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- PDB-6eht: Modulation of PCNA sliding surface by p15PAF suggests a suppressi... -

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Basic information

Entry
Database: PDB / ID: 6eht
TitleModulation of PCNA sliding surface by p15PAF suggests a suppressive mechanism for cisplatin-induced DNA lesion bypass by pol eta holoenzyme
Components
  • (Proliferating cell nuclear ...) x 2
  • DNA (5'-D(P*AP*TP*AP*CP*GP*AP*TP*GP*GP*G)-3')
  • DNA (5'-D(P*CP*CP*CP*AP*TP*CP*GP*TP*AP*T)-3')
  • PCNA-associated factor
KeywordsDNA BINDING PROTEIN / Structural analysis / human PCNA P15 DNA macro complex
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 / positive regulation of DNA-directed DNA polymerase activity / MutLalpha complex binding / nuclear lamina / Polymerase switching / Telomere C-strand (Lagging Strand) Synthesis ...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 / positive regulation of DNA-directed DNA polymerase activity / MutLalpha complex binding / nuclear lamina / Polymerase switching / Telomere C-strand (Lagging Strand) Synthesis / Processive synthesis on the lagging strand / PCNA complex / Processive synthesis on the C-strand of the telomere / Removal of the Flap Intermediate / Mismatch repair (MMR) directed by MSH2:MSH3 (MutSbeta) / Mismatch repair (MMR) directed by MSH2:MSH6 (MutSalpha) / Polymerase switching on the C-strand of the telomere / Transcription of E2F targets under negative control by DREAM complex / Removal of the Flap Intermediate from the C-strand / replisome / centrosome cycle / response to L-glutamate / histone acetyltransferase binding / leading strand elongation / DNA polymerase processivity factor activity / replication fork processing / G1/S-Specific Transcription / response to dexamethasone / nuclear replication fork / SUMOylation of DNA replication proteins / estrous cycle / PCNA-Dependent Long Patch Base Excision Repair / mismatch repair / cyclin-dependent protein kinase holoenzyme complex / translesion synthesis / response to cadmium ion / DNA polymerase binding / response to UV / base-excision repair, gap-filling / positive regulation of DNA repair / epithelial cell differentiation / Translesion synthesis by REV1 / Translesion synthesis by POLK / Translesion synthesis by POLI / Gap-filling DNA repair synthesis and ligation in GG-NER / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / replication fork / positive regulation of DNA replication / male germ cell nucleus / liver regeneration / nuclear estrogen receptor binding / Recognition of DNA damage by PCNA-containing replication complex / Termination of translesion DNA synthesis / Translesion Synthesis by POLH / HDR through Homologous Recombination (HRR) / Dual Incision in GG-NER / receptor tyrosine kinase binding / cellular response to hydrogen peroxide / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / cellular response to UV / cellular response to xenobiotic stimulus / response to estradiol / E3 ubiquitin ligases ubiquitinate target proteins / heart development / DNA replication / damaged DNA binding / chromosome, telomeric region / molecular adaptor activity / nuclear body / regulation of cell cycle / centrosome / DNA damage response / chromatin binding / chromatin / protein-containing complex binding / perinuclear region of cytoplasm / negative regulation of transcription by RNA polymerase II / enzyme binding / 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
DNA / Proliferating cell nuclear antigen / PCNA-associated factor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsDe March, M. / Barrera-Vilarmau, S. / Mentegari, E. / Merino, N. / Bressan, E. / Maga, G. / Crehuet, R. / Onesti, S. / Blanco, F.J. / De Biasio, A.
Citation
#1: Journal: 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.
#2: Journal: Nat Commun / Year: 2017
Title: Structural basis of human PCNA sliding on DNA.
Authors: De March, M. / Merino, N. / Barrera-Vilarmau, S. / Crehuet, R. / Onesti, S. / Blanco, F.J. / De Biasio, A.
History
DepositionSep 15, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 8, 2018Provider: repository / Type: Initial release
Revision 1.1Aug 22, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Oct 24, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Jan 17, 2024Group: 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_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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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: PCNA-associated factor
E: PCNA-associated factor
F: DNA (5'-D(P*AP*TP*AP*CP*GP*AP*TP*GP*GP*G)-3')
G: DNA (5'-D(P*CP*CP*CP*AP*TP*CP*GP*TP*AP*T)-3')


Theoretical massNumber of molelcules
Total (without water)95,1747
Polymers95,1747
Non-polymers00
Water1629
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8050 Å2
ΔGint-58 kcal/mol
Surface area38050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.993, 42.300, 141.827
Angle α, β, γ (deg.)90.00, 102.70, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13B
23C
14D
24E

NCS domain segments:

Component-ID: 0 / Refine code: 0

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11PHEPHEPROPROAA2 - 2532 - 253
21PHEPHEPROPROBB2 - 2532 - 253
12METMETPROPROAA1 - 2531 - 253
22METMETPROPROCC1 - 2532 - 254
13PHEPHEPROPROBB2 - 2532 - 253
23PHEPHEPROPROCC2 - 2533 - 254
14VALVALARGARGDD53 - 702 - 19
24VALVALARGARGEE53 - 702 - 19

NCS ensembles :
ID
1
2
3
4

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Components

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Proliferating cell nuclear ... , 2 types, 3 molecules ABC

#1: Protein Proliferating cell nuclear antigen / / PCNA / Cyclin


Mass: 28036.033 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PCNA / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: P12004
#2: Protein Proliferating cell nuclear antigen / / PCNA / Cyclin


