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- PDB-6gws: Crystal structure of human PCNA in complex with three p15 peptides -

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Basic information

Entry
Database: PDB / ID: 6gws
TitleCrystal structure of human PCNA in complex with three p15 peptides
Components
  • PCNA-associated factor
  • Proliferating cell nuclear antigen
KeywordsREPLICATION / PCNA / p15 / p15PAF / PAF15 / crystal / complex / DNA repair.
Function / homology
Function and homology information


positive regulation of deoxyribonuclease activity / dinucleotide insertion or deletion binding / PCNA-p21 complex / mitotic telomere maintenance via semi-conservative replication / purine-specific mismatch base pair DNA N-glycosylase activity / positive regulation of DNA-directed DNA polymerase activity / MutLalpha complex binding / nuclear lamina / Polymerase switching / Telomere C-strand (Lagging Strand) Synthesis ...positive regulation of deoxyribonuclease activity / dinucleotide insertion or deletion binding / PCNA-p21 complex / mitotic telomere maintenance via semi-conservative replication / purine-specific mismatch base pair DNA N-glycosylase activity / positive regulation of DNA-directed DNA polymerase activity / MutLalpha complex binding / nuclear lamina / Polymerase switching / Telomere C-strand (Lagging Strand) Synthesis / Processive synthesis on the lagging strand / PCNA complex / Removal of the Flap Intermediate / Processive synthesis on the C-strand of the telomere / Polymerase switching on the C-strand of the telomere / Mismatch repair (MMR) directed by MSH2:MSH3 (MutSbeta) / Mismatch repair (MMR) directed by MSH2:MSH6 (MutSalpha) / Removal of the Flap Intermediate from the C-strand / Transcription of E2F targets under negative control by DREAM complex / replisome / centrosome cycle / response to L-glutamate / histone acetyltransferase binding / leading strand elongation / DNA polymerase processivity factor activity / G1/S-Specific Transcription / response to dexamethasone / replication fork processing / nuclear replication fork / SUMOylation of DNA replication proteins / PCNA-Dependent Long Patch Base Excision Repair / estrous cycle / mismatch repair / translesion synthesis / response to cadmium ion / DNA polymerase binding / cyclin-dependent protein kinase holoenzyme complex / response to UV / base-excision repair, gap-filling / epithelial cell differentiation / positive regulation of DNA repair / Translesion synthesis by REV1 / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / Translesion synthesis by POLK / Translesion synthesis by POLI / Gap-filling DNA repair synthesis and ligation in GG-NER / positive regulation of DNA replication / male germ cell nucleus / replication fork / nuclear estrogen receptor binding / liver regeneration / Recognition of DNA damage by PCNA-containing replication complex / Termination of translesion DNA synthesis / Translesion Synthesis by POLH / HDR through Homologous Recombination (HRR) / Dual Incision in GG-NER / receptor tyrosine kinase binding / cellular response to hydrogen peroxide / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / cellular response to UV / cellular response to xenobiotic stimulus / E3 ubiquitin ligases ubiquitinate target proteins / response to estradiol / heart development / DNA replication / damaged DNA binding / chromosome, telomeric region / molecular adaptor activity / regulation of cell cycle / nuclear body / centrosome / DNA damage response / chromatin binding / protein-containing complex binding / chromatin / perinuclear region of cytoplasm / negative regulation of transcription by RNA polymerase II / enzyme binding / extracellular exosome / nucleoplasm / identical protein binding / nucleus
Similarity search - Function
PCNA-associated factor, histone-like domain / PCNA-associated factor / PCNA-associated factor histone like domain / 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 ...PCNA-associated factor, histone-like domain / PCNA-associated factor / PCNA-associated factor histone like domain / 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 / : / Alpha Beta
Similarity search - Domain/homology
Proliferating cell nuclear antigen / PCNA-associated factor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsDe March, M. / Merino, N. / Gonzalez-Magana, A. / Romano-Moreno, M. / Onesti, S. / Blanco, F.J. / De Biasio, A.
Funding support Spain, 1items
OrganizationGrant numberCountry
Spanish Ministry of Economy and CompetitivenessCTQ2017-83810-R Spain
CitationJournal: Nucleic Acids Res. / Year: 2018
Title: p15PAF binding to PCNA modulates the DNA sliding surface.
Authors: De March, M. / Barrera-Vilarmau, S. / Crespan, E. / Mentegari, E. / Merino, N. / Gonzalez-Magana, A. / Romano-Moreno, M. / Maga, G. / Crehuet, R. / Onesti, S. / Blanco, F.J. / De Biasio, A.
History
DepositionJun 25, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 22, 2018Provider: repository / Type: Initial release
Revision 1.1Sep 5, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 24, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Proliferating cell nuclear antigen
B: Proliferating cell nuclear antigen
C: Proliferating cell nuclear antigen
D: PCNA-associated factor
E: PCNA-associated factor
F: PCNA-associated factor


