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- PDB-7kq0: PCNA bound to peptide mimetic -

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Basic information

Entry
Database: PDB / ID: 7kq0
TitlePCNA bound to peptide mimetic
Components
  • LYS-ARG-ARG-GLN-THR-SER-MET-THR-ASP-TYR-TYR-HIS-SER-LYS-ARG
  • Proliferating cell nuclear antigen
KeywordsREPLICATION / PCNA / DNA replication / peptide mimetic
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
Proliferating cell nuclear antigen
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsVandborg, B.A. / Bruning, J.B.
CitationJournal: J.Biol.Chem. / Year: 2021
Title: Unlocking the PIP-box: A peptide library reveals interactions that drive high-affinity binding to human PCNA.
Authors: Horsfall, A.J. / Vandborg, B.A. / Kowalczyk, W. / Chav, T. / Scanlon, D.B. / Abell, A.D. / Bruning, J.B.
History
DepositionNov 13, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 19, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 6, 2021Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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: LYS-ARG-ARG-GLN-THR-SER-MET-THR-ASP-TYR-TYR-HIS-SER-LYS-ARG
C: Proliferating cell nuclear antigen
D: LYS-ARG-ARG-GLN-THR-SER-MET-THR-ASP-TYR-TYR-HIS-SER-LYS-ARG
E: Proliferating cell nuclear antigen
F: LYS-ARG-ARG-GLN-THR-SER-MET-THR-ASP-TYR-TYR-HIS-SER-LYS-ARG


Theoretical massNumber of molelcules
Total (without water)91,8456
Polymers91,8456
Non-polymers00
Water1,982110
1
A: Proliferating cell nuclear antigen
B: LYS-ARG-ARG-GLN-THR-SER-MET-THR-ASP-TYR-TYR-HIS-SER-LYS-ARG

A: Proliferating cell nuclear antigen
B: LYS-ARG-ARG-GLN-THR-SER-MET-THR-ASP-TYR-TYR-HIS-SER-LYS-ARG

A: Proliferating cell nuclear antigen
B: LYS-ARG-ARG-GLN-THR-SER-MET-THR-ASP-TYR-TYR-HIS-SER-LYS-ARG


Theoretical massNumber of molelcules
Total (without water)91,8456
Polymers91,8456
Non-polymers00
Water1086
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 area8240 Å2
ΔGint-49 kcal/mol
Surface area34110 Å2
MethodPISA
2
C: Proliferating cell nuclear antigen
D: LYS-ARG-ARG-GLN-THR-SER-MET-THR-ASP-TYR-TYR-HIS-SER-LYS-ARG

C: Proliferating cell nuclear antigen
D: LYS-ARG-ARG-GLN-THR-SER-MET-THR-ASP-TYR-TYR-HIS-SER-LYS-ARG

C: Proliferating cell nuclear antigen
D: LYS-ARG-ARG-GLN-THR-SER-MET-THR-ASP-TYR-TYR-HIS-SER-LYS-ARG


Theoretical massNumber of molelcules
Total (without water)91,8456
Polymers91,8456
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_445-y-1,x-y-1,z1
crystal symmetry operation3_545-x+y,-x-1,z1
Buried area8250 Å2
ΔGint-52 kcal/mol
Surface area34090 Å2
MethodPISA
3
E: Proliferating cell nuclear antigen
F: LYS-ARG-ARG-GLN-THR-SER-MET-THR-ASP-TYR-TYR-HIS-SER-LYS-ARG

E: Proliferating cell nuclear antigen
F: LYS-ARG-ARG-GLN-THR-SER-MET-THR-ASP-TYR-TYR-HIS-SER-LYS-ARG

E: Proliferating cell nuclear antigen
F: LYS-ARG-ARG-GLN-THR-SER-MET-THR-ASP-TYR-TYR-HIS-SER-LYS-ARG


Theoretical massNumber of molelcules
Total (without water)91,8456
Polymers91,8456
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area8100 Å2
ΔGint-50 kcal/mol
Surface area34060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)142.563, 142.563, 41.030
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number143
Space group name H-MP3
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 1 through 2 or (resid 3...
21(chain C and (resid 1 through 2 or (resid 3...
31(chain E and (resid 1 through 7 or (resid 8...
12(chain B and resid 143 through 154)
22(chain D and (resid 143 through 152 or (resid 153...
32(chain F and ((resid 143 and (name N or name...

