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- PDB-5e0u: Human PCNA variant (S228I) complexed with p21 at 1.9 Angstroms -

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Basic information

Entry
Database: PDB / ID: 5e0u
TitleHuman PCNA variant (S228I) complexed with p21 at 1.9 Angstroms
Components
  • Cyclin-dependent kinase inhibitor 1Cyclin-dependent kinase inhibitor protein
  • Proliferating cell nuclear antigen
KeywordsDNA BINDING PROTEIN / DNA replication / sliding clamp
Function / homology
Function and homology information


cyclin-dependent protein kinase activating kinase activity / negative regulation of cardiac muscle tissue regeneration / negative regulation of cyclin-dependent protein kinase activity / positive regulation of deoxyribonuclease activity / dinucleotide insertion or deletion binding / PCNA-p21 complex / TFAP2 (AP-2) family regulates transcription of cell cycle factors / FOXO-mediated transcription of cell cycle genes / mitotic telomere maintenance via semi-conservative replication / purine-specific mismatch base pair DNA N-glycosylase activity ...cyclin-dependent protein kinase activating kinase activity / negative regulation of cardiac muscle tissue regeneration / negative regulation of cyclin-dependent protein kinase activity / positive regulation of deoxyribonuclease activity / dinucleotide insertion or deletion binding / PCNA-p21 complex / TFAP2 (AP-2) family regulates transcription of cell cycle factors / FOXO-mediated transcription of cell cycle genes / mitotic telomere maintenance via semi-conservative replication / purine-specific mismatch base pair DNA N-glycosylase activity / intestinal epithelial cell maturation / 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 / tissue regeneration / regulation of cell cycle G1/S phase transition / Transcriptional regulation by RUNX2 / negative regulation of phosphorylation / 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 / cyclin-dependent protein serine/threonine kinase inhibitor activity / negative regulation of DNA biosynthetic process / response to arsenic-containing substance / replisome / oncogene-induced cell senescence / positive regulation of programmed cell death / Transcriptional activation of cell cycle inhibitor p21 / RUNX3 regulates CDKN1A transcription / AKT phosphorylates targets in the cytosol / response to L-glutamate / DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator / histone acetyltransferase binding / leading strand elongation / stress-induced premature senescence / DNA polymerase processivity factor activity / response to aldosterone / negative regulation of G1/S transition of mitotic cell cycle / response to corticosterone / replication fork processing / cellular response to UV-B / G1/S-Specific Transcription / molecular function inhibitor activity / response to dexamethasone / protein kinase inhibitor activity / STAT5 activation downstream of FLT3 ITD mutants / nuclear replication fork / p53-Dependent G1 DNA Damage Response / regulation of cyclin-dependent protein serine/threonine kinase activity / regulation of G1/S transition of mitotic cell cycle / Constitutive Signaling by AKT1 E17K in Cancer / mitotic G2 DNA damage checkpoint signaling / negative regulation of vascular associated smooth muscle cell proliferation / Defective binding of RB1 mutants to E2F1,(E2F2, E2F3) / SUMOylation of DNA replication proteins / estrous cycle / keratinocyte proliferation / PCNA-Dependent Long Patch Base Excision Repair / response to X-ray / replicative senescence / mismatch repair / cyclin-dependent protein kinase holoenzyme complex / response to hyperoxia / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / translesion synthesis / positive regulation of protein kinase activity / positive regulation of DNA replication / animal organ regeneration / response to cadmium ion / TP53 Regulates Transcription of Genes Involved in G1 Cell Cycle Arrest / DNA polymerase binding / Cyclin E associated events during G1/S transition / DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest / positive regulation of B cell proliferation / Cyclin A:Cdk2-associated events at S phase entry / base-excision repair, gap-filling / keratinocyte differentiation / response to organonitrogen compound / positive regulation of DNA repair / epithelial cell differentiation / cellular response to amino acid starvation / regulation of G2/M transition of mitotic cell cycle / Signaling by FLT3 fusion proteins / Translesion synthesis by REV1 / Translesion synthesis by POLK / cyclin binding / Translesion synthesis by POLI / Gap-filling DNA repair synthesis and ligation in GG-NER / protein sequestering activity / intrinsic apoptotic signaling pathway / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest
Similarity search - Function
Cyclin-dependent kinase inhibitor 1 / Cyclin-dependent kinase inhibitor domain / Cyclin-dependent kinase inhibitor domain superfamily / Cyclin-dependent kinase inhibitor / 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. ...Cyclin-dependent kinase inhibitor 1 / Cyclin-dependent kinase inhibitor domain / Cyclin-dependent kinase inhibitor domain superfamily / Cyclin-dependent kinase inhibitor / 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 / Cyclin-dependent kinase inhibitor 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.93 Å
AuthorsDuffy, C.M. / Hilbert, B.J. / Kelch, B.A.
CitationJournal: J.Mol.Biol. / Year: 2016
Title: A Disease-Causing Variant in PCNA Disrupts a Promiscuous Protein Binding Site.
Authors: Duffy, C.M. / Hilbert, B.J. / Kelch, B.A.
History
DepositionSep 29, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 20, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Database references / Derived calculations / Refinement description
Category: citation / pdbx_struct_oper_list / software
Item: _citation.journal_id_CSD / _pdbx_struct_oper_list.symmetry_operation / _software.classification
Revision 1.2Sep 27, 2023Group: 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
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: Cyclin-dependent kinase inhibitor 1
E: Cyclin-dependent kinase inhibitor 1
F: Cyclin-dependent kinase inhibitor 1


