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- PDB-4rr2: Crystal structure of human primase -

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Basic information

Entry
Database: PDB / ID: 4rr2
TitleCrystal structure of human primase
Components
  • DNA primase large subunitPrimase
  • DNA primase small subunitPrimase
KeywordsTRANSFERASE / POL ALPHA / PRIMASE / DNA REPLICATION / POLYMERASE / IRON-SULFUR CLUSTER / DNA-BINDING / DNA-DIRECTED RNA POLYMERASE / METAL-BINDING / NUCLEOTIDYLTRANSFERASE / PHOSPHOPROTEIN / PRIMOSOME
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
IRON/SULFUR CLUSTER / DNA primase small subunit / DNA primase large subunit
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.65 Å
AuthorsBaranovskiy, A.G. / Gu, J. / Suwa, Y. / Babayeva, N.D. / Tahirov, T.H.
CitationJournal: J.Biol.Chem. / Year: 2015
Title: Crystal structure of the human primase.
Authors: Baranovskiy, A.G. / Zhang, Y. / Suwa, Y. / Babayeva, N.D. / Gu, J. / Pavlov, Y.I. / Tahirov, T.H.
History
DepositionNov 5, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 21, 2015Provider: repository / Type: Initial release
Revision 1.1Mar 11, 2015Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)218,2267
Polymers217,7444
Non-polymers4823
Water1,58588
1
A: DNA primase small subunit
B: DNA primase large subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,9373
Polymers108,8722
Non-polymers651
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1620 Å2
ΔGint-7 kcal/mol
Surface area30630 Å2
MethodPISA
2
C: DNA primase small subunit
D: DNA primase large subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,2894
Polymers108,8722
Non-polymers4172
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1990 Å2
ΔGint-31 kcal/mol
Surface area39310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.195, 88.899, 94.682
Angle α, β, γ (deg.)93.82, 96.57, 111.72
Int Tables number1
Space group name H-MP1

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Components

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


Mass: 49981.012 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PRIM1 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta-2(DE3)
References: UniProt: P49642, Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases
#2: Protein DNA primase large subunit / Primase / DNA primase 58 kDa subunit / p58


Mass: 58890.918 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PRIM2, PRIM2A / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta-2(DE3)
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-SF4 / IRON/SULFUR CLUSTER / Iron–sulfur cluster


Mass: 351.640 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe4S4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 88 / 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: 3.05 Å3/Da / Density % sol: 59.72 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 50 mM Tris-HCl pH 8.5, 7.5% v/v ethanol and 2 mM TCEP, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Jan 1, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 72404 / % possible obs: 91.5 % / Observed criterion σ(I): -1 / Redundancy: 3.8 % / Biso Wilson estimate: 45.8 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 27.8
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allDiffraction-ID% possible all
2.69-2.743.40.48523645193.6
2.64-2.693.40.5841.633732193.2
2.6-2.643.30.6531.533697193.5

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Processing

Software
NameVersionClassification
PHENIXmodel building
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.65→48.48 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 1705624.57 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: ZONAL SCALING AND BULK SOLVENT CORRECTION WERE APPLIED TO STRUCTURE FACTORS
RfactorNum. reflection% reflectionSelection details
Rfree0.271 3385 5.1 %RANDOM
Rwork0.229 ---
obs0.229 66240 88.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 60.5284 Å2 / ksol: 0.404389 e/Å3
Displacement parametersBiso mean: 53.2 Å2
Baniso -1Baniso -2Baniso -3
1-0.23 Å24.85 Å22.05 Å2
2---0.16 Å21.32 Å2
3----0.07 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.44 Å0.36 Å
Luzzati d res low-5 Å
Luzzati sigma a0.62 Å0.54 Å
Refinement stepCycle: LAST / Resolution: 2.65→48.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11798 0 10 88 11896
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d21.3
X-RAY DIFFRACTIONc_improper_angle_d1.09
X-RAY DIFFRACTIONc_mcbond_it3.731.5
X-RAY DIFFRACTIONc_mcangle_it5.632
X-RAY DIFFRACTIONc_scbond_it5.062
X-RAY DIFFRACTIONc_scangle_it6.922.5
Refine LS restraints NCSNCS model details: NONE
LS refinement shellResolution: 2.65→2.82 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.386 513 4.9 %
Rwork0.369 10002 -
obs--84.4 %
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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