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- PDB-8gcj: PCNA -

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Basic information

Entry
Database: PDB / ID: 8gcj
TitlePCNA
ComponentsProliferating cell nuclear antigen
KeywordsREPLICATION / PCNA / 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 / nuclear lamina / positive regulation of DNA-directed DNA polymerase activity / Polymerase switching / Telomere C-strand (Lagging Strand) Synthesis / MutLalpha complex binding ...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 / nuclear lamina / positive regulation of DNA-directed DNA polymerase activity / Polymerase switching / Telomere C-strand (Lagging Strand) Synthesis / MutLalpha complex binding / 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 / Removal of the Flap Intermediate from the C-strand / Mismatch repair (MMR) directed by MSH2:MSH3 (MutSbeta) / Mismatch repair (MMR) directed by MSH2:MSH6 (MutSalpha) / Transcription of E2F targets under negative control by DREAM complex / replisome / response to L-glutamate / histone acetyltransferase binding / DNA polymerase processivity factor activity / leading strand elongation / 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 / translesion synthesis / mismatch repair / response to cadmium ion / estrous cycle / cyclin-dependent protein kinase holoenzyme complex / base-excision repair, gap-filling / DNA polymerase binding / epithelial cell differentiation / positive regulation of DNA repair / male germ cell nucleus / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / Translesion synthesis by REV1 / Translesion synthesis by POLK / liver regeneration / Translesion synthesis by POLI / replication fork / Gap-filling DNA repair synthesis and ligation in GG-NER / positive regulation of DNA replication / nuclear estrogen receptor binding / Termination of translesion DNA synthesis / Recognition of DNA damage by PCNA-containing replication complex / Translesion Synthesis by POLH / receptor tyrosine kinase binding / HDR through Homologous Recombination (HRR) / Dual Incision in GG-NER / 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 / damaged DNA binding / chromosome, telomeric region / nuclear body / centrosome / chromatin binding / protein-containing complex binding / chromatin / enzyme binding / negative regulation of transcription by RNA polymerase II / extracellular exosome / nucleoplasm / identical protein binding / nucleus
Similarity search - Function
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 / :
Similarity search - Domain/homology
Proliferating cell nuclear antigen
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.85 Å
AuthorsVandborg, B.C. / Bruning, J.B.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Crystal structure of apo pcna
Authors: Vandborg, B.C. / Bruning, J.B.
History
DepositionMar 1, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 29, 2024Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Proliferating cell nuclear antigen
C: Proliferating cell nuclear antigen
E: Proliferating cell nuclear antigen
F: Proliferating cell nuclear antigen
B: Proliferating cell nuclear antigen
D: Proliferating cell nuclear antigen


Theoretical massNumber of molelcules
Total (without water)172,7756
Polymers172,7756
Non-polymers00
Water2,216123
1
A: Proliferating cell nuclear antigen
C: Proliferating cell nuclear antigen
E: Proliferating cell nuclear antigen


Theoretical massNumber of molelcules
Total (without water)86,3873
Polymers86,3873
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3900 Å2
ΔGint-16 kcal/mol
Surface area33380 Å2
MethodPISA
2
F: Proliferating cell nuclear antigen
B: Proliferating cell nuclear antigen
D: Proliferating cell nuclear antigen


Theoretical massNumber of molelcules
Total (without water)86,3873
Polymers86,3873
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3720 Å2
ΔGint-14 kcal/mol
Surface area33720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)147.104, 85.186, 149.806
Angle α, β, γ (deg.)90.00, 116.87, 90.00
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 28795.752 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PCNA / Production host: Escherichia coli (E. coli) / References: UniProt: P12004
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 123 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.45 Å3/Da / Density % sol: 49.72 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, hanging drop
Details: 0.2 M Magnesium chloride hexahydrate, 0.1 M HEPES pH 7.5, 25% w/v Polyethylene glycol 3,350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9537 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 22, 2022 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.85→48.39 Å / Num. obs: 38188 / % possible obs: 98.5 % / Redundancy: 6.8 % / CC1/2: 0.999 / Rmerge(I) obs: 0.058 / Rpim(I) all: 0.024 / Rrim(I) all: 0.063 / Χ2: 1.06 / Net I/σ(I): 17.5 / Num. measured all: 261519
Reflection shellResolution: 2.85→2.98 Å / % possible obs: 98.8 % / Redundancy: 7.1 % / Rmerge(I) obs: 0.3 / Num. measured all: 32613 / Num. unique obs: 4618 / CC1/2: 0.982 / Rpim(I) all: 0.121 / Rrim(I) all: 0.324 / Χ2: 0.95 / Net I/σ(I) obs: 5.7

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Processing

Software
NameVersionClassification
Aimless0.7.4data scaling
PHENIX1.18.2_3874refinement
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.85→48.39 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 38.45 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2775 1989 5.24 %
Rwork0.2311 --
obs0.2336 37982 97.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.85→48.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11117 0 0 123 11240
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00611268
X-RAY DIFFRACTIONf_angle_d1.11115268
X-RAY DIFFRACTIONf_dihedral_angle_d14.4411583
X-RAY DIFFRACTIONf_chiral_restr0.0661858
X-RAY DIFFRACTIONf_plane_restr0.0071946
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.85-2.920.43111430.32632571X-RAY DIFFRACTION98
2.92-30.36861360.29262551X-RAY DIFFRACTION99
3-3.090.36371410.28952553X-RAY DIFFRACTION98
3.09-3.190.35761490.27782581X-RAY DIFFRACTION98
3.19-3.30.34281350.26932543X-RAY DIFFRACTION98
3.3-3.430.31121390.24812505X-RAY DIFFRACTION96
3.43-3.590.34421360.25642564X-RAY DIFFRACTION98
3.59-3.780.33871390.24042566X-RAY DIFFRACTION98
3.78-4.020.28811490.24542568X-RAY DIFFRACTION98
4.02-4.330.24421480.22192589X-RAY DIFFRACTION99
4.33-4.760.2371390.18382595X-RAY DIFFRACTION99
4.76-5.450.23191500.19752593X-RAY DIFFRACTION99
5.45-6.860.28951390.24582546X-RAY DIFFRACTION96
6.86-48.390.20141460.19942668X-RAY DIFFRACTION98

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