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- PDB-6e49: Pif1 peptide bound to PCNA trimer -

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Basic information

Entry
Database: PDB / ID: 6.0E+49
TitlePif1 peptide bound to PCNA trimer
Components
  • ATP-dependent DNA helicase PIF1
  • Proliferating cell nuclear antigen
KeywordsDNA BINDING PROTEIN / Complex / PCNA / Pif1 peptide
Function / homology
Function and homology information


telomerase inhibitor activity / Mismatch repair (MMR) directed by MSH2:MSH6 (MutSalpha) / meiotic mismatch repair / Processive synthesis on the lagging strand / G-quadruplex DNA unwinding / Removal of the Flap Intermediate / E3 ubiquitin ligases ubiquitinate target proteins / Polymerase switching / G-quadruplex DNA binding / SUMOylation of DNA replication proteins ...telomerase inhibitor activity / Mismatch repair (MMR) directed by MSH2:MSH6 (MutSalpha) / meiotic mismatch repair / Processive synthesis on the lagging strand / G-quadruplex DNA unwinding / Removal of the Flap Intermediate / E3 ubiquitin ligases ubiquitinate target proteins / Polymerase switching / G-quadruplex DNA binding / SUMOylation of DNA replication proteins / positive regulation of DNA metabolic process / maintenance of DNA trinucleotide repeats / telomere maintenance via recombination / Translesion Synthesis by POLH / mitochondrial genome maintenance / Translesion synthesis by REV1 / Translesion synthesis by POLK / Translesion synthesis by POLI / establishment of mitotic sister chromatid cohesion / PCNA complex / replication fork reversal / Termination of translesion DNA synthesis / lagging strand elongation / double-strand break repair via break-induced replication / postreplication repair / silent mating-type cassette heterochromatin formation / DNA duplex unwinding / mitotic sister chromatid cohesion / error-free translesion synthesis / DNA polymerase processivity factor activity / leading strand elongation / DNA unwinding involved in DNA replication / nuclear replication fork / negative regulation of telomere maintenance via telomerase / Dual incision in TC-NER / subtelomeric heterochromatin formation / chromosome organization / mismatch repair / translesion synthesis / DNA helicase activity / positive regulation of DNA repair / telomere maintenance / replication fork / positive regulation of DNA replication / mitochondrial membrane / nucleotide-excision repair / mitotic cell cycle / single-stranded DNA binding / 5'-3' DNA helicase activity / DNA recombination / DNA replication / DNA helicase / mitochondrial inner membrane / chromosome, telomeric region / nucleolus / ATP hydrolysis activity / mitochondrion / DNA binding / ATP binding / identical protein binding / nucleus
Similarity search - Function
: / : / DNA helicase Pif1, 2B domain / DNA helicase Pif1-like / PIF1-like helicase / Box / Proliferating Cell Nuclear Antigen / Proliferating Cell Nuclear Antigen - #10 / Proliferating cell nuclear antigen signature 2. / Proliferating cell nuclear antigen, PCNA, conserved site ...: / : / DNA helicase Pif1, 2B domain / DNA helicase Pif1-like / PIF1-like helicase / Box / Proliferating Cell Nuclear Antigen / Proliferating Cell Nuclear Antigen - #10 / Proliferating cell nuclear antigen signature 2. / Proliferating cell nuclear antigen, PCNA, conserved site / Proliferating cell nuclear antigen signature 1. / Proliferating cell nuclear antigen, PCNA / Proliferating cell nuclear antigen, PCNA, N-terminal / Proliferating cell nuclear antigen, PCNA, C-terminal / Proliferating cell nuclear antigen, N-terminal domain / Proliferating cell nuclear antigen, C-terminal domain / : / P-loop containing nucleoside triphosphate hydrolase / Alpha Beta
Similarity search - Domain/homology
ATP-dependent DNA helicase PIF1 / Proliferating cell nuclear antigen
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsBuzovetsky, O. / Kwon, Y. / Pham, N.T. / Kim, C. / Ira, G. / Sung, P. / Xiong, Y.
CitationJournal: Cell Rep / Year: 2017
Title: Role of the Pif1-PCNA Complex in Pol delta-Dependent Strand Displacement DNA Synthesis and Break-Induced Replication.
Authors: Buzovetsky, O. / Kwon, Y. / Pham, N.T. / Kim, C. / Ira, G. / Sung, P. / Xiong, Y.
History
DepositionJul 17, 2018Deposition site: RCSB / Processing site: RCSB
SupersessionAug 22, 2018ID: 6B8I
Revision 1.0Aug 22, 2018Provider: repository / Type: Initial release
Revision 1.1Mar 13, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Proliferating cell nuclear antigen
B: Proliferating cell nuclear antigen
C: Proliferating cell nuclear antigen
D: ATP-dependent DNA helicase PIF1
E: ATP-dependent DNA helicase PIF1
F: ATP-dependent DNA helicase PIF1


Theoretical massNumber of molelcules
Total (without water)97,7826
Polymers97,7826
Non-polymers00
Water1448
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7010 Å2
ΔGint-34 kcal/mol
Surface area36500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)169.346, 41.795, 146.968
Angle α, β, γ (deg.)90.00, 92.26, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13B
23C

