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- PDB-4d2g: Crystal structure of human PCNA in complex with p15 peptide -

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Basic information

Entry
Database: PDB / ID: 4d2g
TitleCrystal structure of human PCNA in complex with p15 peptide
Components
  • P15
  • PROLIFERATING CELL NUCLEAR ANTIGEN
KeywordsTRANSCRIPTION
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 / Polymerase switching / positive regulation of DNA-directed DNA polymerase activity / Processive synthesis on the lagging strand / 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 / Polymerase switching / positive regulation of DNA-directed DNA polymerase activity / Processive synthesis on the lagging strand / MutLalpha complex binding / PCNA complex / Telomere C-strand (Lagging Strand) Synthesis / Removal of the Flap Intermediate / 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 / Polymerase switching on the C-strand of the telomere / replisome / Processive synthesis on the C-strand of the telomere / response to L-glutamate / Removal of the Flap Intermediate from the C-strand / centrosome cycle / response to dexamethasone / histone acetyltransferase binding / DNA polymerase processivity factor activity / G1/S-Specific Transcription / leading strand elongation / nuclear replication fork / replication fork processing / SUMOylation of DNA replication proteins / PCNA-Dependent Long Patch Base Excision Repair / response to cadmium ion / estrous cycle / mismatch repair / translesion synthesis / response to UV / cyclin-dependent protein kinase holoenzyme complex / base-excision repair, gap-filling / DNA polymerase binding / epithelial cell differentiation / liver regeneration / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / positive regulation of DNA replication / nuclear estrogen receptor binding / replication fork / positive regulation of DNA repair / Translesion synthesis by REV1 / Translesion synthesis by POLK / Translesion synthesis by POLI / Gap-filling DNA repair synthesis and ligation in GG-NER / male germ cell nucleus / Termination of translesion DNA synthesis / Translesion Synthesis by POLH / Recognition of DNA damage by PCNA-containing replication complex / receptor tyrosine kinase binding / HDR through Homologous Recombination (HRR) / cellular response to xenobiotic stimulus / 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 / response to estradiol / E3 ubiquitin ligases ubiquitinate target proteins / heart development / chromatin organization / molecular adaptor activity / damaged DNA binding / DNA replication / chromosome, telomeric region / regulation of cell cycle / nuclear body / DNA repair / DNA damage response / chromatin binding / centrosome / chromatin / protein-containing complex binding / perinuclear region of cytoplasm / enzyme binding / negative regulation of transcription by RNA polymerase II / extracellular exosome / nucleoplasm / identical protein binding / nucleus
Similarity search - Function
PCNA-associated factor, histone-like domain / PCNA-associated factor / PCNA-associated factor histone like 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 ...PCNA-associated factor, histone-like domain / PCNA-associated factor / PCNA-associated factor histone like 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 / PCNA-associated factor
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
SYNTHETIC CONSTRUCT (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.65 Å
AuthorsDeBiasio, A. / Ibanez, A. / Mortuza, G. / Molina, R. / Cordeiro, T.N. / Castillo, F. / Villate, M. / Merino, N. / Lelli, M. / Diercks, T. ...DeBiasio, A. / Ibanez, A. / Mortuza, G. / Molina, R. / Cordeiro, T.N. / Castillo, F. / Villate, M. / Merino, N. / Lelli, M. / Diercks, T. / Luque, I. / Bernardo, P. / Montoya, G. / Blanco, F.J.
CitationJournal: Nat.Commun. / Year: 2015
Title: Structure of P15(Paf)-PCNA Complex and Implications for Clamp Sliding During DNA Replication and Repair.
Authors: De Biasio, A. / De Opakua, A.I. / Mortuza, G.B. / Molina, R. / Cordeiro, T.N. / Castillo, F. / Villate, M. / Merino, N. / Delgado, S. / Gil-Carton, D. / Luque, I. / Diercks, T. / Bernado, P. ...Authors: De Biasio, A. / De Opakua, A.I. / Mortuza, G.B. / Molina, R. / Cordeiro, T.N. / Castillo, F. / Villate, M. / Merino, N. / Delgado, S. / Gil-Carton, D. / Luque, I. / Diercks, T. / Bernado, P. / Montoya, G. / Blanco, F.J.
History
DepositionMay 9, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 18, 2015Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2015Group: Database references
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
Revision 1.3Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PROLIFERATING CELL NUCLEAR ANTIGEN
B: PROLIFERATING CELL NUCLEAR ANTIGEN
C: PROLIFERATING CELL NUCLEAR ANTIGEN
D: P15
E: P15


Theoretical massNumber of molelcules
Total (without water)91,8765
Polymers91,8765
Non-polymers00
Water3,531196
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8760 Å2
ΔGint-44.7 kcal/mol
Surface area35580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.053, 41.228, 141.121
Angle α, β, γ (deg.)90.00, 105.39, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein PROLIFERATING CELL NUCLEAR ANTIGEN / PCNA / CYCLIN


Mass: 29088.061 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: CDFDUET1 / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P12004
#2: Protein/peptide P15


Mass: 2305.716 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) SYNTHETIC CONSTRUCT (others) / References: UniProt: Q15004*PLUS
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 196 / 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

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Sample preparation

CrystalDensity Matthews: 2.46 Å3/Da / Density % sol: 50 % / Description: NONE
Crystal growDetails: 40% PEG 300 IN 0.1 MM PHOSPHATE-CITRATE PH 4.2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.65→44.35 Å / Num. obs: 24870 / % possible obs: 98.8 % / Observed criterion σ(I): 2 / Redundancy: 3.5 % / Biso Wilson estimate: 49.91 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 9.3
Reflection shellResolution: 2.65→2.74 Å / Redundancy: 3 % / Rmerge(I) obs: 0.51 / Mean I/σ(I) obs: 2 / % possible all: 89.1

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1VYM

1vym


Resolution: 2.65→44.35 Å / SU ML: 0.34 / σ(F): 2 / Phase error: 26.82 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2499 1241 5 %
Rwork0.1703 --
obs0.1744 24817 98.55 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.65→44.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6265 0 0 196 6461
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0166361
X-RAY DIFFRACTIONf_angle_d1.7868596
X-RAY DIFFRACTIONf_dihedral_angle_d16.3562374
X-RAY DIFFRACTIONf_chiral_restr0.0731005
X-RAY DIFFRACTIONf_plane_restr0.0081105
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6501-2.75620.34021260.22642387X-RAY DIFFRACTION90
2.7562-2.88160.30891380.20722616X-RAY DIFFRACTION100
2.8816-3.03350.29161370.19442606X-RAY DIFFRACTION100
3.0335-3.22350.27091380.18372630X-RAY DIFFRACTION100
3.2235-3.47230.28511390.1632637X-RAY DIFFRACTION100
3.4723-3.82160.24371380.15682624X-RAY DIFFRACTION99
3.8216-4.37410.21211390.15312630X-RAY DIFFRACTION99
4.3741-5.50930.19841400.14532674X-RAY DIFFRACTION99
5.5093-44.35440.27111460.18912772X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 7.4415 Å / Origin y: -4.7876 Å / Origin z: -35.7624 Å
111213212223313233
T0.1999 Å20.0116 Å20.0039 Å2-0.1575 Å2-0.0094 Å2--0.1907 Å2
L0.1712 °20.0134 °20.0078 °2-0.0715 °2-0.1409 °2--0.2615 °2
S0.0252 Å °-0.0164 Å °-0.0015 Å °-0.0138 Å °-0.0161 Å °0.0049 Å °-0.0106 Å °0.0091 Å °0 Å °
Refinement TLS groupSelection details: ALL

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