Theoretical massNumber of molelcules
Total (without water)95,1136
Polymers95,1136
Non-polymers00
Water12,629701
1
A: Proliferating cell nuclear antigen
D: Cyclin-dependent kinase inhibitor 1


Theoretical massNumber of molelcules
Total (without water)31,7042
Polymers31,7042
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2060 Å2
ΔGint-11 kcal/mol
Surface area13430 Å2
MethodPISA
2
B: Proliferating cell nuclear antigen
E: Cyclin-dependent kinase inhibitor 1


Theoretical massNumber of molelcules
Total (without water)31,7042
Polymers31,7042
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2210 Å2
ΔGint-10 kcal/mol
Surface area13310 Å2
MethodPISA
3
C: Proliferating cell nuclear antigen
F: Cyclin-dependent kinase inhibitor 1


Theoretical massNumber of molelcules
Total (without water)31,7042
Polymers31,7042
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2160 Å2
ΔGint-10 kcal/mol
Surface area13180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)143.295, 143.295, 41.402
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number143
Space group name H-MP3

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Components

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


Mass: 28821.830 Da / Num. of mol.: 3 / Mutation: S228I
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PCNA / Plasmid: pET3c / Production host: Escherichia coli (E. coli) / Strain (production host): BLR(DE3) / References: UniProt: P12004
#2: Protein/peptide Cyclin-dependent kinase inhibitor 1 / Cyclin-dependent kinase inhibitor protein / CDK-interacting protein 1 / Melanoma differentiation-associated protein 6 / MDA-6 / p21


Mass: 2882.376 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P38936
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 701 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.58 Å3/Da / Density % sol: 52.33 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 100mM HEPES pH 7.5, 25% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 12.3.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 14, 2015
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.93→34.44 Å / Num. obs: 71746 / % possible obs: 99.8 % / Redundancy: 7.7 % / Rmerge(I) obs: 0.09 / Net I/av σ(I): 14 / Net I/σ(I): 20.7
Reflection shellResolution: 1.93→1.96 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.568 / Mean I/σ(I) obs: 2.96 / % possible all: 98.65

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-3000phasing
HKL-3000data scaling
PHASERphasing
HKL-3000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1AXC

1axc


Resolution: 1.93→34.439 Å / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 26.14 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.2211 2002 2.79 %
Rwork0.1623 --
obs0.1699 71743 99.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.93→34.439 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6384 0 0 701 7085
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0166471
X-RAY DIFFRACTIONf_angle_d1.5928728
X-RAY DIFFRACTIONf_dihedral_angle_d14.972431
X-RAY DIFFRACTIONf_chiral_restr0.0691024
X-RAY DIFFRACTIONf_plane_restr0.0081116
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.93-1.97630.26131420.29025012X-RAY DIFFRACTION97
1.9763-2.02970.24421420.25124928X-RAY DIFFRACTION97
2.0297-2.08950.30711480.25334985X-RAY DIFFRACTION97
2.0895-2.15690.28011440.2374988X-RAY DIFFRACTION97
2.1569-2.23390.27721440.2324966X-RAY DIFFRACTION97
2.2339-2.32330.30411420.22974970X-RAY DIFFRACTION97
2.3233-2.4290.25741440.22725027X-RAY DIFFRACTION97
2.429-2.5570.22541480.21314928X-RAY DIFFRACTION97
2.557-2.71710.23181420.19974991X-RAY DIFFRACTION97
2.7171-2.92670.23571420.18775006X-RAY DIFFRACTION97
2.9267-3.22090.22471460.16674964X-RAY DIFFRACTION97
3.2209-3.68610.21241420.13714955X-RAY DIFFRACTION97
3.6861-4.64080.20531400.10854965X-RAY DIFFRACTION97
4.6408-28.47290.17611360.11974957X-RAY DIFFRACTION97

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