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and (resid 1 through 2 or (resid 3...A1 - 2
121(chain A and (resid 1 through 2 or (resid 3...A3
131(chain A and (resid 1 through 2 or (resid 3...A1 - 257
141(chain A and (resid 1 through 2 or (resid 3...A1 - 257
151(chain A and (resid 1 through 2 or (resid 3...A1 - 257
161(chain A and (resid 1 through 2 or (resid 3...A1 - 257
171(chain A and (resid 1 through 2 or (resid 3...A1 - 257
181(chain A and (resid 1 through 2 or (resid 3...A1 - 257
211(chain C and (resid 1 through 2 or (resid 3...C1 - 2
221(chain C and (resid 1 through 2 or (resid 3...C3
231(chain C and (resid 1 through 2 or (resid 3...C1 - 256
241(chain C and (resid 1 through 2 or (resid 3...C1 - 256
251(chain C and (resid 1 through 2 or (resid 3...C1 - 256
261(chain C and (resid 1 through 2 or (resid 3...C1 - 256
271(chain C and (resid 1 through 2 or (resid 3...C1 - 256
281(chain C and (resid 1 through 2 or (resid 3...C1 - 256
291(chain C and (resid 1 through 2 or (resid 3...C1 - 256
311(chain E and (resid 1 through 7 or (resid 8...E1 - 7
321(chain E and (resid 1 through 7 or (resid 8...E8
331(chain E and (resid 1 through 7 or (resid 8...E1 - 256
112(chain B and resid 143 through 154)B143 - 154
212(chain D and (resid 143 through 152 or (resid 153...D0
312(chain F and ((resid 143 and (name N or name...F143
322(chain F and ((resid 143 and (name N or name...F143 - 155
332(chain F and ((resid 143 and (name N or name...F143 - 155
342(chain F and ((resid 143 and (name N or name...F143 - 155
352(chain F and ((resid 143 and (name N or name...F143 - 155

NCS ensembles :
ID
1
2

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Components

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


Mass: 28651.621 Da / Num. of mol.: 3
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 LYS-ARG-ARG-GLN-THR-SER-MET-THR-ASP-TYR-TYR-HIS-SER-LYS-ARG


Mass: 1963.226 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 110 / 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: 2.62 Å3/Da / Density % sol: 53.07 % / Description: needles
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.18M magnesium acetate, 20% poly(ethylene) glycol 3350

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: liquid nitrogen cryostat / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9537 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 21, 2019 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
Reflection twinOperator: -h,-k,l / Fraction: 0.43
ReflectionResolution: 2.4→46.66 Å / Num. obs: 32885 / % possible obs: 90.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 10.7 % / CC1/2: 1 / Rmerge(I) obs: 0.043 / Rpim(I) all: 0.014 / Rrim(I) all: 0.046 / Net I/σ(I): 40.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.4-2.4911.10.1824228738180.9870.0570.19113.6100
8.98-46.6611.60.026811169710.0080.0278799.5

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
Aimless0.7.4data scaling
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4RJF

4rjf


Resolution: 2.4→46.66 Å / Cross valid method: THROUGHOUT / σ(F): 64.77 / Phase error: 29.36 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflectionSelection details
Rfree0.2011 2032 6.18 %random selection
Rwork0.1537 30852 --
obs0.164 32883 90.15 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 99.45 Å2 / Biso mean: 32.2253 Å2 / Biso min: 15.59 Å2
Refinement stepCycle: final / Resolution: 2.4→46.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5962 0 0 110 6072
Biso mean---31.69 -
Num. residues----807
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A3187X-RAY DIFFRACTION10.126TORSIONAL
12C3187X-RAY DIFFRACTION10.126TORSIONAL
13E3187X-RAY DIFFRACTION10.126TORSIONAL
21B146X-RAY DIFFRACTION10.126TORSIONAL
22D146X-RAY DIFFRACTION10.126TORSIONAL
23F146X-RAY DIFFRACTION10.126TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 15

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.4-2.460.28641460.212276242294
2.46-2.520.26591540.20772266242094
2.52-2.590.22341500.20152294244494
2.59-2.640.32411010.19831588168965
2.7-2.750.2727800.1911300138053
2.75-2.850.22451500.19142241239194
2.85-2.960.27841540.18322304245894
2.96-3.090.23271520.17732273242594
3.09-3.260.22921410.16732252239394
3.26-3.410.2151220.16011750187271
3.47-3.70.171360.15042004214082
3.8-4.10.20321170.14281823194075
4.1-4.70.18391280.12211897202579
4.7-5.910.15721470.12592318246594
5.92-46.660.19081530.17052266241994

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