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- PDB-3pge: Structure of sumoylated PCNA -

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Basic information

Entry
Database: PDB / ID: 3pge
TitleStructure of sumoylated PCNA
Components
  • Proliferating cell nuclear antigen
  • SUMO-modified proliferating cell nuclear antigen
KeywordsDNA BINDING PROTEIN / DNA replication
Function / homology
Function and homology information


positive regulation of DNA metabolic process / Mismatch repair (MMR) directed by MSH2:MSH6 (MutSalpha) / SUMO is conjugated to E1 (UBA2:SAE1) / meiotic mismatch repair / SUMOylation of nuclear envelope proteins / SUMO is transferred from E1 to E2 (UBE2I, UBC9) / SUMO is proteolytically processed / Processive synthesis on the lagging strand / SUMOylation of transcription factors / Removal of the Flap Intermediate ...positive regulation of DNA metabolic process / Mismatch repair (MMR) directed by MSH2:MSH6 (MutSalpha) / SUMO is conjugated to E1 (UBA2:SAE1) / meiotic mismatch repair / SUMOylation of nuclear envelope proteins / SUMO is transferred from E1 to E2 (UBE2I, UBC9) / SUMO is proteolytically processed / Processive synthesis on the lagging strand / SUMOylation of transcription factors / Removal of the Flap Intermediate / SUMOylation of transcription cofactors / Postmitotic nuclear pore complex (NPC) reformation / Polymerase switching / septin ring / E3 ubiquitin ligases ubiquitinate target proteins / SUMOylation of DNA damage response and repair proteins / maintenance of DNA trinucleotide repeats / Transcriptional and post-translational regulation of MITF-M expression and activity / 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 / SUMOylation of SUMOylation proteins / Termination of translesion DNA synthesis / PCNA complex / lagging strand elongation / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / SUMOylation of RNA binding proteins / DNA damage tolerance / SUMOylation of chromatin organization proteins / silent mating-type cassette heterochromatin formation / mitotic sister chromatid cohesion / error-free translesion synthesis / DNA polymerase processivity factor activity / leading strand elongation / ubiquitin-like protein ligase binding / Dual incision in TC-NER / protein sumoylation / subtelomeric heterochromatin formation / translesion synthesis / mismatch repair / positive regulation of DNA repair / positive regulation of DNA replication / replication fork / condensed nuclear chromosome / nucleotide-excision repair / protein tag activity / mitotic cell cycle / chromosome, telomeric region / DNA binding / identical protein binding / nucleus
Similarity search - Function
DNA Polymerase III; Chain A, domain 2 / DNA Polymerase III, subunit A, domain 2 / Rad60/SUMO-like domain / Ubiquitin-2 like Rad60 SUMO-like / 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 ...DNA Polymerase III; Chain A, domain 2 / DNA Polymerase III, subunit A, domain 2 / Rad60/SUMO-like domain / Ubiquitin-2 like Rad60 SUMO-like / 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 / : / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Ubiquitin-like (UB roll) / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
Proliferating cell nuclear antigen / Ubiquitin-like protein SMT3
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsFreudenthal, B.D. / Brogie, J.E. / Gakhar, L. / Washington, T.
CitationJournal: J.Mol.Biol. / Year: 2011
Title: Crystal Structure of SUMO-Modified Proliferating Cell Nuclear Antigen.
Authors: Freudenthal, B.D. / Brogie, J.E. / Gakhar, L. / Kondratick, C.M. / Washington, M.T.
History
DepositionNov 1, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 29, 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

Downloads & links

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Assembly

Deposited unit
A: SUMO-modified proliferating cell nuclear antigen
B: Proliferating cell nuclear antigen


Theoretical massNumber of molelcules
Total (without water)42,0342
Polymers42,0342
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5750 Å2
ΔGint-39 kcal/mol
Surface area17560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)268.816, 268.816, 268.816
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number209
Space group name H-MF432

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Components

#1: Protein SUMO-modified proliferating cell nuclear antigen


Mass: 22626.527 Da / Num. of mol.: 1 / Fragment: sumo-C fragment of PCNA
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Plasmid: petduet-1 / Production host: Escherichia coli (E. coli) / Strain (production host): Rossetta / References: UniProt: Q12306, UniProt: P15873
#2: Protein Proliferating cell nuclear antigen / PCNA


Mass: 19406.984 Da / Num. of mol.: 1 / Fragment: N fragment of PCNA
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Plasmid: petduet-1 / Production host: Escherichia coli (E. coli) / Strain (production host): Rossetta / 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: 4.81 Å3/Da / Density % sol: 74.45 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 2.0M Ammonium Sulfate, 0.1M sodium Citrate, pH 5.6, 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: Oct 6, 2010
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→45.438 Å / Num. all: 20836 / Num. obs: 20836 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 2 / Redundancy: 12.6 % / Biso Wilson estimate: 78.7 Å2 / Rmerge(I) obs: 0.089 / Net I/σ(I): 14.8
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 8.83 % / Rmerge(I) obs: 0.433 / Mean I/σ(I) obs: 4.4 / Num. unique all: 2029 / % possible all: 99.5

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Processing

Software
NameVersionClassification
StructureStudiodata collection
PHASERphasing
PHENIX(phenix.refine: 1.6.4_486)refinement
d*TREKdata reduction
d*TREKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1PLQ

1plq


Resolution: 2.8→45.4 Å / SU ML: 0.32 / Cross valid method: THROUGHOUT / σ(F): 2.34 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2534 1071 5.14 %Random
Rwork0.2313 ---
obs0.2324 20836 98.93 %-
all-20836 --
Solvent computationShrinkage radii: 1.06 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 56.51 Å2 / ksol: 0.311 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.8→45.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2647 0 0 0 2647
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0122666
X-RAY DIFFRACTIONf_angle_d1.453589
X-RAY DIFFRACTIONf_dihedral_angle_d18.5821006
X-RAY DIFFRACTIONf_chiral_restr0.092417
X-RAY DIFFRACTIONf_plane_restr0.006464
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-2.92760.40991270.39422411X-RAY DIFFRACTION99
2.9276-3.08190.35811250.32772426X-RAY DIFFRACTION100
3.0819-3.27490.30891380.27622436X-RAY DIFFRACTION99
3.2749-3.52770.31611530.24562426X-RAY DIFFRACTION100
3.5277-3.88250.29571450.23682444X-RAY DIFFRACTION99
3.8825-4.44390.23751340.21292454X-RAY DIFFRACTION99
4.4439-5.59730.21191270.1932522X-RAY DIFFRACTION99
5.5973-45.44420.21221220.21922642X-RAY DIFFRACTION97

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