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- PDB-5l2x: Crystal structure of human PrimPol ternary complex -

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Basic information

Entry
Database: PDB / ID: 5l2x
TitleCrystal structure of human PrimPol ternary complex
Components
  • DNA (5'-D(P*GP*GP*TP*AP*GP*CP*(DDG))-3')
  • DNA (5'-D(P*TP*CP*GP*CP*(5IU)P*AP*CP*C)-3')
  • DNA-directed primase/polymerase protein
KeywordsTRANSFERASE/DNA / Protein-DNA complex / TRANSFERASE-DNA complex
Function / homology
Function and homology information


DNA primase AEP / R-loop processing / mitochondrial DNA replication / DNA primase activity / mitochondrial DNA repair / replication fork processing / translesion synthesis / error-prone translesion synthesis / response to UV / DNA-directed RNA polymerase complex ...DNA primase AEP / R-loop processing / mitochondrial DNA replication / DNA primase activity / mitochondrial DNA repair / replication fork processing / translesion synthesis / error-prone translesion synthesis / response to UV / DNA-directed RNA polymerase complex / replication fork / manganese ion binding / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / mitochondrial matrix / chromatin binding / zinc ion binding / nucleus
Similarity search - Function
DNA-directed primase/polymerase protein / Herpesviridae UL52/UL70 DNA primase / DNA primase, small subunit / DNA primase small subunit
Similarity search - Domain/homology
2'-DEOXYADENOSINE 5'-TRIPHOSPHATE / DNA / DNA (> 10) / DNA-directed primase/polymerase protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.2 Å
AuthorsRechkoblit, O. / Gupta, Y.K. / Malik, R. / Rajashankar, K.R. / Johnson, R.E. / Prakash, L. / Prakash, S. / Aggarwal, A.K.
CitationJournal: Sci Adv / Year: 2016
Title: Structure and mechanism of human PrimPol, a DNA polymerase with primase activity.
Authors: Rechkoblit, O. / Gupta, Y.K. / Malik, R. / Rajashankar, K.R. / Johnson, R.E. / Prakash, L. / Prakash, S. / Aggarwal, A.K.
History
DepositionAug 2, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 23, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 6, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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-directed primase/polymerase protein
C: DNA (5'-D(P*TP*CP*GP*CP*(5IU)P*AP*CP*C)-3')
D: DNA (5'-D(P*GP*GP*TP*AP*GP*CP*(DDG))-3')
B: DNA-directed primase/polymerase protein
G: DNA (5'-D(P*TP*CP*GP*CP*(5IU)P*AP*CP*C)-3')
H: DNA (5'-D(P*GP*GP*TP*AP*GP*CP*(DDG))-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,35510
Polymers100,2926
Non-polymers1,0634
Water1,76598
1
A: DNA-directed primase/polymerase protein
C: DNA (5'-D(P*TP*CP*GP*CP*(5IU)P*AP*CP*C)-3')
D: DNA (5'-D(P*GP*GP*TP*AP*GP*CP*(DDG))-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,6775
Polymers50,1463
Non-polymers5312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4140 Å2
ΔGint-2 kcal/mol
Surface area16390 Å2
MethodPISA
2
B: DNA-directed primase/polymerase protein
G: DNA (5'-D(P*TP*CP*GP*CP*(5IU)P*AP*CP*C)-3')
H: DNA (5'-D(P*GP*GP*TP*AP*GP*CP*(DDG))-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,6775
Polymers50,1463
Non-polymers5312
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3560 Å2
ΔGint-0 kcal/mol
Surface area14510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.723, 65.212, 72.463
Angle α, β, γ (deg.)67.89, 85.22, 86.65
Int Tables number1
Space group name H-MP1

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein DNA-directed primase/polymerase protein / hPrimpol1 / Coiled-coil domain-containing protein 111


Mass: 40909.309 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PRIMPOL, CCDC111 / Production host: Saccharomyces cerevisiae (brewer's yeast)
References: UniProt: Q96LW4, Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases

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DNA chain , 2 types, 4 molecules CGDH

#2: DNA chain DNA (5'-D(P*TP*CP*GP*CP*(5IU)P*AP*CP*C)-3')


Mass: 5149.148 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: DNA chain DNA (5'-D(P*GP*GP*TP*AP*GP*CP*(DDG))-3')


Mass: 4087.657 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)

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Non-polymers , 3 types, 102 molecules

#4: Chemical ChemComp-DTP / 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE / Deoxyadenosine triphosphate


Mass: 491.182 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O12P3
#5: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 98 / 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: 2.22 Å3/Da / Density % sol: 50.47 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 17-23% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Feb 8, 2016 / Details: MD2
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.2→39.354 Å / Num. obs: 38848 / % possible obs: 94.2 % / Redundancy: 2.5 % / Rsym value: 0.01 / Net I/σ(I): 6.2

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Processing

Software
NameVersionClassification
PHENIX(dev_2264: ???)refinement
XDSdata reduction
SCALAdata scaling
autoSHARPphasing
RefinementMethod to determine structure: SAD / Resolution: 2.2→39.354 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.98 / Phase error: 29.63 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.255 1826 4.7 %
Rwork0.2056 --
obs0.2079 38848 89.3 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.2→39.354 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4147 694 62 98 5001
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0125098
X-RAY DIFFRACTIONf_angle_d1.1537031
X-RAY DIFFRACTIONf_dihedral_angle_d18.1452871
X-RAY DIFFRACTIONf_chiral_restr0.056776
X-RAY DIFFRACTIONf_plane_restr0.006773
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.25950.37531330.32082142X-RAY DIFFRACTION68
2.2595-2.3260.36251100.2992403X-RAY DIFFRACTION75
2.326-2.4010.32771310.27572634X-RAY DIFFRACTION82
2.401-2.48680.33771540.26452749X-RAY DIFFRACTION87
2.4868-2.58640.30821680.24572977X-RAY DIFFRACTION94
2.5864-2.70410.3021390.23633035X-RAY DIFFRACTION96
2.7041-2.84660.29011440.22173078X-RAY DIFFRACTION95
2.8466-3.02490.28581410.21222989X-RAY DIFFRACTION94
3.0249-3.25830.24621300.21172946X-RAY DIFFRACTION91
3.2583-3.5860.25481430.193058X-RAY DIFFRACTION96
3.586-4.10440.21531430.1763030X-RAY DIFFRACTION95
4.1044-5.16930.2051330.17282979X-RAY DIFFRACTION93
5.1693-39.360.24571570.21083002X-RAY DIFFRACTION94

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