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- PDB-5e0v: Human PCNA variant (S228I) complexed with FEN1 at 2.1 Angstroms -

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Basic information

Entry
Database: PDB / ID: 5e0v
TitleHuman PCNA variant (S228I) complexed with FEN1 at 2.1 Angstroms
Components
  • Flap endonuclease 1
  • Proliferating cell nuclear antigen
KeywordsDNA BINDING PROTEIN / DNA replication / sliding clamp
Function / homology
Function and homology information


positive regulation of sister chromatid cohesion / flap endonuclease activity / telomere maintenance via semi-conservative replication / double-stranded DNA exodeoxyribonuclease activity / positive regulation of deoxyribonuclease activity / dinucleotide insertion or deletion binding / PCNA-p21 complex / mitotic telomere maintenance via semi-conservative replication / nucleic acid metabolic process / purine-specific mismatch base pair DNA N-glycosylase activity ...positive regulation of sister chromatid cohesion / flap endonuclease activity / telomere maintenance via semi-conservative replication / double-stranded DNA exodeoxyribonuclease activity / positive regulation of deoxyribonuclease activity / dinucleotide insertion or deletion binding / PCNA-p21 complex / mitotic telomere maintenance via semi-conservative replication / nucleic acid metabolic process / purine-specific mismatch base pair DNA N-glycosylase activity / 5'-flap endonuclease activity / nuclear lamina / MutLalpha complex binding / DNA replication, removal of RNA primer / positive regulation of DNA-directed DNA polymerase activity / Polymerase switching / Telomere C-strand (Lagging Strand) Synthesis / 5'-3' exonuclease activity / Processive synthesis on the lagging strand / UV protection / PCNA complex / Removal of the Flap Intermediate / Processive synthesis on the C-strand of the telomere / Mismatch repair (MMR) directed by MSH2:MSH3 (MutSbeta) / Polymerase switching on the C-strand of the telomere / Mismatch repair (MMR) directed by MSH2:MSH6 (MutSalpha) / Transcription of E2F targets under negative control by DREAM complex / Removal of the Flap Intermediate from the C-strand / HDR through MMEJ (alt-NHEJ) / replisome / exonuclease activity / response to L-glutamate / histone acetyltransferase binding / DNA polymerase processivity factor activity / G1/S-Specific Transcription / leading strand elongation / response to dexamethasone / replication fork processing / Early Phase of HIV Life Cycle / nuclear replication fork / SUMOylation of DNA replication proteins / POLB-Dependent Long Patch Base Excision Repair / estrous cycle / PCNA-Dependent Long Patch Base Excision Repair / cyclin-dependent protein kinase holoenzyme complex / mismatch repair / translesion synthesis / response to cadmium ion / DNA polymerase binding / epithelial cell differentiation / positive regulation of DNA repair / Translesion synthesis by REV1 / Translesion synthesis by POLK / Translesion synthesis by POLI / Gap-filling DNA repair synthesis and ligation in GG-NER / base-excision repair, gap-filling / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / positive regulation of DNA replication / replication fork / male germ cell nucleus / liver regeneration / nuclear estrogen receptor binding / Recognition of DNA damage by PCNA-containing replication complex / Termination of translesion DNA synthesis / Translesion Synthesis by POLH / double-strand break repair via homologous recombination / base-excision repair / HDR through Homologous Recombination (HRR) / Dual Incision in GG-NER / receptor tyrosine kinase binding / memory / cellular response to hydrogen peroxide / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / cellular response to UV / double-strand break repair / RNA-DNA hybrid ribonuclease activity / cellular response to xenobiotic stimulus / E3 ubiquitin ligases ubiquitinate target proteins / response to estradiol / heart development / manganese ion binding / double-stranded DNA binding / endonuclease activity / DNA replication / chromosome, telomeric region / damaged DNA binding / Hydrolases; Acting on ester bonds / nuclear body / DNA repair / centrosome / chromatin binding / protein-containing complex binding / chromatin / nucleolus / enzyme binding / negative regulation of transcription by RNA polymerase II / magnesium ion binding / protein-containing complex / mitochondrion
Similarity search - Function
Flap endonuclease 1 / XPG protein signature 2. / XPG conserved site / XPG protein signature 1. / XPG/Rad2 endonuclease / XPG, N-terminal / XPG-I domain / XPG N-terminal domain / XPG I-region / Xeroderma pigmentosum G I-region ...Flap endonuclease 1 / XPG protein signature 2. / XPG conserved site / XPG protein signature 1. / XPG/Rad2 endonuclease / XPG, N-terminal / XPG-I domain / XPG N-terminal domain / XPG I-region / Xeroderma pigmentosum G I-region / Xeroderma pigmentosum G N-region / 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 / Helix-hairpin-helix motif, class 2 / Helix-hairpin-helix class 2 (Pol1 family) motifs / 5'-3' exonuclease, C-terminal domain superfamily / PIN-like domain superfamily / : / Alpha Beta
Similarity search - Domain/homology
Flap endonuclease 1 / Proliferating cell nuclear antigen / Flap endonuclease 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.074 Å
AuthorsDuffy, C.M. / Hilbert, B.J. / Kelch, B.A.
CitationJournal: J.Mol.Biol. / Year: 2016
Title: A Disease-Causing Variant in PCNA Disrupts a Promiscuous Protein Binding Site.
Authors: Duffy, C.M. / Hilbert, B.J. / Kelch, B.A.
History
DepositionSep 29, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 20, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Database references / Derived calculations / Refinement description
Category: citation / pdbx_struct_oper_list / software
Item: _citation.journal_id_CSD / _pdbx_struct_oper_list.symmetry_operation / _software.classification
Revision 1.2Sep 27, 2023Group: 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: Flap endonuclease 1
D: Flap endonuclease 1


