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- PDB-6cbi: PCNA in complex with inhibitor -

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Basic information

Entry
Database: PDB / ID: 6cbi
TitlePCNA in complex with inhibitor
Components
  • GLY-ARG-LYS-ARG-ARG-GLN-DAB-SER-MET-THR-GLU-PHE-TYR-HIS
  • Proliferating cell nuclear antigen
KeywordsCELL CYCLE / PCNA / sliding clamp / proliferating cell nuclear antigen
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 / FOXO-mediated transcription of cell cycle genes / TFAP2 (AP-2) family regulates transcription of cell cycle factors / positive regulation of deoxyribonuclease activity / dinucleotide insertion or deletion binding / PCNA-p21 complex / intestinal epithelial cell maturation / mitotic telomere maintenance via semi-conservative replication ...cyclin-dependent protein kinase activating kinase activity / negative regulation of cardiac muscle tissue regeneration / negative regulation of cyclin-dependent protein kinase activity / FOXO-mediated transcription of cell cycle genes / TFAP2 (AP-2) family regulates transcription of cell cycle factors / positive regulation of deoxyribonuclease activity / dinucleotide insertion or deletion binding / PCNA-p21 complex / intestinal epithelial cell maturation / 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 / regulation of cell cycle G1/S phase transition / Polymerase switching / Telomere C-strand (Lagging Strand) Synthesis / tissue regeneration / Transcriptional regulation by RUNX2 / Processive synthesis on the lagging strand / PCNA complex / negative regulation of phosphorylation / Removal of the Flap Intermediate / Processive synthesis on the C-strand of the telomere / cyclin-dependent protein serine/threonine kinase inhibitor activity / 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 / negative regulation of DNA biosynthetic process / Removal of the Flap Intermediate from the C-strand / response to arsenic-containing substance / replisome / positive regulation of programmed cell death / oncogene-induced cell senescence / Transcriptional activation of cell cycle inhibitor p21 / AKT phosphorylates targets in the cytosol / RUNX3 regulates CDKN1A transcription / response to L-glutamate / stress-induced premature senescence / DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator / histone acetyltransferase binding / negative regulation of G1/S transition of mitotic cell cycle / response to aldosterone / regulation of cyclin-dependent protein serine/threonine kinase activity / response to corticosterone / cellular response to UV-B / molecular function inhibitor activity / DNA polymerase processivity factor activity / G1/S-Specific Transcription / STAT5 activation downstream of FLT3 ITD mutants / leading strand elongation / protein kinase inhibitor activity / response to dexamethasone / replication fork processing / p53-Dependent G1 DNA Damage Response / nuclear replication fork / Constitutive Signaling by AKT1 E17K in Cancer / regulation of G1/S transition of mitotic cell cycle / Defective binding of RB1 mutants to E2F1,(E2F2, E2F3) / mitotic G2 DNA damage checkpoint signaling / negative regulation of vascular associated smooth muscle cell proliferation / SUMOylation of DNA replication proteins / keratinocyte proliferation / response to X-ray / replicative senescence / estrous cycle / PCNA-Dependent Long Patch Base Excision Repair / cyclin-dependent protein kinase holoenzyme complex / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / positive regulation of protein kinase activity / response to hyperoxia / animal organ regeneration / TP53 Regulates Transcription of Genes Involved in G1 Cell Cycle Arrest / mismatch repair / translesion synthesis / Cyclin E associated events during G1/S transition / response to cadmium ion / DNA polymerase binding / Cyclin A:Cdk2-associated events at S phase entry / positive regulation of B cell proliferation / keratinocyte differentiation / : / epithelial cell differentiation / protein sequestering activity / regulation of G2/M transition of mitotic cell cycle / Signaling by FLT3 fusion proteins / DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest / positive regulation of DNA repair / cellular response to amino acid starvation / Translesion synthesis by REV1 / intrinsic apoptotic signaling pathway / Translesion synthesis by POLK / cyclin binding / 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 / negative regulation of protein phosphorylation
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: 2.75 Å
AuthorsBruning, J.B. / Wegener, K.L.
CitationJournal: Chemistry / Year: 2018
Title: Rational Design of a 310-Helical PIP-Box Mimetic Targeting PCNA, the Human Sliding Clamp.
Authors: Wegener, K.L. / McGrath, A.E. / Dixon, N.E. / Oakley, A.J. / Scanlon, D.B. / Abell, A.D. / Bruning, J.B.
History
DepositionFeb 3, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 4, 2018Provider: repository / Type: Initial release
Revision 1.1Aug 1, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Aug 29, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Jan 29, 2020Group: Derived calculations
Category: pdbx_struct_assembly_gen / pdbx_struct_assembly_prop
Item: _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_assembly_prop.value

