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- PDB-7kq1: PCNA bound to truncated peptide mimetic -

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Basic information

Entry
Database: PDB / ID: 7kq1
TitlePCNA bound to truncated peptide mimetic
Components
  • LYS-ARG-ARG-GLN-THR-SER-MET-THR-ASP-PHE-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 / positive regulation of DNA-directed DNA polymerase activity / nuclear lamina / MutLalpha complex binding / 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 / positive regulation of DNA-directed DNA polymerase activity / nuclear lamina / MutLalpha complex binding / 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: 3.3 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 ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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


Theoretical massNumber of molelcules
Total (without water)91,7976
Polymers91,7976
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8950 Å2
ΔGint-46 kcal/mol
Surface area35460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)136.660, 136.660, 104.005
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 1 through 4 or (resid 5...
21(chain C and (resid 1 through 4 or (resid 5...
31(chain E and (resid 1 through 16 or (resid 17...
12(chain B and ((resid 142 through 143 and (name N...
22(chain D and ((resid 142 through 143 and (name N...
32(chain F and ((resid 142 through 143 and (name N...

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111METMETALAALA(chain A and (resid 1 through 4 or (resid 5...AA1 - 41 - 4
121ARGARGARGARG(chain A and (resid 1 through 4 or (resid 5...AA55
131METMETASPASP(chain A and (resid 1 through 4 or (resid 5...AA1 - 2571 - 257
141METMETASPASP(chain A and (resid 1 through 4 or (resid 5...AA1 - 2571 - 257
151METMETASPASP(chain A and (resid 1 through 4 or (resid 5...AA1 - 2571 - 257
161METMETASPASP(chain A and (resid 1 through 4 or (resid 5...AA1 - 2571 - 257
171METMETASPASP(chain A and (resid 1 through 4 or (resid 5...AA1 - 2571 - 257
181METMETASPASP(chain A and (resid 1 through 4 or (resid 5...AA1 - 2571 - 257
191METMETASPASP(chain A and (resid 1 through 4 or (resid 5...AA1 - 2571 - 257
1101METMETASPASP(chain A and (resid 1 through 4 or (resid 5...AA1 - 2571 - 257
211METMETALAALA(chain C and (resid 1 through 4 or (resid 5...CC1 - 41 - 4
221ARGARGARGARG(chain C and (resid 1 through 4 or (resid 5...CC55
231METMETASPASP(chain C and (resid 1 through 4 or (resid 5...CC1 - 2571 - 257
241METMETASPASP(chain C and (resid 1 through 4 or (resid 5...CC1 - 2571 - 257
251METMETASPASP(chain C and (resid 1 through 4 or (resid 5...CC1 - 2571 - 257
261METMETASPASP(chain C and (resid 1 through 4 or (resid 5...CC1 - 2571 - 257
271METMETASPASP(chain C and (resid 1 through 4 or (resid 5...CC1 - 2571 - 257
281METMETASPASP(chain C and (resid 1 through 4 or (resid 5...CC1 - 2571 - 257
291METMETASPASP(chain C and (resid 1 through 4 or (resid 5...CC1 - 2571 - 257
2101METMETASPASP(chain C and (resid 1 through 4 or (resid 5...CC1 - 2571 - 257
311METMETLEULEU(chain E and (resid 1 through 16 or (resid 17...EE1 - 161 - 16
321GLUGLUALAALA(chain E and (resid 1 through 16 or (resid 17...EE17 - 1817 - 18
331METMETGLUGLU(chain E and (resid 1 through 16 or (resid 17...EE1 - 2591 - 259
341METMETGLUGLU(chain E and (resid 1 through 16 or (resid 17...EE1 - 2591 - 259
351METMETGLUGLU(chain E and (resid 1 through 16 or (resid 17...EE1 - 2591 - 259
361METMETGLUGLU(chain E and (resid 1 through 16 or (resid 17...EE1 - 2591 - 259
112ARGARGARGARG(chain B and ((resid 142 through 143 and (name N...BB142 - 1432 - 3
122LYSLYSARGARG(chain B and ((resid 142 through 143 and (name N...BB141 - 1551 - 15
132LYSLYSARGARG(chain B and ((resid 142 through 143 and (name N...BB141 - 1551 - 15
142LYSLYSARGARG(chain B and ((resid 142 through 143 and (name N...BB141 - 1551 - 15
152LYSLYSARGARG(chain B and ((resid 142 through 143 and (name N...BB141 - 1551 - 15
212ARGARGARGARG(chain D and ((resid 142 through 143 and (name N...DD142 - 1432 - 3
222LYSLYSARGARG(chain D and ((resid 142 through 143 and (name N...DD141 - 1551 - 15
232LYSLYSARGARG(chain D and ((resid 142 through 143 and (name N...DD141 - 1551 - 15
242LYSLYSARGARG(chain D and ((resid 142 through 143 and (name N...DD141 - 1551 - 15
252LYSLYSARGARG(chain D and ((resid 142 through 143 and (name N...DD141 - 1551 - 15
312ARGARGARGARG(chain F and ((resid 142 through 143 and (name N...FF142 - 1432 - 3
322ARGARGLYSLYS(chain F and ((resid 142 through 143 and (name N...FF142 - 1542 - 14
332ARGARGLYSLYS(chain F and ((resid 142 through 143 and (name N...FF142 - 1542 - 14
342ARGARGLYSLYS(chain F and ((resid 142 through 143 and (name N...FF142 - 1542 - 14
352ARGARGLYSLYS(chain F and ((resid 142 through 143 and (name N...FF142 - 1542 - 14

