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- PDB-6k3a: Crystal structure of human PCNA in complex with DNMT1 PIP box motif. -

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Basic information

Entry
Database: PDB / ID: 6k3a
TitleCrystal structure of human PCNA in complex with DNMT1 PIP box motif.
Components
  • Peptide from DNA (cytosine-5)-methyltransferase 1
  • Proliferating cell nuclear antigen
KeywordsREPLICATION / DNMT1 / PCNA / DNA methylation / PIP box
Function / homology
Function and homology information


chromosomal DNA methylation maintenance following DNA replication / negative regulation of vascular associated smooth muscle cell differentiation involved in phenotypic switching / epigenetic programming of gene expression / DNA-methyltransferase activity / negative regulation of vascular associated smooth muscle cell apoptotic process / positive regulation of deoxyribonuclease activity / dinucleotide insertion or deletion binding / PCNA-p21 complex / mitotic telomere maintenance via semi-conservative replication / cellular response to bisphenol A ...chromosomal DNA methylation maintenance following DNA replication / negative regulation of vascular associated smooth muscle cell differentiation involved in phenotypic switching / epigenetic programming of gene expression / DNA-methyltransferase activity / negative regulation of vascular associated smooth muscle cell apoptotic process / positive regulation of deoxyribonuclease activity / dinucleotide insertion or deletion binding / PCNA-p21 complex / mitotic telomere maintenance via semi-conservative replication / cellular response to bisphenol A / DNA (cytosine-5-)-methyltransferase / DNA (cytosine-5-)-methyltransferase activity / purine-specific mismatch base pair DNA N-glycosylase activity / nuclear lamina / positive regulation of DNA-directed DNA polymerase activity / Polymerase switching / MutLalpha complex binding / Telomere C-strand (Lagging Strand) Synthesis / SUMOylation of DNA methylation proteins / Processive synthesis on the lagging strand / PCNA complex / Removal of the Flap Intermediate / female germ cell nucleus / Processive synthesis on the C-strand of the telomere / STAT3 nuclear events downstream of ALK signaling / Polymerase switching on the C-strand of the telomere / Mismatch repair (MMR) directed by MSH2:MSH3 (MutSbeta) / Mismatch repair (MMR) directed by MSH2:MSH6 (MutSalpha) / Removal of the Flap Intermediate from the C-strand / methyl-CpG binding / Transcription of E2F targets under negative control by DREAM complex / replisome / response to L-glutamate / DNA methylation-dependent constitutive heterochromatin formation / negative regulation of gene expression via chromosomal CpG island methylation / response to dexamethasone / histone acetyltransferase binding / lncRNA binding / DNA polymerase processivity factor activity / leading strand elongation / G1/S-Specific Transcription / replication fork processing / nuclear replication fork / pericentric heterochromatin / SUMOylation of DNA replication proteins / PCNA-Dependent Long Patch Base Excision Repair / response to cadmium ion / translesion synthesis / mismatch repair / estrous cycle / cyclin-dependent protein kinase holoenzyme complex / Nuclear events stimulated by ALK signaling in cancer / positive regulation of vascular associated smooth muscle cell proliferation / Translesion synthesis by REV1 / Translesion synthesis by POLK / base-excision repair, gap-filling / DNA polymerase binding / Translesion synthesis by POLI / Gap-filling DNA repair synthesis and ligation in GG-NER / epithelial cell differentiation / liver regeneration / positive regulation of DNA repair / DNA methylation / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / positive regulation of DNA replication / Termination of translesion DNA synthesis / replication fork / Recognition of DNA damage by PCNA-containing replication complex / nuclear estrogen receptor binding / PRC2 methylates histones and DNA / Translesion Synthesis by POLH / Defective pyroptosis / male germ cell nucleus / cellular response to amino acid stimulus / promoter-specific chromatin binding / HDR through Homologous Recombination (HRR) / Dual Incision in GG-NER / NoRC negatively regulates rRNA expression / receptor tyrosine kinase binding / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / cellular response to xenobiotic stimulus / cellular response to hydrogen peroxide / cellular response to UV / E3 ubiquitin ligases ubiquitinate target proteins / response to estradiol / heart development / chromatin organization / methylation / damaged DNA binding / chromosome, telomeric region / nuclear body / negative regulation of gene expression / DNA-templated transcription / centrosome / chromatin binding / positive regulation of gene expression / chromatin / protein-containing complex binding / enzyme binding
