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- PDB-4lik: Crystal structure of the catalytic subunit of human primase -

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Basic information

Entry
Database: PDB / ID: 4lik
TitleCrystal structure of the catalytic subunit of human primase
ComponentsDNA primase small subunitPrimase
KeywordsTRANSFERASE / Prim fold
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 / Polymerase switching / Processive synthesis on the lagging strand / alpha DNA polymerase:primase complex / Removal of the Flap Intermediate / DNA primase activity ...DNA primase AEP / ribonucleotide binding / DNA replication initiation / 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 / 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
CITRIC ACID / DNA primase small subunit
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsVaithiyalingam, S. / Eichman, B.F. / Chazin, W.J.
CitationJournal: J.Mol.Biol. / Year: 2014
Title: Insights into Eukaryotic Primer Synthesis from Structures of the p48 Subunit of Human DNA Primase.
Authors: Vaithiyalingam, S. / Arnett, D.R. / Aggarwal, A. / Eichman, B.F. / Fanning, E. / Chazin, W.J.
History
DepositionJul 2, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 11, 2013Provider: repository / Type: Initial release
Revision 1.1Feb 5, 2014Group: 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_ref_seq_dif / 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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_seq_id / _struct_ref_seq_dif.details / _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

Downloads & links

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Assembly

Deposited unit
A: DNA primase small subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,1135
Polymers46,4711
Non-polymers6424
Water5,801322
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)101.812, 71.916, 84.797
Angle α, β, γ (deg.)90.00, 122.04, 90.00
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 46471.223 Da / Num. of mol.: 1
Fragment: Catalytic subunit p48, UNP residues 1-390 (delta 360-379)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PRIM1 / Production host: Escherichia coli (E. coli)
References: UniProt: P49642, Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-CIT / CITRIC ACID / Citric acid


Mass: 192.124 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H8O7
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 322 / 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: 2.84 Å3/Da / Density % sol: 56.7 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 200 mM Sodium Citrate and 20% PEG3350, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.9787 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 15, 2012
RadiationMonochromator: 0.99 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9787 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. all: 56665 / Num. obs: 56665 / % possible obs: 98.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.9 % / Rsym value: 0.066 / Net I/σ(I): 23.4
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 4.7 % / Mean I/σ(I) obs: 3.3 / Num. unique all: 5130 / Rsym value: 0.416 / % possible all: 89.7

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.8.1_1168)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→30.399 Å / SU ML: 0.17 / σ(F): 1.36 / Phase error: 21.12 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.198 2865 5.06 %
Rwork0.1749 --
obs0.176 56577 98.48 %
all-56665 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.7→30.399 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3052 0 40 322 3414
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093261
X-RAY DIFFRACTIONf_angle_d1.2354423
X-RAY DIFFRACTIONf_dihedral_angle_d14.3521271
X-RAY DIFFRACTIONf_chiral_restr0.088469
X-RAY DIFFRACTIONf_plane_restr0.006566
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.72580.25891260.23062274X-RAY DIFFRACTION83
1.7258-1.75710.23351250.22192525X-RAY DIFFRACTION93
1.7571-1.79090.23061350.20932693X-RAY DIFFRACTION99
1.7909-1.82750.2631310.19852725X-RAY DIFFRACTION100
1.8275-1.86720.21861520.18542668X-RAY DIFFRACTION100
1.8672-1.91060.22491590.1872707X-RAY DIFFRACTION100
1.9106-1.95840.2181480.18292731X-RAY DIFFRACTION100
1.9584-2.01140.21021510.18592714X-RAY DIFFRACTION100
2.0114-2.07050.19831510.17582711X-RAY DIFFRACTION100
2.0705-2.13730.23351490.17112679X-RAY DIFFRACTION100
2.1373-2.21370.20571560.17222718X-RAY DIFFRACTION100
2.2137-2.30230.18821320.16822750X-RAY DIFFRACTION100
2.3023-2.40710.20681110.17152755X-RAY DIFFRACTION100
2.4071-2.53390.19911590.17612685X-RAY DIFFRACTION100
2.5339-2.69260.20261450.18182748X-RAY DIFFRACTION100
2.6926-2.90030.18811540.17592709X-RAY DIFFRACTION100
2.9003-3.19190.19471440.17892734X-RAY DIFFRACTION100
3.1919-3.65310.19621320.16222760X-RAY DIFFRACTION99
3.6531-4.60.1521520.14712713X-RAY DIFFRACTION99
4.6-30.40390.21591530.19192713X-RAY DIFFRACTION97
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.0416-0.0481-0.01470.31520.17020.09650.16640.08-0.0086-0.5268-0.11680.0051-0.2628-0.2574-0.00410.30530.0853-0.04850.2130.00890.1506-24.215411.095364.4321
20.4944-0.2987-0.31320.65330.12390.27840.02430.0253-0.0313-0.28510.0071-0.1263-0.0589-0.00050.00120.1348-0.02190.00910.0983-0.00780.1191-7.26892.693772.3087
30.8661-0.1166-0.17310.111-0.1484-0.1021-0.5281-0.6272-0.18990.00110.2336-0.02620.3721-0.1582-0.13940.1057-0.07870.07180.16310.04110.1495-15.7013-5.377784.8462
40.12470.0515-0.22590.0745-0.11790.3128-0.0553-0.16780.17460.07180.04280.1328-0.0564-0.36100.1355-0.01160.01960.29830.01650.1656-31.09194.465291.3725
50.27430.0777-0.30950.367-0.28520.4376-0.0340.0025-0.05520.02890.02110.00280.104-0.012600.135-0.0126-0.00080.1476-0.01220.1096-14.66141.440291.1382
61.520.95730.49232.3465-0.3582.33460.0042-0.38330.17460.25050.04090.1696-0.1665-0.6224-0.04340.1713-0.07790.04730.34280.0090.149-30.3186-2.4811102.2067
72.0993-0.87520.23721.87890.44391.4435-0.0014-0.5126-0.63951.2684-0.25851.92560.954-1.8189-0.15680.7219-0.36660.45961.4517-0.00451.0815-48.4614-3.8917103.5126
80.1476-0.01820.22920.0755-0.03360.27520.0319-0.0965-0.0961-0.0472-0.0383-0.02170.1769-0.21010.00440.1225-0.07590.00110.1970.00630.1382-24.6408-3.683992.223
90.4559-0.28350.33020.3752-0.31070.2203-0.0151-0.07610.0113-0.00570.0320.0765-0.2011-0.2030.01280.19760.057-0.01290.1366-0.00540.1612-25.07915.784675.4887
10-0.00460.01010.05170.0827-0.12260.37760.03-0.14210.4808-0.2061-0.1674-0.0464-0.60330.2206-0.04380.2153-0.0189-0.02540.1156-0.08810.1972-10.54417.003785.8501
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 19 )
2X-RAY DIFFRACTION2chain 'A' and (resid 20 through 93 )
3X-RAY DIFFRACTION3chain 'A' and (resid 94 through 118 )
4X-RAY DIFFRACTION4chain 'A' and (resid 119 through 148 )
5X-RAY DIFFRACTION5chain 'A' and (resid 149 through 189 )
6X-RAY DIFFRACTION6chain 'A' and (resid 190 through 227 )
7X-RAY DIFFRACTION7chain 'A' and (resid 228 through 276 )
8X-RAY DIFFRACTION8chain 'A' and (resid 292 through 321 )
9X-RAY DIFFRACTION9chain 'A' and (resid 322 through 388 )
10X-RAY DIFFRACTION10chain 'A' and (resid 389 through 407 )

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