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-PHE-TYR-HIS-SER-LYS-ARG


Mass: 1947.226 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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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: 3.05 Å3/Da / Density % sol: 59.73 % / Description: needles
Crystal growTemperature: 289.15 K / Method: vapor diffusion, hanging drop
Details: 0.1M sodium malonate and 8% 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 EIGER2 X 9M / Detector: PIXEL / Date: Mar 30, 2019 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 3.3→44.73 Å / Num. obs: 17231 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 19.9 % / CC1/2: 0.999 / Rmerge(I) obs: 0.283 / Rpim(I) all: 0.065 / Rrim(I) all: 0.291 / Net I/σ(I): 10.4
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
3.3-3.5618.23.1656378634970.6260.7553.2551.299.9
8.73-44.7317.60.0491770110070.9990.0120.054999.4

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Processing

Software
NameVersionClassification
Aimless0.7.4data scaling
PHENIX1.18.2_3874refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5MLO

5mlo


Resolution: 3.3→41.38 Å / SU ML: 0.52 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 32.99 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2674 1716 9.98 %
Rwork0.2417 15477 -
obs0.2443 17193 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 172.15 Å2 / Biso mean: 108.5069 Å2 / Biso min: 77.63 Å2
Refinement stepCycle: final / Resolution: 3.3→41.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6084 0 0 0 6084
Num. residues----816
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2313X-RAY DIFFRACTION10.882TORSIONAL
12C2313X-RAY DIFFRACTION10.882TORSIONAL
13E2313X-RAY DIFFRACTION10.882TORSIONAL
21B108X-RAY DIFFRACTION10.882TORSIONAL
22D108X-RAY DIFFRACTION10.882TORSIONAL
23F108X-RAY DIFFRACTION10.882TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 12 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
3.3-3.40.37451430.365512601403
3.4-3.510.37321440.339112741418
3.51-3.630.31871340.29612561390
3.63-3.780.3091420.288412761418
3.78-3.950.28091410.295412791420
3.95-4.160.34211440.270512791423
4.16-4.420.23561500.218712881438
4.42-4.760.26731410.205412761417
4.76-5.240.24711350.218713021437
5.24-5.990.28011480.261912921440
5.99-7.540.31131410.275713301471
7.54-41.380.20331530.192713651518

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