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- PDB-8gla: Co-crystal structure of caPCNA bound to the AOH1996 derivative, A... -

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Basic information

Entry
Database: PDB / ID: 8gla
TitleCo-crystal structure of caPCNA bound to the AOH1996 derivative, AOH1996-1LE
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 / positive regulation of DNA-directed DNA polymerase activity / Polymerase switching / MutLalpha complex binding / 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 / positive regulation of DNA-directed DNA polymerase activity / Polymerase switching / MutLalpha complex binding / 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 / Polymerase switching on the C-strand of the telomere / 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 / Removal of the Flap Intermediate from the C-strand / replisome / response to L-glutamate / response to dexamethasone / histone acetyltransferase binding / DNA polymerase processivity factor activity / leading strand elongation / G1/S-Specific Transcription / nuclear replication fork / replication fork processing / SUMOylation of DNA replication proteins / PCNA-Dependent Long Patch Base Excision Repair / response to cadmium ion / translesion synthesis / estrous cycle / mismatch repair / cyclin-dependent protein kinase holoenzyme complex / base-excision repair, gap-filling / DNA polymerase binding / liver regeneration / epithelial cell differentiation / positive regulation of DNA repair / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / Translesion synthesis by REV1 / Translesion synthesis by POLK / Translesion synthesis by POLI / positive regulation of DNA replication / Gap-filling DNA repair synthesis and ligation in GG-NER / replication fork / nuclear estrogen receptor binding / male germ cell nucleus / Termination of translesion DNA synthesis / Recognition of DNA damage by PCNA-containing replication complex / Translesion Synthesis by POLH / receptor tyrosine kinase binding / HDR through Homologous Recombination (HRR) / Dual Incision in GG-NER / cellular response to xenobiotic stimulus / 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 / centrosome / chromatin binding / 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
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-ZQZ / Proliferating cell nuclear antigen
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.77 Å
AuthorsJossart, 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
Revision 1.5Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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: Proliferating cell nuclear antigen
hetero molecules


Theoretical massNumber of molelcules
Total (without water)118,45818
Polymers115,1834
Non-polymers3,27514
Water00
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)89,59115
Polymers86,3873
Non-polymers3,20412
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4500 Å2
ΔGint-74 kcal/mol
Surface area32120 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
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-y,x-y-1,z1
crystal symmetry operation3_655-x+y+1,-x,z1
Buried area4460 Å2
ΔGint-73 kcal/mol
Surface area33060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)199.492, 199.492, 129.413
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-ZQZ / N-[2-(3-methoxyphenoxy)phenyl]-N~2~-(naphthalene-1-carbonyl)-L-alpha-glutamine


Mass: 498.527 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C29H26N2O6
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Cl
Has ligand of interestY
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: 4.29 Å3/Da / Density % sol: 71.31 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1 M sodium cacodylate pH 6.5, 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: May 20, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 3.77→39.59 Å / Num. obs: 19342 / % possible obs: 99.6 % / Redundancy: 5.9 % / CC1/2: 0.993 / Rmerge(I) obs: 0.202 / Rpim(I) all: 0.09 / Rrim(I) all: 0.221 / Χ2: 0.97 / Net I/σ(I): 6.9 / Num. measured all: 114061
Reflection shellResolution: 3.77→4.13 Å / % possible obs: 99.1 % / Redundancy: 5.9 % / Rmerge(I) obs: 0.788 / Num. measured all: 27122 / Num. unique obs: 4598 / CC1/2: 0.774 / Rpim(I) all: 0.347 / Rrim(I) all: 0.862 / Χ2: 0.98 / Net I/σ(I) obs: 2.4

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Processing

Software
NameVersionClassification
PHENIX(1.19.1_4122: ???)refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3VKX

3vkx


Resolution: 3.77→39.59 Å / SU ML: 0.47 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 29.07 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.26 1895 9.8 %
Rwork0.2051 --
obs0.2105 19329 99.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.77→39.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7341 0 230 0 7571
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0037665
X-RAY DIFFRACTIONf_angle_d0.68710331
X-RAY DIFFRACTIONf_dihedral_angle_d8.1021015
X-RAY DIFFRACTIONf_chiral_restr0.0491208
X-RAY DIFFRACTIONf_plane_restr0.0041296
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.77-3.860.33761260.28171210X-RAY DIFFRACTION97
3.86-3.970.34861390.26751286X-RAY DIFFRACTION100
3.97-4.080.32351560.25821197X-RAY DIFFRACTION100
4.08-4.210.26661350.23881252X-RAY DIFFRACTION100
4.21-4.360.26451210.20811264X-RAY DIFFRACTION100
4.36-4.540.2271380.18321245X-RAY DIFFRACTION100
4.54-4.750.22271340.1711256X-RAY DIFFRACTION100
4.75-4.990.22651480.17541236X-RAY DIFFRACTION100
5-5.310.23541380.18141248X-RAY DIFFRACTION100
5.31-5.720.26131340.19791241X-RAY DIFFRACTION100
5.72-6.290.27381320.24331256X-RAY DIFFRACTION100
6.29-7.190.31971440.24621242X-RAY DIFFRACTION99
7.19-9.040.22581150.19431260X-RAY DIFFRACTION100
9.05-39.590.24191350.17411241X-RAY DIFFRACTION99

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