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- PDB-5e0t: Human PCNA mutant - S228I -

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Basic information

Entry
Database: PDB / ID: 5e0t
TitleHuman PCNA mutant - S228I
ComponentsProliferating cell nuclear antigen
KeywordsDNA BINDING PROTEIN / DNA replication
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 / Processive synthesis on the C-strand of the telomere / Removal of the Flap Intermediate / Mismatch repair (MMR) directed by MSH2:MSH3 (MutSbeta) / Mismatch repair (MMR) directed by MSH2:MSH6 (MutSalpha) / Polymerase switching on the C-strand of the telomere / Transcription of E2F targets under negative control by DREAM complex / Removal of the Flap Intermediate from the C-strand / replisome / response to L-glutamate / histone acetyltransferase binding / leading strand elongation / DNA polymerase processivity factor activity / replication fork processing / G1/S-Specific Transcription / response to dexamethasone / nuclear replication fork / SUMOylation of DNA replication proteins / estrous cycle / PCNA-Dependent Long Patch Base Excision Repair / mismatch repair / cyclin-dependent protein kinase holoenzyme complex / translesion synthesis / positive regulation of DNA replication / response to cadmium ion / DNA polymerase binding / base-excision repair, gap-filling / positive regulation of DNA repair / epithelial cell differentiation / Translesion synthesis by REV1 / Translesion synthesis by POLK / Translesion synthesis by POLI / Gap-filling DNA repair synthesis and ligation in GG-NER / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / 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 / 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 / response to estradiol / E3 ubiquitin ligases ubiquitinate target proteins / heart development / damaged DNA binding / chromosome, telomeric region / nuclear body / centrosome / chromatin binding / chromatin / protein-containing complex binding / negative regulation of transcription by RNA polymerase II / enzyme binding / extracellular exosome / nucleoplasm / identical protein binding / nucleus
Similarity search - Function
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 ...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
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6653 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

Downloads & links

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Assembly

Deposited unit
A: Proliferating cell nuclear antigen
B: Proliferating cell nuclear antigen
C: Proliferating cell nuclear antigen


Theoretical massNumber of molelcules
Total (without water)86,4653
Polymers86,4653
Non-polymers00
Water4,252236
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4300 Å2
ΔGint-14 kcal/mol
Surface area33110 Å2
MethodPISA
2
A: Proliferating cell nuclear antigen
B: Proliferating cell nuclear antigen
C: Proliferating cell nuclear antigen

A: Proliferating cell nuclear antigen
B: Proliferating cell nuclear antigen
C: Proliferating cell nuclear antigen


Theoretical massNumber of molelcules
Total (without water)172,9316
Polymers172,9316
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area14220 Å2
ΔGint-38 kcal/mol
Surface area60620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)162.324, 162.324, 139.837
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

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


Mass: 28821.830 Da / Num. of mol.: 3 / Mutation: S228I
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PCNA / Variant: S228I / Production host: Escherichia coli (E. coli) / Strain (production host): BLR (DE3) / References: UniProt: P12004
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 236 / 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: 5.33 Å3/Da / Density % sol: 76.91 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: 100mM sodium acetate, pH4.5, 2M ammonium sulfate

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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: Nov 8, 2014
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 2.6653→42.8599 Å / Num. obs: 53711 / % possible obs: 99.78 % / Redundancy: 8 % / Net I/σ(I): 12.3
Reflection shellResolution: 2.6653→2.72 Å / Redundancy: 7.7 % / Rmerge(I) obs: 0.851 / Mean I/σ(I) obs: 2.28 / % possible all: 98

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Processing

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

1vym


Resolution: 2.6653→42.854 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.98 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2263 2143 3.99 %
Rwork0.1888 --
obs0.1904 53652 99.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.6653→42.854 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5804 0 0 236 6040
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0145879
X-RAY DIFFRACTIONf_angle_d1.6297939
X-RAY DIFFRACTIONf_dihedral_angle_d16.2032199
X-RAY DIFFRACTIONf_chiral_restr0.065942
X-RAY DIFFRACTIONf_plane_restr0.0071016
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6653-2.72730.2991370.25753289X-RAY DIFFRACTION98
2.7273-2.79550.29861400.24723390X-RAY DIFFRACTION100
2.7955-2.87110.32231410.24083374X-RAY DIFFRACTION100
2.8711-2.95550.27821420.23013405X-RAY DIFFRACTION100
2.9555-3.05090.2711400.21873395X-RAY DIFFRACTION100
3.0509-3.15990.28131420.21283394X-RAY DIFFRACTION100
3.1599-3.28640.25451410.20853410X-RAY DIFFRACTION100
3.2864-3.43590.21981420.19533413X-RAY DIFFRACTION100
3.4359-3.61690.19661430.17813420X-RAY DIFFRACTION100
3.6169-3.84340.23161420.17573426X-RAY DIFFRACTION100
3.8434-4.13990.19311440.16773451X-RAY DIFFRACTION100
4.1399-4.55610.19011430.14853456X-RAY DIFFRACTION100
4.5561-5.21440.18921450.14893493X-RAY DIFFRACTION100
5.2144-6.56580.24661460.20263514X-RAY DIFFRACTION100
6.5658-42.85990.20611550.2023679X-RAY DIFFRACTION100

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