Mass: 28287.336 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PCNA
Production host: Escherichia coli O103:H2 str. 12009 (bacteria)
References: UniProt: P12004

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DNA chain , 2 types, 2 molecules FG

#4: DNA chain DNA (5'-D(P*AP*TP*AP*CP*GP*AP*TP*GP*GP*G)-3')


Mass: 3109.053 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#5: DNA chain DNA (5'-D(P*CP*CP*CP*AP*TP*CP*GP*TP*AP*T)-3')


Mass: 2979.968 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)

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Protein/peptide / Non-polymers , 2 types, 11 molecules DE

#3: Protein/peptide PCNA-associated factor / Hepatitis C virus NS5A-transactivated protein 9 / HCV NS5A-transactivated protein 9 / Overexpressed ...Hepatitis C virus NS5A-transactivated protein 9 / HCV NS5A-transactivated protein 9 / Overexpressed in anaplastic thyroid carcinoma 1 / OEATC-1 / PCNA-associated factor of 15 kDa / p15PAF / PCNA-clamp-associated factor


Mass: 2362.834 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q15004
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 9 / Source method: isolated from a natural source / Formula: H2O

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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: 2.34 Å3/Da / Density % sol: 47.36 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 10% polyethylene glycol 3350 0.1 M sodium acetate pH 4.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Feb 7, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.2→46.12 Å / Num. obs: 14271 / % possible obs: 95.3 % / Redundancy: 2.2 % / Rmerge(I) obs: 0.105 / Net I/av σ(I): 4.5 / Net I/σ(I): 5.7
Reflection shellResolution: 3.2→3.37 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.32 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 2122 / % possible all: 98.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0222refinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4D2G

4d2g


Resolution: 3.2→40.48 Å / Cor.coef. Fo:Fc: 0.835 / Cor.coef. Fo:Fc free: 0.806 / SU B: 91.608 / SU ML: 0.68 / Cross valid method: THROUGHOUT / ESU R Free: 0.721 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.32715 716 5.1 %RANDOM
Rwork0.26063 ---
obs0.26401 13440 94.23 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 63.479 Å2
Baniso -1Baniso -2Baniso -3
1-5.01 Å2-0 Å23.76 Å2
2--0.27 Å20 Å2
3----6.33 Å2
Refinement stepCycle: 1 / Resolution: 3.2→40.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5506 410 0 9 5925
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0146055
X-RAY DIFFRACTIONr_bond_other_d0.0010.0175048
X-RAY DIFFRACTIONr_angle_refined_deg1.3961.6038346
X-RAY DIFFRACTIONr_angle_other_deg1.0211.71511593
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.6725797
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.54523.258178
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.60215748
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.6141514
X-RAY DIFFRACTIONr_chiral_restr0.0650.2887
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.026756
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021160
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9642.4553203
X-RAY DIFFRACTIONr_mcbond_other0.9642.4553202
X-RAY DIFFRACTIONr_mcangle_it1.6523.6843995
X-RAY DIFFRACTIONr_mcangle_other1.6523.6843996
X-RAY DIFFRACTIONr_scbond_it1.6544.1912852
X-RAY DIFFRACTIONr_scbond_other1.6544.1872851
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.8066.2814352
X-RAY DIFFRACTIONr_long_range_B_refined4.50736.4085626
X-RAY DIFFRACTIONr_long_range_B_other4.50636.3975625
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A51440.08
12B51440.08
21A55440.09
22C55440.09
31B51590.09
32C51590.09
41D3550.13
42E3550.13
LS refinement shellResolution: 3.2→3.283 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.377 53 -
Rwork0.281 1028 -
obs--98.27 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.66580.62560.00111.6962-1.0273.1678-0.07250.15770.043-0.1003-0.0406-0.2006-0.14980.16690.11310.0467-0.027-0.08070.58370.05520.429753.34487.269733.8035
21.07430.953-0.73961.1385-0.83812.16960.17020.01660.0357-0.0084-0.27110.071-0.1623-0.04960.10090.19910.1122-0.17610.7656-0.03030.32913.8154.309714.8005
34.2529-0.35471.01611.3942-0.80471.96820.17480.2733-0.1551-0.1215-0.117-0.07820.19560.0159-0.05780.05630.0274-0.09270.3041-0.07730.252422.074-12.993254.2781
48.6433-3.2184-8.24281.45072.8848.0210.5594-0.2770.49220.1929-0.1335-0.0993-0.85310.4753-0.42590.7165-0.38930.02730.4289-0.01160.54668.8177-4.243456.9163
51.5118-0.5704-1.16185.68-2.38522.3536-0.10360.1320.4724-0.1584-0.0069-1.05120.1857-0.13470.11050.46260.08130.01570.3469-0.05180.557916.004422.468313.3566
62.6434-0.5984-0.061713.2789-0.581.84570.01550.21460.1903-0.202-0.1452-0.0661-0.1335-0.06790.12970.9947-0.06220.00671.48980.08180.941432.05382.325134.9201
75.251-3.9380.79447.0782-2.41740.97350.17720.2934-0.307-0.1516-0.19490.29980.1921-0.11730.01771.0218-0.02950.01921.4010.07211.066432.11281.237335.0362
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 254
2X-RAY DIFFRACTION2B2 - 254
3X-RAY DIFFRACTION3C0 - 255
4X-RAY DIFFRACTION4D52 - 71
5X-RAY DIFFRACTION5E53 - 71
6X-RAY DIFFRACTION6F1 - 10
7X-RAY DIFFRACTION7G1 - 10

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