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- PDB-3gpn: Structure of the non-trimeric form of the E113G PCNA mutant protein -

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Basic information

Entry
Database: PDB / ID: 3gpn
TitleStructure of the non-trimeric form of the E113G PCNA mutant protein
ComponentsProliferating cell nuclear antigen
KeywordsDNA BINDING PROTEIN / Replication / DNA damage / DNA repair / DNA replication / DNA-binding / Isopeptide bond / Nucleus / Ubl conjugation
Function / homology
Function and homology information


positive regulation of DNA metabolic process / Mismatch repair (MMR) directed by MSH2:MSH6 (MutSalpha) / meiotic mismatch repair / Processive synthesis on the lagging strand / Removal of the Flap Intermediate / E3 ubiquitin ligases ubiquitinate target proteins / Polymerase switching / maintenance of DNA trinucleotide repeats / SUMOylation of DNA replication proteins / Translesion synthesis by REV1 ...positive regulation of DNA metabolic process / Mismatch repair (MMR) directed by MSH2:MSH6 (MutSalpha) / meiotic mismatch repair / Processive synthesis on the lagging strand / Removal of the Flap Intermediate / E3 ubiquitin ligases ubiquitinate target proteins / Polymerase switching / maintenance of DNA trinucleotide repeats / SUMOylation of DNA replication proteins / Translesion synthesis by REV1 / Translesion synthesis by POLK / Translesion synthesis by POLI / Translesion Synthesis by POLH / establishment of mitotic sister chromatid cohesion / PCNA complex / Termination of translesion DNA synthesis / lagging strand elongation / DNA damage tolerance / silent mating-type cassette heterochromatin formation / mitotic sister chromatid cohesion / error-free translesion synthesis / DNA polymerase processivity factor activity / leading strand elongation / Dual incision in TC-NER / translesion synthesis / subtelomeric heterochromatin formation / mismatch repair / positive regulation of DNA repair / positive regulation of DNA replication / replication fork / nucleotide-excision repair / mitotic cell cycle / chromosome, telomeric region / DNA binding / 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 speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsFreudenthal, B.D. / Gakhar, L. / Ramaswamy, S. / Washington, M.T.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2009
Title: A charged residue at the subunit interface of PCNA promotes trimer formation by destabilizing alternate subunit interactions.
Authors: Freudenthal, B.D. / Gakhar, L. / Ramaswamy, S. / Washington, M.T.
History
DepositionMar 23, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 16, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 20, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.3Sep 6, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Proliferating cell nuclear antigen


Theoretical massNumber of molelcules
Total (without water)28,8721
Polymers28,8721
Non-polymers00
Water00
1
A: Proliferating cell nuclear antigen

A: Proliferating cell nuclear antigen


Theoretical massNumber of molelcules
Total (without water)57,7442
Polymers57,7442
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_556x,-y,-z+11
Buried area1680 Å2
ΔGint-11 kcal/mol
Surface area24910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.590, 147.509, 81.442
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Proliferating cell nuclear antigen / PCNA


Mass: 28871.988 Da / Num. of mol.: 1 / Mutation: E113G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: POL30, YBR0811, YBR088C / Plasmid: Pet11-a / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta / References: UniProt: P15873

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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: 3.97 Å3/Da / Density % sol: 68.99 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.8
Details: 1.6 M ammonium sulfate and 0.1 M sodium Citrate, pH 5.8, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1.072 Å
DetectorType: NOIR-1 / Detector: CCD / Date: Feb 4, 2008 / Details: saggital focusing mirrors
RadiationMonochromator: Sagitally focused Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.072 Å / Relative weight: 1
ReflectionResolution: 2.5→81.38 Å / Num. all: 15940 / Num. obs: 14864 / % possible obs: 98.18 % / Redundancy: 4.75 % / Biso Wilson estimate: 42.619 Å2 / Rsym value: 0.09 / Net I/σ(I): 11.4
Reflection shellResolution: 2.5→2.565 Å / Redundancy: 4.75 % / Rmerge(I) obs: 0.365 / Mean I/σ(I) obs: 3.2 / Num. unique all: 1041 / Rsym value: 0.365 / % possible all: 96.79

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
d*TREKdata reduction
d*TREKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1PLQ

1plq


Resolution: 2.5→81.38 Å / Cor.coef. Fo:Fc: 0.924 / Cor.coef. Fo:Fc free: 0.904 / SU B: 10.022 / SU ML: 0.221 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0.02 / ESU R: 0.32 / ESU R Free: 0.255 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2734 784 5 %RANDOM
Rwork0.23443 ---
obs0.23636 14864 98.18 %-
all-14864 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 42.619 Å2
Baniso -1Baniso -2Baniso -3
1--0.04 Å20 Å20 Å2
2---1.2 Å20 Å2
3---1.24 Å2
Refinement stepCycle: LAST / Resolution: 2.5→81.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1979 0 0 0 1979
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0222008
X-RAY DIFFRACTIONr_angle_refined_deg1.6761.9942708
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2645252
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.29525.58186
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.0315382
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.811158
X-RAY DIFFRACTIONr_chiral_restr0.1010.2321
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021460
X-RAY DIFFRACTIONr_nbd_refined0.2170.2698
X-RAY DIFFRACTIONr_nbtor_refined0.3130.21349
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1450.250
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2570.250
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0850.21
X-RAY DIFFRACTIONr_mcbond_it0.9751.51299
X-RAY DIFFRACTIONr_mcangle_it1.71622042
X-RAY DIFFRACTIONr_scbond_it2.1823784
X-RAY DIFFRACTIONr_scangle_it3.5134.5666
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)
2.5-2.5650.384740.3271041115296.79
2.565-2.6350.338490.32114195.53
2.635-2.7120.362490.309108998.163
2.712-2.7950.378620.301105597.441
2.795-2.8870.307490.287105498.197
2.887-2.9880.324570.30899898.397
2.988-3.10.294550.27196398.754
3.1-3.2270.308470.26394299.682
3.227-3.370.285410.24188899.324
3.37-3.5340.229410.22977498.853
3.534-3.7250.268420.21572399.4

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