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- PDB-6hvo: Crystal structure of human PCNA in complex with three peptides of... -

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Basic information

Entry
Database: PDB / ID: 6hvo
TitleCrystal structure of human PCNA in complex with three peptides of p12 subunit of human polymerase delta
Components
  • DNA polymerase delta subunit 4
  • Proliferating cell nuclear antigen
KeywordsREPLICATION / PCNA / POLD4 / p12 / polymerase delta / crystal
Function / homology
Function and homology information


delta DNA polymerase complex / 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 / Processive synthesis on the lagging strand / PCNA complex / MutLalpha complex binding ...delta DNA polymerase complex / 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 / Processive synthesis on the lagging strand / PCNA complex / MutLalpha complex binding / 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 / Processive synthesis on the C-strand of the telomere / replisome / Removal of the Flap Intermediate from the C-strand / response to L-glutamate / response to dexamethasone / histone acetyltransferase binding / G1/S-Specific Transcription / leading strand elongation / DNA polymerase processivity factor activity / DNA synthesis involved in DNA repair / nuclear replication fork / SUMOylation of DNA replication proteins / replication fork processing / PCNA-Dependent Long Patch Base Excision Repair / response to cadmium ion / estrous cycle / mismatch repair / cyclin-dependent protein kinase holoenzyme complex / base-excision repair, gap-filling / translesion synthesis / DNA polymerase binding / epithelial cell differentiation / positive regulation of endothelial cell proliferation / liver regeneration / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / positive regulation of DNA replication / nuclear estrogen receptor binding / positive regulation of DNA repair / Translesion synthesis by REV1 / replication fork / Translesion synthesis by POLK / Translesion synthesis by POLI / male germ cell nucleus / Gap-filling DNA repair synthesis and ligation in GG-NER / Termination of translesion DNA synthesis / Translesion Synthesis by POLH / Recognition of DNA damage by PCNA-containing replication complex / receptor tyrosine kinase binding / DNA-templated DNA replication / 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 / damaged DNA binding / chromosome, telomeric region / nuclear body / chromatin binding / centrosome / chromatin / protein-containing complex binding / enzyme binding / negative regulation of transcription by RNA polymerase II / extracellular exosome / nucleoplasm / identical protein binding / nucleus
Similarity search - Function
DNA polymerase delta, subunit 4 / DNA polymerase delta, subunit 4 / 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 ...DNA polymerase delta, subunit 4 / DNA polymerase delta, subunit 4 / 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
DNA sliding clamp PCNA / DNA polymerase delta subunit 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsGonzalez-Magana, A. / Romano-Moreno, M. / Rojas, A.L. / Blanco, F.J. / De Biasio, A.
Funding support Spain, 1items
OrganizationGrant numberCountry
Spanish Ministry of Economy and CompetitivenessCTQ2017-83810-R Spain
CitationJournal: J.Biol.Chem. / Year: 2019
Title: The p12 subunit of human polymerase delta uses an atypical PIP box for molecular recognition of proliferating cell nuclear antigen (PCNA).
Authors: Gonzalez-Magana, A. / Ibanez de Opakua, A. / Romano-Moreno, M. / Murciano-Calles, J. / Merino, N. / Luque, I. / Rojas, A.L. / Onesti, S. / Blanco, F.J. / De Biasio, A.
History
DepositionOct 11, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 23, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 30, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.pdbx_database_id_DOI ..._citation.journal_abbrev / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Mar 27, 2019Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Item: _citation.journal_abbrev / _citation.journal_volume ..._citation.journal_abbrev / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID
Revision 1.3Nov 20, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Proliferating cell nuclear antigen
B: Proliferating cell nuclear antigen
C: Proliferating cell nuclear antigen
D: DNA polymerase delta subunit 4
F: DNA polymerase delta subunit 4
E: DNA polymerase delta subunit 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,74013
Polymers94,0676
Non-polymers6727
Water4,378243
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9540 Å2
ΔGint-121 kcal/mol
Surface area35750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.965, 83.888, 154.982
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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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) / Gene: PCNA / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P12004
#2: Protein/peptide DNA polymerase delta subunit 4 / DNA polymerase delta subunit p12


Mass: 2267.698 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: POLD4, POLDS / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9HCU8
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 243 / 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 / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.61 Å3/Da / Density % sol: 52.96 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: Bis Tris 6.5 , Li2SO4 (0.2M), PEG 3350 24%

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97925 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 2, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97925 Å / Relative weight: 1
ReflectionResolution: 2.1→154.98 Å / Num. obs: 55602 / % possible obs: 100 % / Redundancy: 12.9 % / CC1/2: 0.996 / Rmerge(I) obs: 0.166 / Rpim(I) all: 0.048 / Rrim(I) all: 0.173 / Net I/σ(I): 10.7 / Num. measured all: 718873 / Scaling rejects: 96
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Num. unique obsCC1/2Rpim(I) all% possible allRmerge(I) obsRrim(I) all
2.1-2.1613.244930.4470.775100
8.91-154.9810.18460.9910.03199.50.0960.101

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Processing

Software
NameVersionClassification
REFMAC5.8.0222refinement
Aimless0.5.17data scaling
PDB_EXTRACT3.24data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→73.88 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.94 / SU B: 6.148 / SU ML: 0.155 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.206 / ESU R Free: 0.184
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2444 2779 5 %RANDOM
Rwork0.1949 ---
obs0.1975 52745 99.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 139.76 Å2 / Biso mean: 48.838 Å2 / Biso min: 26.16 Å2
Baniso -1Baniso -2Baniso -3
1-1.38 Å20 Å20 Å2
2---0.41 Å20 Å2
3----0.97 Å2
Refinement stepCycle: final / Resolution: 2.1→73.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6147 0 35 243 6425
Biso mean--70.83 51.61 -
Num. residues----795
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0156381
X-RAY DIFFRACTIONr_bond_other_d0.0010.0175947
X-RAY DIFFRACTIONr_angle_refined_deg1.4451.7318658
X-RAY DIFFRACTIONr_angle_other_deg0.491.70113968
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.835830
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.57920.273183
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.474151016
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.4481529
X-RAY DIFFRACTIONr_chiral_restr0.0670.2873
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.027050
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021070
LS refinement shellResolution: 2.1→2.155 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.349 199 -
Rwork0.306 3833 -
all-4032 -
obs--100 %

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