Theoretical massNumber of molelcules
Total (without water)98,1916
Polymers98,1916
Non-polymers00
Water18010
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11530 Å2
ΔGint-66 kcal/mol
Surface area36510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.240, 89.750, 85.130
Angle α, β, γ (deg.)90.000, 117.250, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Proliferating cell nuclear antigen / PCNA / Cyclin


Mass: 29088.061 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PCNA / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P12004
#2: Protein/peptide PCNA-associated factor / Hepatitis C virus NS5A-transactivated protein 9 / HCV NS5A-transactivated protein 9 / Overexpressed ...Hepatitis C virus NS5A-transactivated protein 9 / HCV NS5A-transactivated protein 9 / Overexpressed in anaplastic thyroid carcinoma 1 / OEATC-1 / PCNA-associated factor of 15 kDa / p15PAF / PCNA-clamp-associated factor


Mass: 3642.217 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PCLAF, KIAA0101, NS5ATP9, PAF, L5 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q15004
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 10 / 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: 2.92 Å3/Da / Density % sol: 57.81 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 28% PEG 400, 0.2 M CaCl2, 0.1 M Hepes / PH range: 6.5-7

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Oct 30, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.9→89.75 Å / Num. obs: 42698 / % possible obs: 92.2 % / Redundancy: 1.768 % / Biso Wilson estimate: 90.9 Å2 / CC1/2: 0.986 / Rmerge(I) obs: 0.105 / Χ2: 1.024 / Net I/σ(I): 4.77
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Mean I/σ(I) obsNum. unique obsCC1/2% possible allRmerge(I) obsRrim(I) all
2.9-3.081.7620.7368440.76391.3
3.08-3.291.7781.3965890.87993.80.4250.583
3.29-3.551.82.9661670.95894.30.1990.274
3.55-3.891.794.6656330.96893.80.1390.191
3.89-4.341.7655.8449770.9892.10.1090.15
4.34-5.011.7078.2543110.98189.30.0810.112
5.01-6.111.6748.0335970.98288.40.080.111
6.11-8.561.84610.0429480.98693.40.0640.09

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Processing

Software
NameVersionClassification
XSCALEdata scaling
REFMAC5.8.0135refinement
PDB_EXTRACT3.24data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1VYM

1vym


Resolution: 2.9→75.69 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.927 / SU B: 26.897 / SU ML: 0.443 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.42
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2632 1097 4.7 %RANDOM
Rwork0.2 ---
obs0.203 22217 98.43 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 273.23 Å2 / Biso mean: 98.238 Å2 / Biso min: 46.81 Å2
Baniso -1Baniso -2Baniso -3
1-6.71 Å20 Å25.99 Å2
2---5.61 Å20 Å2
3----4.76 Å2
Refinement stepCycle: final / Resolution: 2.9→75.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6420 0 0 10 6430
Biso mean---70.65 -
Num. residues----831
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0196524
X-RAY DIFFRACTIONr_bond_other_d0.0030.026329
X-RAY DIFFRACTIONr_angle_refined_deg2.3961.9798813
X-RAY DIFFRACTIONr_angle_other_deg1.274314628
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.1595825
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.18925.435276
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.187151205
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.9411530
X-RAY DIFFRACTIONr_chiral_restr0.1240.21028
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.027299
X-RAY DIFFRACTIONr_gen_planes_other0.0030.021353
LS refinement shellResolution: 2.9→2.975 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.552 67 -
Rwork0.52 1675 -
obs--98.64 %

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