Theoretical massNumber of molelcules
Total (without water)61,1904
Polymers61,1904
Non-polymers00
Water1,78399
1
A: Proliferating cell nuclear antigen
C: Flap endonuclease 1


Theoretical massNumber of molelcules
Total (without water)30,5952
Polymers30,5952
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1480 Å2
ΔGint-8 kcal/mol
Surface area13110 Å2
MethodPISA
2
B: Proliferating cell nuclear antigen
D: Flap endonuclease 1


Theoretical massNumber of molelcules
Total (without water)30,5952
Polymers30,5952
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1410 Å2
ΔGint-8 kcal/mol
Surface area12880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.721, 80.721, 66.556
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number143
Space group name H-MP3
Components on special symmetry positions
IDModelComponents
11A-324-

HOH

21A-329-

HOH

31A-348-

HOH

41B-323-

HOH

51B-325-

HOH

61B-341-

HOH

71B-342-

HOH

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Components

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


Mass: 28821.830 Da / Num. of mol.: 2 / Mutation: S228I
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PCNA / Plasmid: pET3c / Production host: Escherichia coli (E. coli) / Strain (production host): BLR(DE3) / References: UniProt: P12004
#2: Protein/peptide Flap endonuclease 1 / FEN-1 / Flap structure-specific endonuclease 1


Mass: 1772.954 Da / Num. of mol.: 2 / Fragment: UNP residues 299-314 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
References: UniProt: B4DWZ4, UniProt: P39748*PLUS, Hydrolases; Acting on ester bonds
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 99 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.05 Å3/Da / Density % sol: 39.88 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 2.35 M ammonium sulfate, 100 mM sodium acetate pH 4.6, 40% (v/v) -1,3-Butanediol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.033 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 16, 2015
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 2.074→30.95 Å / Num. obs: 29298 / % possible obs: 99.7 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.078 / Net I/σ(I): 16.68
Reflection shellResolution: 2.074→2.12 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.636 / Mean I/σ(I) obs: 2.1 / % possible all: 98.33

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-3000data scaling
HKL-3000phasing
PHASERphasing
HKL-3000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1UL7

1ul7


Resolution: 2.074→30.945 Å / Cross valid method: FREE R-VALUE / σ(F): 1.99 / Phase error: 37.63 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.2292 1450 4.95 %
Rwork0.202 --
obs0.2155 29297 99.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.074→30.945 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4030 0 0 99 4129
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0044084
X-RAY DIFFRACTIONf_angle_d0.7265508
X-RAY DIFFRACTIONf_dihedral_angle_d13.9831518
X-RAY DIFFRACTIONf_chiral_restr0.027654
X-RAY DIFFRACTIONf_plane_restr0.003702
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.074-2.15050.32471490.33192767X-RAY DIFFRACTION95
2.1505-2.23650.35431420.30752769X-RAY DIFFRACTION95
2.2365-2.3380.28941460.28852771X-RAY DIFFRACTION95
2.338-2.46090.34791380.28712797X-RAY DIFFRACTION95
2.4609-2.61460.28121500.26372772X-RAY DIFFRACTION95
2.6146-2.81560.27181450.24532773X-RAY DIFFRACTION95
2.8156-3.09740.25061460.22562771X-RAY DIFFRACTION95
3.0974-3.54210.261420.20712783X-RAY DIFFRACTION95
3.5421-4.44940.21631380.1732790X-RAY DIFFRACTION95
4.4494-16.99090.20791530.16912757X-RAY DIFFRACTION94

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