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

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Basic information

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


Mismatch repair (MMR) directed by MSH2:MSH6 (MutSalpha) / positive regulation of DNA metabolic process / Processive synthesis on the lagging strand / Removal of the Flap Intermediate / meiotic mismatch repair / maintenance of DNA repeat elements / Polymerase switching / maintenance of DNA trinucleotide repeats / SUMOylation of DNA replication proteins / establishment of mitotic sister chromatid cohesion ...Mismatch repair (MMR) directed by MSH2:MSH6 (MutSalpha) / positive regulation of DNA metabolic process / Processive synthesis on the lagging strand / Removal of the Flap Intermediate / meiotic mismatch repair / maintenance of DNA repeat elements / Polymerase switching / maintenance of DNA trinucleotide repeats / SUMOylation of DNA replication proteins / establishment of mitotic sister chromatid cohesion / PCNA complex / lagging strand elongation / DNA damage tolerance / silent mating-type cassette heterochromatin formation / mitotic sister chromatid cohesion / error-free translesion synthesis / leading strand elongation / DNA polymerase processivity factor activity / Dual incision in TC-NER / subtelomeric heterochromatin formation / mismatch repair / positive regulation of DNA replication / positive regulation of DNA repair / 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, C-terminal / Proliferating cell nuclear antigen, C-terminal domain / 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 ...Box / Proliferating Cell Nuclear Antigen / Proliferating Cell Nuclear Antigen - #10 / Proliferating cell nuclear antigen signature 2. / Proliferating cell nuclear antigen, PCNA, C-terminal / Proliferating cell nuclear antigen, C-terminal domain / 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, N-terminal domain / : / Alpha Beta
Similarity search - Domain/homology
DNA sliding clamp PCNA
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.8 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

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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

A: Proliferating cell nuclear antigen


Theoretical massNumber of molelcules
Total (without water)86,6163
Polymers86,6163
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-z,x+1/2,-y+1/21
crystal symmetry operation11_455y-1/2,-z+1/2,-x1
Buried area3480 Å2
ΔGint-10 kcal/mol
Surface area36390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)122.093, 122.093, 122.093
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number198
Space group name H-MP213

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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 / 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: 5.25 Å3/Da / Density % sol: 76.59 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.8
Details: 2.0 M ammonium sulfate and 0.1 M sodium citrate, pH 5.8, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 0.97 Å
DetectorType: NOIR-1 / Detector: CCD / Date: Jan 8, 2008 / Details: saggital focusing mirrors
RadiationMonochromator: Sagitally focused Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 3.8→29.62 Å / Num. all: 6194 / Num. obs: 6146 / % possible obs: 99.57 % / Redundancy: 10.56 % / Biso Wilson estimate: 92.254 Å2 / Rsym value: 0.072 / Net I/σ(I): 17.9
Reflection shellResolution: 3.8→3.903 Å / Redundancy: 9.84 % / Rmerge(I) obs: 0.294 / Mean I/σ(I) obs: 6.8 / Num. unique all: 439 / Rsym value: 0.294 / % possible all: 99.57

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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: 3.8→29.62 Å / Cor.coef. Fo:Fc: 0.889 / Cor.coef. Fo:Fc free: 0.876 / SU B: 46.347 / SU ML: 0.669 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0.02 / ESU R Free: 0.699 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.31215 282 4.6 %RANDOM
Rwork0.27331 ---
obs0.27531 5860 99.22 %-
all-6187 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 92.254 Å2
Refinement stepCycle: LAST / Resolution: 3.8→29.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1990 0 0 0 1990
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0221989
X-RAY DIFFRACTIONr_angle_refined_deg1.3761.9892687
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2255253
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.9925.24482
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.06915363
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.184158
X-RAY DIFFRACTIONr_chiral_restr0.0970.2321
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.021451
X-RAY DIFFRACTIONr_nbd_refined0.2390.2972
X-RAY DIFFRACTIONr_nbtor_refined0.3140.21362
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1540.277
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1610.222
X-RAY DIFFRACTIONr_mcbond_it0.5551.51288
X-RAY DIFFRACTIONr_mcangle_it1.0122038
X-RAY DIFFRACTIONr_scbond_it0.7643766
X-RAY DIFFRACTIONr_scangle_it1.324.5649
LS refinement shellResolution: 3.8→3.903 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.343 19 -
Rwork0.308 439 -
obs--99.57 %

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