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- PDB-3l0w: Structure of split monoubiquitinated PCNA with ubiquitin in posit... -

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Basic information

Entry
Database: PDB / ID: 3l0w
TitleStructure of split monoubiquitinated PCNA with ubiquitin in position two
Components
  • Monoubiquitinated Proliferating cell nuclear antigen
  • Proliferating cell nuclear antigen
KeywordsREPLICATION / DNA damage / DNA repair / DNA replication / DNA-binding / Isopeptide bond / Nucleus / Ubl conjugation
Function / homology
Function and homology information


: / : / : / : / : / Regulation of TP53 Degradation / Regulation of PTEN localization / ER Quality Control Compartment (ERQC) / UCH proteinases / Interleukin-1 signaling ...: / : / : / : / : / Regulation of TP53 Degradation / Regulation of PTEN localization / ER Quality Control Compartment (ERQC) / UCH proteinases / Interleukin-1 signaling / Aggrephagy / Peroxisomal protein import / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / ABC-family proteins mediated transport / Mismatch repair (MMR) directed by MSH2:MSH6 (MutSalpha) / meiotic mismatch repair / Metalloprotease DUBs / Endosomal Sorting Complex Required For Transport (ESCRT) / Processive synthesis on the lagging strand / Removal of the Flap Intermediate / E3 ubiquitin ligases ubiquitinate target proteins / Polymerase switching / SUMOylation of DNA replication proteins / positive regulation of DNA metabolic process / maintenance of DNA trinucleotide repeats / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, LSU-rRNA,5S) / Translesion Synthesis by POLH / Translesion synthesis by REV1 / Translesion synthesis by POLK / Translesion synthesis by POLI / establishment of mitotic sister chromatid cohesion / PCNA complex / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / Termination of translesion DNA synthesis / Negative regulators of DDX58/IFIH1 signaling / lagging strand elongation / postreplication repair / silent mating-type cassette heterochromatin formation / Formation of the ternary complex, and subsequently, the 43S complex / Translation initiation complex formation / Ribosomal scanning and start codon recognition / mitotic sister chromatid cohesion / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / error-free translesion synthesis / Regulation of PTEN stability and activity / DNA polymerase processivity factor activity / CDK-mediated phosphorylation and removal of Cdc6 / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis / Formation of TC-NER Pre-Incision Complex / Major pathway of rRNA processing in the nucleolus and cytosol / leading strand elongation / Orc1 removal from chromatin / MAPK6/MAPK4 signaling / SRP-dependent cotranslational protein targeting to membrane / GTP hydrolysis and joining of the 60S ribosomal subunit / Gap-filling DNA repair synthesis and ligation in TC-NER / Formation of a pool of free 40S subunits / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / Antigen processing: Ubiquitination & Proteasome degradation / L13a-mediated translational silencing of Ceruloplasmin expression / Dual incision in TC-NER / ribosomal large subunit export from nucleus / subtelomeric heterochromatin formation / Ub-specific processing proteases / mismatch repair / translesion synthesis / positive regulation of DNA repair / replication fork / positive regulation of DNA replication / nucleotide-excision repair / ribosomal large subunit assembly / modification-dependent protein catabolic process / protein tag activity / ribosome biogenesis / mitotic cell cycle / ribosomal small subunit assembly / cytosolic small ribosomal subunit / cytosolic large ribosomal subunit / chromosome, telomeric region / cytoplasmic translation / protein ubiquitination / structural constituent of ribosome / ubiquitin protein ligase binding / DNA binding / identical protein binding / nucleus / metal ion binding / cytoplasm / cytosol
Similarity search - Function
DNA Polymerase III; Chain A, domain 2 / DNA Polymerase III, subunit A, domain 2 / 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 ...DNA Polymerase III; Chain A, domain 2 / DNA Polymerase III, subunit A, domain 2 / 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 / : / S27a-like superfamily / Ribosomal protein S27a / Ribosomal protein S27a / Ribosomal protein S27a / Ribosomal L40e family / Ribosomal_L40e / Ribosomal protein L40e / Ribosomal protein L40e superfamily / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Ubiquitin domain signature. / Ubiquitin conserved site / Ubiquitin domain / Ubiquitin-like (UB roll) / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Zinc-binding ribosomal protein / Ubiquitin-like domain superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
Ubiquitin-ribosomal protein eS31 fusion protein / Proliferating cell nuclear antigen / Ubiquitin-60S ribosomal protein L40
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsFreudenthal, B.D. / Gakhar, L. / Ramaswamy, S. / Washington, M.T.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2010
Title: Structure of monoubiquitinated PCNA and implications for translesion synthesis and DNA polymerase exchange.
Authors: Freudenthal, B.D. / Gakhar, L. / Ramaswamy, S. / Washington, M.T.
History
DepositionDec 10, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 23, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 2, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 1.3Sep 6, 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)37,9532
Polymers37,9532
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5790 Å2
ΔGint-40 kcal/mol
Surface area16550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)122.516, 122.516, 122.516
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number198
Space group name H-MP213