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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
H: GLY-ARG-LYS-ARG-ARG-GLN-DAB-SER-MET-THR-GLU-PHE-TYR-HIS
I: GLY-ARG-LYS-ARG-ARG-GLN-DAB-SER-MET-THR-GLU-PHE-TYR-HIS
J: GLY-ARG-LYS-ARG-ARG-GLN-DAB-SER-MET-THR-GLU-PHE-TYR-HIS
K: GLY-ARG-LYS-ARG-ARG-GLN-DAB-SER-MET-THR-GLU-PHE-TYR-HIS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)180,17112
Polymers179,97910
Non-polymers1922
Water3,819212
1
A: Proliferating cell nuclear antigen
C: Proliferating cell nuclear antigen
E: Proliferating cell nuclear antigen
H: GLY-ARG-LYS-ARG-ARG-GLN-DAB-SER-MET-THR-GLU-PHE-TYR-HIS
I: GLY-ARG-LYS-ARG-ARG-GLN-DAB-SER-MET-THR-GLU-PHE-TYR-HIS
K: GLY-ARG-LYS-ARG-ARG-GLN-DAB-SER-MET-THR-GLU-PHE-TYR-HIS


Theoretical massNumber of molelcules
Total (without water)91,7906
Polymers91,7906
Non-polymers00
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7260 Å2
ΔGint-45 kcal/mol
Surface area33880 Å2
MethodPISA
2
B: Proliferating cell nuclear antigen
D: Proliferating cell nuclear antigen
F: Proliferating cell nuclear antigen
J: GLY-ARG-LYS-ARG-ARG-GLN-DAB-SER-MET-THR-GLU-PHE-TYR-HIS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,3806
Polymers88,1884
Non-polymers1922
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5690 Å2
ΔGint-56 kcal/mol
Surface area33320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.260, 144.820, 174.480
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 28795.752 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) / Strain (production host): BL21(DE3) / References: UniProt: P12004
#2: Protein/peptide
GLY-ARG-LYS-ARG-ARG-GLN-DAB-SER-MET-THR-GLU-PHE-TYR-HIS


Mass: 1801.061 Da / Num. of mol.: 4 / Source method: obtained synthetically
Details: peptide mimetic with covalent lactam bridge between DAB and Glu side chains
Source: (synth.) Homo sapiens (human) / References: UniProt: P38936*PLUS
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 212 / 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: 2.75 Å3/Da / Density % sol: 55.22 %
Crystal growTemperature: 289 K / Method: vapor diffusion / Details: 2M ammonium sulfate 0.1M Tris pH8.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Jul 8, 2015 / Details: mirror
RadiationMonochromator: Double Si with sagittaly bent second crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.75→46.68 Å / Num. obs: 47028 / % possible obs: 91 % / Redundancy: 3.6 % / Biso Wilson estimate: 57.7 Å2 / CC1/2: 0.98 / Rmerge(I) obs: 0.196 / Rpim(I) all: 0.108 / Rrim(I) all: 0.225 / Net I/σ(I): 4.8 / Num. measured all: 171431 / Scaling rejects: 4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
2.75-2.843.51.89938910.2061.0762.281.9
11-46.684.30.0487880.9940.0250.05590.2

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
PHENIX(1.11.1_2575: ???)refinement
MOSFLMdata reduction
Aimless0.3.11data scaling
PHASERphasing
PDB_EXTRACT3.24data extraction
RefinementResolution: 2.75→41.086 Å / SU ML: 0.45 / σ(F): 1.33 / Phase error: 28.37 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2523 2328 4.96 %
Rwork0.2082 --
obs0.2104 46931 89.61 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.75→41.086 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11682 0 10 212 11904
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00611893
X-RAY DIFFRACTIONf_angle_d1.01116059
X-RAY DIFFRACTIONf_dihedral_angle_d13.797331
X-RAY DIFFRACTIONf_chiral_restr0.0521909
X-RAY DIFFRACTIONf_plane_restr0.0092038
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.75-2.80620.35771120.34212322X-RAY DIFFRACTION80
2.8062-2.86720.39751280.32672338X-RAY DIFFRACTION81
2.8672-2.93380.38071320.32522353X-RAY DIFFRACTION82
2.9338-3.00720.34451210.31212369X-RAY DIFFRACTION82
3.0072-3.08850.38251440.2992419X-RAY DIFFRACTION85
3.0885-3.17930.33981350.29222494X-RAY DIFFRACTION87
3.1793-3.28190.33441540.2672565X-RAY DIFFRACTION89
3.2819-3.39910.32671220.24072667X-RAY DIFFRACTION91
3.3991-3.53520.28631380.22282673X-RAY DIFFRACTION92
3.5352-3.6960.2411470.21232705X-RAY DIFFRACTION94
3.696-3.89070.22931470.19842763X-RAY DIFFRACTION94
3.8907-4.13420.23241280.18442799X-RAY DIFFRACTION95
4.1342-4.45310.19921400.16362797X-RAY DIFFRACTION95
4.4531-4.90060.19681400.13932831X-RAY DIFFRACTION96
4.9006-5.60820.19151490.15732826X-RAY DIFFRACTION96
5.6082-7.05990.22431400.21472845X-RAY DIFFRACTION95
7.0599-41.09040.21991510.19662837X-RAY DIFFRACTION91

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