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- PDB-5mav: Crystal structure of human PCNA in complex with PARG (poly(ADP-ri... -

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Basic information

Entry
Database: PDB / ID: 5mav
TitleCrystal structure of human PCNA in complex with PARG (poly(ADP-ribose) glycohydrolase) peptide.
Components
  • Poly (ADP-ribose) glycohydrolase
  • Proliferating cell nuclear antigen
KeywordsTRANSCRIPTION / PCNA / PARG / interactions
Function / homology
Function and homology information


poly(ADP-ribose) glycohydrolase / poly(ADP-ribose) glycohydrolase activity / 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 ...poly(ADP-ribose) glycohydrolase / poly(ADP-ribose) glycohydrolase activity / 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 / carbohydrate metabolic process / 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
Poly(ADP-ribose) glycohydrolase / Poly (ADP-ribose) glycohydrolase (PARG), Macro domain fold / 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 ...Poly(ADP-ribose) glycohydrolase / Poly (ADP-ribose) glycohydrolase (PARG), Macro domain fold / 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 / Poly(ADP-ribose) glycohydrolase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.575 Å
AuthorsGrishkovskaya, I. / Djinovic-Carugo, K. / Slade, D.
CitationJournal: Nucleic Acids Res. / Year: 2017
Title: A novel non-canonical PIP-box mediates PARG interaction with PCNA.
Authors: Kaufmann, T. / Grishkovskaya, I. / Polyansky, A.A. / Kostrhon, S. / Kukolj, E. / Olek, K.M. / Herbert, S. / Beltzung, E. / Mechtler, K. / Peterbauer, T. / Gotzmann, J. / Zhang, L. / Hartl, M. ...Authors: Kaufmann, T. / Grishkovskaya, I. / Polyansky, A.A. / Kostrhon, S. / Kukolj, E. / Olek, K.M. / Herbert, S. / Beltzung, E. / Mechtler, K. / Peterbauer, T. / Gotzmann, J. / Zhang, L. / Hartl, M. / Zagrovic, B. / Elsayad, K. / Djinovic-Carugo, K. / Slade, D.
History
DepositionNov 6, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 2, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 6, 2017Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Oct 16, 2019Group: Data collection / Category: reflns_shell
Revision 1.3Jan 17, 2024Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms
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
C: Proliferating cell nuclear antigen
E: Proliferating cell nuclear antigen
B: Proliferating cell nuclear antigen
D: Proliferating cell nuclear antigen
F: Proliferating cell nuclear antigen
G: Poly (ADP-ribose) glycohydrolase
H: Poly (ADP-ribose) glycohydrolase
K: Poly (ADP-ribose) glycohydrolase
L: Poly (ADP-ribose) glycohydrolase
N: Poly (ADP-ribose) glycohydrolase
M: Poly (ADP-ribose) glycohydrolase


Theoretical massNumber of molelcules
Total (without water)187,59412
Polymers187,59412
Non-polymers00
Water57632
1
A: Proliferating cell nuclear antigen
C: Proliferating cell nuclear antigen
E: Proliferating cell nuclear antigen
G: Poly (ADP-ribose) glycohydrolase
H: Poly (ADP-ribose) glycohydrolase
M: Poly (ADP-ribose) glycohydrolase


Theoretical massNumber of molelcules
Total (without water)93,7976
Polymers93,7976
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8270 Å2
ΔGint-45 kcal/mol
Surface area35880 Å2
MethodPISA
2
B: Proliferating cell nuclear antigen
D: Proliferating cell nuclear antigen
F: Proliferating cell nuclear antigen
K: Poly (ADP-ribose) glycohydrolase
L: Poly (ADP-ribose) glycohydrolase
N: Poly (ADP-ribose) glycohydrolase


Theoretical massNumber of molelcules
Total (without water)93,7976
Polymers93,7976
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8190 Å2
ΔGint-37 kcal/mol
Surface area35190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.597, 153.604, 85.512
Angle α, β, γ (deg.)90.00, 96.90, 90.00
Int Tables number4
Space group name H-MP1211
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

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


Mass: 29020.990 Da / Num. of mol.: 6
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: Protein/peptide
Poly (ADP-ribose) glycohydrolase


Mass: 2244.637 Da / Num. of mol.: 6 / Fragment: UNP residues 402-420 / Source method: obtained synthetically / Details: peptide / Source: (synth.) Homo sapiens (human) / References: UniProt: Q0MQR4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 32 / 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: 2.9 Å3/Da / Density % sol: 57.62 %
Crystal growTemperature: 295.15 K / Method: vapor diffusion, sitting drop
Details: 0.1 M Tris-HCl pH 7.5, 20% PEG 3350, 0.2 M ammonium acetate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.968 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 29, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.968 Å / Relative weight: 1
ReflectionResolution: 2.57→47.671 Å / Num. obs: 62473 / % possible obs: 99.1 % / Redundancy: 4.8 % / Biso Wilson estimate: 58.38713131 Å2 / Rmerge(I) obs: 0.26 / Rpim(I) all: 0.132 / Rrim(I) all: 0.293 / Net I/σ(I): 5.6

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Processing

Software
NameVersionClassification
PHENIX(1.10_2155: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1VYM

1vym


Resolution: 2.575→47.671 Å / SU ML: 0.53 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 37.7
RfactorNum. reflection% reflection
Rfree0.2909 3032 4.88 %
Rwork0.2387 --
obs0.2412 62098 98.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.575→47.671 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12149 0 0 32 12181
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00712321
X-RAY DIFFRACTIONf_angle_d1.04116617
X-RAY DIFFRACTIONf_dihedral_angle_d16.3517615
X-RAY DIFFRACTIONf_chiral_restr0.0561962
X-RAY DIFFRACTIONf_plane_restr0.0062119
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5751-2.61530.43531110.41592140X-RAY DIFFRACTION79
2.6153-2.65820.40641360.4072694X-RAY DIFFRACTION99
2.6582-2.7040.39921620.39252662X-RAY DIFFRACTION99
2.704-2.75320.42711520.3892680X-RAY DIFFRACTION99
2.7532-2.80610.38791310.37112697X-RAY DIFFRACTION100
2.8061-2.86340.42391110.36782727X-RAY DIFFRACTION100
2.8634-2.92570.33831480.35452686X-RAY DIFFRACTION100
2.9257-2.99370.39231230.34322728X-RAY DIFFRACTION100
2.9937-3.06860.38791380.32732719X-RAY DIFFRACTION100
3.0686-3.15150.36781620.32262661X-RAY DIFFRACTION100
3.1515-3.24420.43961290.3172718X-RAY DIFFRACTION100
3.2442-3.34890.40191370.28852697X-RAY DIFFRACTION100
3.3489-3.46860.34341480.26612687X-RAY DIFFRACTION100
3.4686-3.60740.32141520.24012719X-RAY DIFFRACTION100
3.6074-3.77150.29371310.2312721X-RAY DIFFRACTION100
3.7715-3.97030.2931340.21272711X-RAY DIFFRACTION100
3.9703-4.21890.21231340.18972729X-RAY DIFFRACTION100
4.2189-4.54440.23981280.17622756X-RAY DIFFRACTION100
4.5444-5.00130.22221360.16442700X-RAY DIFFRACTION100
5.0013-5.72390.25371210.1872754X-RAY DIFFRACTION100
5.7239-7.20760.25251540.22082731X-RAY DIFFRACTION100
7.2076-47.67890.20241540.1792749X-RAY DIFFRACTION100

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