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Components

#1: Protein Proliferating cell nuclear antigen / PCNA


Mass: 19238.893 Da / Num. of mol.: 1 / Fragment: N fragment
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: POL30, YBR0811, YBR088C / Plasmid: petduet-1 / Production host: Escherichia coli (E. coli) / Strain (production host): Rossetta / References: UniProt: P15873
#2: Protein Monoubiquitinated Proliferating cell nuclear antigen


Mass: 18714.408 Da / Num. of mol.: 1 / Fragment: ubi-C fragment
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: POL30, UBI1 & Pol30, YBR0811, YBR088C / Plasmid: petduet-1 / Production host: Escherichia coli (E. coli) / Strain (production host): Rossetta
References: UniProt: P61864, UniProt: P15873, UniProt: P05759*PLUS

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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: 4.04 Å3/Da / Density % sol: 69.54 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.2
Details: 2.04 M ammonium sulfate, 0.1 M sodium citrate, 3% ethanol, pH 6.2, 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: 0.97 Å
DetectorType: NOIR-1 / Detector: CCD / Date: Mar 25, 2009 / Details: saggitally focused mirrors
RadiationMonochromator: saggitally focused mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 2.8→86.63 Å / Num. obs: 15333 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 2 / Redundancy: 8.74 % / Biso Wilson estimate: 88.237 Å2 / Rmerge(I) obs: 0.109 / Net I/σ(I): 10.5
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 5.38 % / Rmerge(I) obs: 0.604 / Mean I/σ(I) obs: 2.4 / Num. unique all: 1471 / % possible all: 100

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Processing

Software
NameVersionClassificationNB
PHASERphasing
REFMACrefinement
PDB_EXTRACT3.005data extraction
StructureStudiodata collection
d*TREKdata reduction
d*TREKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1PLQ

1plq


Resolution: 2.8→86 Å / Cor.coef. Fo:Fc: 0.909 / Cor.coef. Fo:Fc free: 0.875 / WRfactor Rfree: 0.323 / WRfactor Rwork: 0.285 / Occupancy max: 1 / Occupancy min: 0.25 / FOM work R set: 0.751 / SU B: 18.201 / SU ML: 0.365 / SU R Cruickshank DPI: 1.084 / SU Rfree: 0.421 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 2 / ESU R: 1.084 / ESU R Free: 0.421 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.314 766 5 %RANDOM
Rwork0.277 ---
all0.279 15333 --
obs0.279 14567 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 125.95 Å2 / Biso mean: 84.621 Å2 / Biso min: 20 Å2
Refinement stepCycle: LAST / Resolution: 2.8→86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2590 0 0 0 2590
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0223255
X-RAY DIFFRACTIONr_angle_refined_deg1.5871.9954385
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.035405
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.38525.625144
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.31215631
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.3771516
X-RAY DIFFRACTIONr_chiral_restr0.1040.2518
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0212371
X-RAY DIFFRACTIONr_mcbond_it0.811.52031
X-RAY DIFFRACTIONr_mcangle_it1.52523296
X-RAY DIFFRACTIONr_scbond_it1.76931224
X-RAY DIFFRACTIONr_scangle_it3.1834.51089
LS refinement shellResolution: 2.8→2.873 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.48 50 -
Rwork0.413 1064 -
all-1114 -
obs-1471 99.46 %

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