP*CP*AP*TP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,25210
Polymers55,5006
Non-polymers7524
Water1,17165
1
A: DNA primase large subunit
C: RNA (5'-R(P*GP*GP*CP*GP*GP*C)-3')
D: DNA (5'-D(*GP*CP*CP*GP*CP*CP*AP*AP*CP*AP*TP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,1265
Polymers27,7503
Non-polymers3762
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3360 Å2
ΔGint-46 kcal/mol
Surface area11940 Å2
MethodPISA
2
B: DNA primase large subunit
E: RNA (5'-R(P*GP*GP*CP*GP*GP*C)-3')
F: DNA (5'-D(*GP*CP*CP*GP*CP*CP*AP*AP*CP*AP*TP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,1265
Polymers27,7503
Non-polymers3762
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2970 Å2
ΔGint-45 kcal/mol
Surface area11580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)122.507, 126.002, 83.942
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Detailstrimer according to electrophoresis

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Components

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Protein / RNA chain / DNA chain , 3 types, 6 molecules ABCEDF

#1: Protein DNA primase large subunit / Primase / DNA primase 58 kDa subunit / p58


Mass: 22027.273 Da / Num. of mol.: 2 / Fragment: UNP residues 266-456
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PRIM2, PRIM2A / Production host: Escherichia coli (E. coli)
References: UniProt: P49643, Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases
#2: RNA chain RNA (5'-R(P*GP*GP*CP*GP*GP*C)-3')


Mass: 2106.188 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: contain 5'-triphosphate / Source: (synth.) Homo sapiens (human)
#3: DNA chain DNA (5'-D(*GP*CP*CP*GP*CP*CP*AP*AP*CP*AP*TP*A)-3')


Mass: 3616.383 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)

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Non-polymers , 3 types, 69 molecules

#4: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER / Iron–sulfur cluster


Mass: 351.640 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe4S4
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 65 / 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: 2.94 Å3/Da / Density % sol: 58.1 %
Description: needle-like prisms with a square in cross-section
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.18 M lithium sulfate, 50 mM sodium citrate, 2 mM TCEP, 0.1 M sodium malonate, 0.1 M Hepes-NaOH (pH 7.0), 19.7% PEG 8,000 and 0.02 M magnesium chloride

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.987 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Aug 16, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 31361 / % possible obs: 95.4 % / Redundancy: 5.3 % / Biso Wilson estimate: 31.7 Å2 / Rmerge(I) obs: 0.062 / Rpim(I) all: 0.027 / Rrim(I) all: 0.068 / Χ2: 1.379 / Net I/av σ(I): 31.213 / Net I/σ(I): 9.6 / Num. measured all: 165370
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.2-2.242.70.3791.559370.7450.2350.4490.64858.3
2.24-2.282.90.38711790.740.2340.4560.7472.5
2.28-2.323.10.38614090.760.2290.4520.67387.2
2.32-2.373.70.4215710.8140.2330.4830.66896.1
2.37-2.424.30.38716020.8860.2020.4380.68798.7
2.42-2.484.50.34915860.9110.1770.3930.7499.2
2.48-2.544.40.30816090.9230.1580.3480.7798.5
2.54-2.614.80.27816280.940.1360.3110.80899.6
2.61-2.695.40.26316340.960.1210.2910.86599.7
2.69-2.775.60.21916140.9760.0990.2410.98199.6
2.77-2.875.70.18416220.9780.0830.2021.0799.6
2.87-2.995.80.15316410.9850.0680.1671.21999.8
2.99-3.1260.12316460.9890.0540.1351.44399.8
3.12-3.295.80.09616220.9920.0420.1051.78199.5
3.29-3.496.10.08116520.9950.0340.0882.01499.6
3.49-3.766.70.0716430.9960.0290.0762.04199.9
3.76-4.146.60.06316510.9950.0260.0682.1299.9
4.14-4.746.30.05216640.9960.0230.0572.00499.9
4.74-5.976.40.04516870.9980.0190.0491.66999.6
5.97-506.20.0417640.9950.0170.0441.59799.4

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Processing

Software
NameVersionClassification
HKL-3000data collection
HKL-3000data scaling
CNS1.1refinement
PDB_EXTRACT3.15data extraction
HKL-3000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4RR2

4rr2


Resolution: 2.21→49.48 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 92148 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.258 1532 5 %RANDOM
Rwork0.223 ---
obs-30821 93.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 56.4797 Å2 / ksol: 0.3515 e/Å3
Displacement parametersBiso max: 127.11 Å2 / Biso mean: 63.8 Å2 / Biso min: 30.15 Å2
Baniso -1Baniso -2Baniso -3
1-8.81 Å20 Å20 Å2
2--7.28 Å20 Å2
3----16.09 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.43 Å0.36 Å
Luzzati d res low-5 Å
Luzzati sigma a0.62 Å0.55 Å
Refinement stepCycle: final / Resolution: 2.21→49.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3035 721 18 65 3839
Biso mean--53.39 53.8 -
Num. residues----406
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d19.9
X-RAY DIFFRACTIONc_improper_angle_d1.8
X-RAY DIFFRACTIONc_mcbond_it3.191.5
X-RAY DIFFRACTIONc_mcangle_it4.782
X-RAY DIFFRACTIONc_scbond_it4.932
X-RAY DIFFRACTIONc_scangle_it6.552.5
LS refinement shellResolution: 2.2→2.34 Å / Rfactor Rfree error: 0.034 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.455 178 5.2 %
Rwork0.409 3246 -
all-3424 -
obs--62.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2dna-rna_rep.paramdna-rna.top
X-RAY DIFFRACTION3ion.paramion.top
X-RAY DIFFRACTION4sf4.parsf4.top
X-RAY DIFFRACTION5water_rep.paramwater.top

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