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- PDB-8gl9: Co-crystal structure of caPCNA bound to AOH1160 derivative 1LE -

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Basic information

Entry
Database: PDB / ID: 8gl9
TitleCo-crystal structure of caPCNA bound to AOH1160 derivative 1LE
ComponentsProliferating cell nuclear antigen
KeywordsDNA BINDING PROTEIN / PCNA / transcription-replication conflict / DNA replication stress / DNA repair / AOH1160 / AOH1996
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 / MutLalpha complex binding / positive regulation of DNA-directed DNA polymerase activity / 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 / nuclear lamina / MutLalpha complex binding / positive regulation of DNA-directed DNA polymerase activity / Polymerase switching / Telomere C-strand (Lagging Strand) Synthesis / Processive synthesis on the lagging strand / PCNA complex / Removal of the Flap Intermediate / Processive synthesis on the C-strand of the telomere / Mismatch repair (MMR) directed by MSH2:MSH3 (MutSbeta) / Polymerase switching on the C-strand of the telomere / Mismatch repair (MMR) directed by MSH2:MSH6 (MutSalpha) / Transcription of E2F targets under negative control by DREAM complex / Removal of the Flap Intermediate from the C-strand / replisome / response to L-glutamate / histone acetyltransferase binding / DNA polymerase processivity factor activity / G1/S-Specific Transcription / leading strand elongation / response to dexamethasone / replication fork processing / nuclear replication fork / SUMOylation of DNA replication proteins / estrous cycle / PCNA-Dependent Long Patch Base Excision Repair / cyclin-dependent protein kinase holoenzyme complex / mismatch repair / translesion synthesis / response to cadmium ion / DNA polymerase binding / epithelial cell differentiation / 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 / base-excision repair, gap-filling / 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 / E3 ubiquitin ligases ubiquitinate target proteins / response to estradiol / heart development / chromosome, telomeric region / damaged DNA binding / nuclear body / centrosome / chromatin binding / protein-containing complex binding / chromatin / enzyme binding / negative regulation of transcription by RNA polymerase II / extracellular exosome / nucleoplasm / identical protein binding / nucleus
Similarity search - Function
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 / :
Similarity search - Domain/homology
Chem-ZQW / Proliferating cell nuclear antigen
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.81 Å
AuthorsJossart, J. / Kenjic, N. / Malkas, L.H. / Hickey, R.J. / Perry, J.J.
Funding support United States, 1items
OrganizationGrant numberCountry
Department of Defense (DOD, United States)W81XWH1910327 United States
CitationJournal: Cell Chem Biol / Year: 2023
Title: Small molecule targeting of transcription-replication conflict for selective chemotherapy.
Authors: Gu, L. / Li, M. / Li, C.M. / Haratipour, P. / Lingeman, R. / Jossart, J. / Gutova, M. / Flores, L. / Hyde, C. / Kenjic, N. / Li, H. / Chung, V. / Li, H. / Lomenick, B. / Von Hoff, D.D. / ...Authors: Gu, L. / Li, M. / Li, C.M. / Haratipour, P. / Lingeman, R. / Jossart, J. / Gutova, M. / Flores, L. / Hyde, C. / Kenjic, N. / Li, H. / Chung, V. / Li, H. / Lomenick, B. / Von Hoff, D.D. / Synold, T.W. / Aboody, K.S. / Liu, Y. / Horne, D. / Hickey, R.J. / Perry, J.J.P. / Malkas, L.H.
History
DepositionMar 21, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 26, 2023Provider: repository / Type: Initial release
Revision 1.1Aug 2, 2023Group: Author supporting evidence / Database references / Structure summary
Category: citation_author / pdbx_contact_author / pdbx_entity_instance_feature
Item: _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Aug 9, 2023Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.title / _citation_author.name
Revision 1.3Aug 16, 2023Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.4Nov 1, 2023Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.page_first

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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: Proliferating cell nuclear antigen
hetero molecules


Theoretical massNumber of molelcules
Total (without water)118,27818
Polymers115,1834
Non-polymers3,09514
Water1267
1
A: Proliferating cell nuclear antigen
B: Proliferating cell nuclear antigen
C: Proliferating cell nuclear antigen
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,41115
Polymers86,3873
Non-polymers3,02412
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4950 Å2
ΔGint-71 kcal/mol
Surface area32480 Å2
MethodPISA
2
D: Proliferating cell nuclear antigen
hetero molecules

D: Proliferating cell nuclear antigen
hetero molecules

D: Proliferating cell nuclear antigen
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,6009
Polymers86,3873
Non-polymers2136
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area4840 Å2
ΔGint-66 kcal/mol
Surface area32200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)197.145, 197.145, 126.979
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

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Components

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


Mass: 28795.752 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PCNA / Production host: Escherichia coli (E. coli) / References: UniProt: P12004
#2: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Cl
#3: Chemical
ChemComp-ZQW / N~2~-(naphthalene-1-carbonyl)-N-(2-phenoxyphenyl)-L-alpha-glutamine


Mass: 468.501 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C28H24N2O5
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 7 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 4.11 Å3/Da / Density % sol: 70.06 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1 M sodium cacodylate, 0.2 M sodium chloride, 2.0 M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 2, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.81→38.89 Å / Num. obs: 44902 / % possible obs: 99.6 % / Redundancy: 7.8 % / CC1/2: 0.994 / Rmerge(I) obs: 0.119 / Rpim(I) all: 0.045 / Rrim(I) all: 0.128 / Χ2: 1.01 / Net I/σ(I): 12.9 / Num. measured all: 351626
Reflection shellResolution: 2.81→2.91 Å / % possible obs: 97.8 % / Redundancy: 7.5 % / Rmerge(I) obs: 1.019 / Num. measured all: 34837 / Num. unique obs: 4659 / CC1/2: 0.74 / Rpim(I) all: 0.391 / Rrim(I) all: 1.093 / Χ2: 0.94 / Net I/σ(I) obs: 2

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Processing

Software
NameVersionClassification
PHENIX(1.19.1_4122: ???)refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.81→38.89 Å / SU ML: 0.42 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 28.34 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2404 2023 4.51 %
Rwork0.1983 --
obs0.2002 44861 99.52 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.81→38.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7414 0 218 7 7639
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.017726
X-RAY DIFFRACTIONf_angle_d1.22310409
X-RAY DIFFRACTIONf_dihedral_angle_d8.9211026
X-RAY DIFFRACTIONf_chiral_restr0.0651216
X-RAY DIFFRACTIONf_plane_restr0.0081311
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.81-2.880.36241260.32733016X-RAY DIFFRACTION97
2.88-2.950.36941590.27983071X-RAY DIFFRACTION100
2.95-3.040.34321330.28893080X-RAY DIFFRACTION100
3.04-3.140.38621420.27043041X-RAY DIFFRACTION99
3.14-3.250.32291590.26183047X-RAY DIFFRACTION100
3.25-3.380.27231350.23073108X-RAY DIFFRACTION100
3.38-3.530.24121400.21123045X-RAY DIFFRACTION100
3.53-3.720.25311540.20063057X-RAY DIFFRACTION100
3.72-3.950.2321400.20033055X-RAY DIFFRACTION99
3.95-4.260.21871440.17153061X-RAY DIFFRACTION100
4.26-4.690.19911400.14893086X-RAY DIFFRACTION100
4.69-5.360.1771490.15423055X-RAY DIFFRACTION100
5.36-6.750.24131430.19833082X-RAY DIFFRACTION100
6.76-38.890.19871590.1713034X-RAY DIFFRACTION99

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