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- PDB-7m5l: PCNA bound to peptide mimetic with linker -

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Basic information

Entry
Database: PDB / ID: 7m5l
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 / 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
PROPANE / Proliferating cell nuclear antigen
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 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
F: Peptide mimetic (ACE)RQCSMTCFYHSK(NH2) with linker
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,2539
Polymers90,1216
Non-polymers1323
Water00
1
B: Proliferating cell nuclear antigen
E: Peptide mimetic (ACE)RQCSMTCFYHSK(NH2) with linker
hetero molecules

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

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


Theoretical massNumber of molelcules
Total (without water)90,2539
Polymers90,1216
Non-polymers1323
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x+1/2,-y,z+1/21
crystal symmetry operation3_545-x,y-1/2,-z+1/21
Buried area7780 Å2
ΔGint-45 kcal/mol
Surface area34930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.960, 84.468, 134.210
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 1 through 7 or (resid 8...
21(chain B and (resid 1 through 2 or (resid 3...
31(chain C and (resid 1 through 2 or (resid 3...
12(chain D and (name C14 or name C15 or name...
22(chain E and (name C14 or name C15 or name...
32(chain F and (name C14 or name C15 or name...

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and (resid 1 through 7 or (resid 8...A1 - 7
121(chain A and (resid 1 through 7 or (resid 8...A8
131(chain A and (resid 1 through 7 or (resid 8...A1 - 257
141(chain A and (resid 1 through 7 or (resid 8...A1 - 257
151(chain A and (resid 1 through 7 or (resid 8...A1 - 257
211(chain B and (resid 1 through 2 or (resid 3...B1 - 2
221(chain B and (resid 1 through 2 or (resid 3...B3 - 4
231(chain B and (resid 1 through 2 or (resid 3...B1 - 257
241(chain B and (resid 1 through 2 or (resid 3...B1 - 257
251(chain B and (resid 1 through 2 or (resid 3...B1 - 257
261(chain B and (resid 1 through 2 or (resid 3...B1 - 257
311(chain C and (resid 1 through 2 or (resid 3...C1 - 2
321(chain C and (resid 1 through 2 or (resid 3...C3 - 4
331(chain C and (resid 1 through 2 or (resid 3...C1 - 255
341(chain C and (resid 1 through 2 or (resid 3...C1 - 255
351(chain C and (resid 1 through 2 or (resid 3...C1 - 255
361(chain C and (resid 1 through 2 or (resid 3...C1 - 255
112(chain D and (name C14 or name C15 or name...D0
212(chain E and (name C14 or name C15 or name...E0
312(chain F and (name C14 or name C15 or name...F0

NCS ensembles :
ID
1
2

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Components

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


Mass: 28522.508 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.: 3 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical ChemComp-TME / PROPANE


Mass: 44.096 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8 / 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: 2.35 Å3/Da / Density % sol: 47.67 % / Description: hexagonal
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.18M magnesium acetate, 19.2% 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: MX2 / Wavelength: 0.9537 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Oct 3, 2020 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 3→48.76 Å / Num. obs: 16781 / % possible obs: 100 % / Redundancy: 13.2 % / CC1/2: 0.999 / Rmerge(I) obs: 0.181 / Rpim(I) all: 0.052 / Rrim(I) all: 0.188 / Net I/σ(I): 9.6 / Num. measured all: 222239 / Scaling rejects: 2
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
3-3.1812.83.5243380226510.4561.0193.6710.7100
9-48.7611.60.0481457030.9990.0120.04146.499.2

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Processing

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

1axc


Resolution: 3→48.76 Å / SU ML: 0.49 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 38.54 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2752 859 5.15 %
Rwork0.2598 15825 -
obs0.2606 16684 99.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 212.54 Å2 / Biso mean: 106.5054 Å2 / Biso min: 55.74 Å2
Refinement stepCycle: final / Resolution: 3→48.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5395 0 241 0 5636
Biso mean--133.71 --
Num. residues----769
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2247X-RAY DIFFRACTION10.823TORSIONAL
12B2247X-RAY DIFFRACTION10.823TORSIONAL
13C2247X-RAY DIFFRACTION10.823TORSIONAL
21D30X-RAY DIFFRACTION10.823TORSIONAL
22E30X-RAY DIFFRACTION10.823TORSIONAL
23F30X-RAY DIFFRACTION10.823TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3-3.190.41541310.39452574270599
3.19-3.430.37221480.356125822730100
3.43-3.780.36631420.307726072749100
3.78-4.330.33321310.281926352766100
4.33-5.450.21481480.224726542802100
5.45-48.760.23881590.228527732932100
Refinement TLS params.Method: refined / Origin x: 17.0965 Å / Origin y: -3.0641 Å / Origin z: 16.3566 Å
111213212223313233
T0.6971 Å20.0108 Å20.0884 Å2-0.7001 Å2-0.0451 Å2--0.7212 Å2
L0.2792 °2-0.1103 °20.0449 °2-0.2205 °2-0.314 °2--0.1572 °2
S0.0232 Å °-0.074 Å °-0.0905 Å °0.0302 Å °-0.0183 Å °0.0855 Å °-0.001 Å °0.0077 Å °-0.0011 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA1 - 257
2X-RAY DIFFRACTION1allB1 - 257
3X-RAY DIFFRACTION1allC1 - 255
4X-RAY DIFFRACTION1allE301
5X-RAY DIFFRACTION1allD401
6X-RAY DIFFRACTION1allF301

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