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: MET / Beg label comp-ID: MET / Refine code: _

Dom-IDEns-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ASNASNAA1 - 25515 - 269
21ASNASNBB1 - 25515 - 269
12LYSLYSAA1 - 25315 - 267
22LYSLYSCC1 - 25315 - 267
13LYSLYSBB1 - 25315 - 267
23LYSLYSCC1 - 25315 - 267

NCS ensembles :
ID
1
2
3

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Components

#1: Protein Proliferating cell nuclear antigen / PCNA


Mass: 30562.740 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: POL30, YBR088C, YBR0811 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: P15873
#2: Protein/peptide ATP-dependent DNA helicase PIF1 / DNA repair and recombination helicase PIF1 / Petite integration frequency protein 1 / Telomere ...DNA repair and recombination helicase PIF1 / Petite integration frequency protein 1 / Telomere stability protein 1


Mass: 2031.412 Da / Num. of mol.: 3 / Fragment: UNP residues 815-831
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: PIF1, TST1, YML061C, YM9958.01C / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: P07271
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 8 / 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: 2.72 Å3/Da / Density % sol: 54.82 %
Crystal growTemperature: 298 K / Method: microbatch / Details: 100 mM MIB (Qiagen), pH 9.0, 25% PEG1500

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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: Jun 13, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.9→18 Å / Num. obs: 21636 / % possible obs: 92.9 % / Redundancy: 3.3 % / CC1/2: 1 / Rmerge(I) obs: 0.08 / Net I/σ(I): 23
Reflection shellResolution: 2.9→3 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.96 / CC1/2: 0.21 / % possible all: 95.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0189refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.9→18 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.919 / SU B: 42 / SU ML: 0.361 / Cross valid method: THROUGHOUT / ESU R Free: 0.422 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25264 1135 5.2 %RANDOM
Rwork0.20109 ---
obs0.20387 20619 92.62 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 70 Å2
Baniso -1Baniso -2Baniso -3
1--2.89 Å20 Å2-0.73 Å2
2--3.47 Å20 Å2
3----0.52 Å2
Refinement stepCycle: 1 / Resolution: 2.9→18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6258 0 0 8 6266
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0196347
X-RAY DIFFRACTIONr_bond_other_d0.0020.026117
X-RAY DIFFRACTIONr_angle_refined_deg1.9891.9918549
X-RAY DIFFRACTIONr_angle_other_deg1.061314235
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.1685791
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.35525.36278
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.883151211
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.4781529
X-RAY DIFFRACTIONr_chiral_restr0.1070.21008
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.026920
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021205
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it5.057.1863182
X-RAY DIFFRACTIONr_mcbond_other5.0457.1833181
X-RAY DIFFRACTIONr_mcangle_it8.30110.763967
X-RAY DIFFRACTIONr_mcangle_other8.30210.7643968
X-RAY DIFFRACTIONr_scbond_it5.277.7773165
X-RAY DIFFRACTIONr_scbond_other5.2697.7793166
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other8.57711.4494583
X-RAY DIFFRACTIONr_long_range_B_refined15.34924606
X-RAY DIFFRACTIONr_long_range_B_other15.34824607
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A154160.08
12B154160.08
21A154780.06
22C154780.06
31B154020.07
32C154020.07
LS refinement shellResolution: 2.9→2.975 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.388 80 -
Rwork0.337 1482 -
obs--90.45 %
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)
13.1627-0.07761.01570.0426-0.07232.5068-0.0081-0.19780.3767-0.0803-0.06570.050.34170.40090.07380.40520.06840.04690.3912-0.0430.38973.6704-2.693921.2719
21.10480.2921-1.24340.8606-0.13262.231-0.11470.10440.02630.146-0.01470.1167-0.0936-0.28150.12940.4652-0.02450.11980.2366-0.00020.4713-45.99122.69723.5772
32.8136-0.19390.78360.4968-0.4720.58210.2321-0.69340.1594-0.0644-0.25820.0110.13110.09610.02620.50610.13440.07770.703-0.0370.0194-19.3763-4.005765.2756
41.9175-0.9777-1.21230.6961.25453.9957-0.3934-0.76870.1680.07790.3522-0.020.44230.84240.04120.47220.2691-0.07130.8416-0.12430.05525.4884-7.105848.1443
52.00960.0608-0.53521.2418-0.17670.59180.14240.1904-0.0430.013-0.2235-0.0295-0.0369-0.04840.08110.5819-0.04590.07220.16380.00560.4129-23.6821-1.07868.3192
62.327-0.65440.84290.4065-0.82052.9633-0.1198-0.6053-0.0613-0.1190.0561-0.0231-0.0203-0.2940.06380.53490.09660.2080.3558-0.03090.3242-43.8544-1.922453.3301
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 127
2X-RAY DIFFRACTION2B1 - 127
3X-RAY DIFFRACTION3C1 - 127
4X-RAY DIFFRACTION4A128 - 255
5X-RAY DIFFRACTION5B128 - 255
6X-RAY DIFFRACTION6C128 - 254

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