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- PDB-7m5n: PCNA bound to peptide mimetic with linker -

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Basic information

Entry
Database: PDB / ID: 7m5n
TitlePCNA bound to peptide mimetic with linker
Components
  • Peptide mimetic (ACE)RQCSMTCFYHSK(NH2) with linker
  • 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 / positive regulation of DNA replication / replication fork / 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
1,3-dimethylbenzene / Proliferating cell nuclear antigen
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.11 Å
AuthorsVandborg, B.A. / Bruning, J.B.
CitationJournal: Rsc Chem Biol / Year: 2021
Title: A cell permeable bimane-constrained PCNA-interacting peptide.
Authors: Horsfall, A.J. / Vandborg, B.A. / Kikhtyak, Z. / Scanlon, D.B. / Tilley, W.D. / Hickey, T.E. / Bruning, J.B. / Abell, A.D.
History
DepositionMar 24, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 11, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 10, 2021Group: 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_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
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: Proliferating cell nuclear antigen
C: Proliferating cell nuclear antigen
E: Peptide mimetic (ACE)RQCSMTCFYHSK(NH2) with linker
D: Peptide mimetic (ACE)RQCSMTCFYHSK(NH2) with linker
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,2037
Polymers88,9905
Non-polymers2122
Water00
1
A: Proliferating cell nuclear antigen
C: Proliferating cell nuclear antigen
D: Peptide mimetic (ACE)RQCSMTCFYHSK(NH2) with linker
hetero molecules

B: Proliferating cell nuclear antigen
E: Peptide mimetic (ACE)RQCSMTCFYHSK(NH2) with linker
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,2037
Polymers88,9905
Non-polymers2122
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_455y-1,x,-z1
Buried area5450 Å2
ΔGint-35 kcal/mol
Surface area35050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.365, 83.365, 181.155
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 2 or (resid 3 through 4...
21(chain B and (resid 2 through 4 or (resid 5...
31(chain C and (resid 2 or (resid 3 through 4...
12(chain D and (name C14 or name C15 or name...
22chain E

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and (resid 2 or (resid 3 through 4...A2
121(chain A and (resid 2 or (resid 3 through 4...A3 - 4
131(chain A and (resid 2 or (resid 3 through 4...A1 - 254
141(chain A and (resid 2 or (resid 3 through 4...A1 - 254
151(chain A and (resid 2 or (resid 3 through 4...A1 - 254
211(chain B and (resid 2 through 4 or (resid 5...B2 - 4
221(chain B and (resid 2 through 4 or (resid 5...B5
231(chain B and (resid 2 through 4 or (resid 5...B2 - 255
241(chain B and (resid 2 through 4 or (resid 5...B2 - 255
251(chain B and (resid 2 through 4 or (resid 5...B2 - 255
261(chain B and (resid 2 through 4 or (resid 5...B2 - 255
271(chain B and (resid 2 through 4 or (resid 5...B2 - 255
281(chain B and (resid 2 through 4 or (resid 5...B2 - 255
311(chain C and (resid 2 or (resid 3 through 4...C2
321(chain C and (resid 2 or (resid 3 through 4...C3 - 4
331(chain C and (resid 2 or (resid 3 through 4...C1 - 255
341(chain C and (resid 2 or (resid 3 through 4...C1 - 255
351(chain C and (resid 2 or (resid 3 through 4...C1 - 255
112(chain D and (name C14 or name C15 or name...D0
212chain EE1

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 Peptide mimetic (ACE)RQCSMTCFYHSK(NH2) with linker


Mass: 1517.798 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical ChemComp-8VH / 1,3-dimethylbenzene


Mass: 106.165 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H10 / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY

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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: 2.09 Å3/Da / Density % sol: 41.13 % / Description: hexagonal
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.18M magnesium acetate, 19.3% poly(ethylene) glycol 3350

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: liquid nitrogen / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9537 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 16, 2020 / 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: 0.12
ReflectionResolution: 3.11→38.37 Å / Num. obs: 13728 / % possible obs: 99.7 % / Redundancy: 13 % / CC1/2: 0.997 / Rmerge(I) obs: 0.201 / Rpim(I) all: 0.054 / Rrim(I) all: 0.209 / Net I/σ(I): 10.9 / Num. measured all: 178503 / Scaling rejects: 851
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
3.11-3.3210.10.6532445324140.9320.2120.6883.598.7
8.79-38.3716.80.105116136920.9990.0250.10824.698.9

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
Aimless0.7.4data scaling
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1AXC

1axc


Resolution: 3.11→38.37 Å / Cross valid method: THROUGHOUT / σ(F): 0.6 / Phase error: 33.06 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.3086 666 5.15 %
Rwork0.2724 12306 -
obs0.278 12930 94.22 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 128.55 Å2 / Biso mean: 60.8255 Å2 / Biso min: 33.43 Å2
Refinement stepCycle: final / Resolution: 3.11→38.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5170 0 151 0 5321
Biso mean--67.61 --
Num. residues----755
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2142X-RAY DIFFRACTION12.727TORSIONAL
12B2142X-RAY DIFFRACTION12.727TORSIONAL
13C2142X-RAY DIFFRACTION12.727TORSIONAL
21D22X-RAY DIFFRACTION12.727TORSIONAL
22E22X-RAY DIFFRACTION12.727TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 4

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.11-3.420.38181410.34162854299585
3.42-3.910.33011520.28843013316589
3.91-4.930.32741650.2423127329291
4.93-38.370.28251660.2733312347893
Refinement TLS params.Method: refined / Origin x: -17.5095 Å / Origin y: 41.862 Å / Origin z: 5.0098 Å
111213212223313233
T0.0613 Å20.1828 Å2-0.0707 Å2-0.0174 Å20.0316 Å2--1.3605 Å2
L0.0053 °20.0992 °2-0.0396 °2-0.3293 °2-0.1723 °2--0.1112 °2
S0.0338 Å °0.0016 Å °0.2517 Å °-0.0306 Å °0.0161 Å °0.041 Å °-0.0656 Å °0.0938 Å °0.0136 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA1 - 254
2X-RAY DIFFRACTION1allB2 - 255
3X-RAY DIFFRACTION1allC1 - 255
4X-RAY DIFFRACTION1allE1
5X-RAY DIFFRACTION1allD301

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