Similarity search - Function
DNA (cytosine-5)-methyltransferase 1-like / DNA (cytosine-5)-methyltransferase 1, replication foci domain / Cytosine specific DNA methyltransferase replication foci domain / DMAP1-binding Domain / DMAP1-binding Domain / DMAP1-binding domain / DMAP1-binding domain profile. / : / DNA methylase, C-5 cytosine-specific, conserved site / C-5 cytosine-specific DNA methylases C-terminal signature. ...DNA (cytosine-5)-methyltransferase 1-like / DNA (cytosine-5)-methyltransferase 1, replication foci domain / Cytosine specific DNA methyltransferase replication foci domain / DMAP1-binding Domain / DMAP1-binding Domain / DMAP1-binding domain / DMAP1-binding domain profile. / : / DNA methylase, C-5 cytosine-specific, conserved site / C-5 cytosine-specific DNA methylases C-terminal signature. / Box / Proliferating Cell Nuclear Antigen / Proliferating Cell Nuclear Antigen - #10 / CXXC zinc finger domain / Zinc finger, CXXC-type / Zinc finger CXXC-type profile. / DNA methylase, C-5 cytosine-specific, active site / C-5 cytosine-specific DNA methylases active site. / C-5 cytosine-specific DNA methylase (Dnmt) domain profile. / C-5 cytosine methyltransferase / C-5 cytosine-specific DNA methylase / Bromo adjacent homology domain / BAH domain / Bromo adjacent homology (BAH) domain / Bromo adjacent homology (BAH) domain superfamily / BAH domain profile. / 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 / : / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Alpha Beta
Similarity search - Domain/homology
DNA methyltransferase 1 / Proliferating cell nuclear antigen / DNA (cytosine-5)-methyltransferase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsJimenji, T. / Kori, S. / Arita, K.
Funding support Japan, 2items
OrganizationGrant numberCountry
Ministry of Education, Culture, Sports, Science and Technology (Japan)18H02392 Japan
Japan Science and Technology14530337 Japan
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2019
Title: Structure of PCNA in complex with DNMT1 PIP box reveals the basis for the molecular mechanism of the interaction.
Authors: Jimenji, T. / Matsumura, R. / Kori, S. / Arita, K.
History
DepositionMay 17, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 26, 2019Provider: repository / Type: Initial release
Revision 1.1Jul 10, 2019Group: Data collection / Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jul 24, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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: Peptide from DNA (cytosine-5)-methyltransferase 1
C: Proliferating cell nuclear antigen
D: Peptide from DNA (cytosine-5)-methyltransferase 1
E: Proliferating cell nuclear antigen
F: Peptide from DNA (cytosine-5)-methyltransferase 1


Theoretical massNumber of molelcules
Total (without water)93,6776
Polymers93,6776
Non-polymers00
Water82946
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8110 Å2
ΔGint-47 kcal/mol
Surface area30950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)141.540, 81.598, 68.105
Angle α, β, γ (deg.)90.00, 90.02, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11C-301-

HOH

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Components

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


Mass: 29006.963 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 from DNA (cytosine-5)-methyltransferase 1


Mass: 2218.557 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: K7ERQ1, UniProt: P26358*PLUS
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 46 / 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: 2.1 Å3/Da / Density % sol: 41.41 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 6.5 / Details: 1.6M sodium citrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 15, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.3→40.84 Å / Num. obs: 34458 / % possible obs: 99.7 % / Redundancy: 3.2 % / CC1/2: 0.997 / Rmerge(I) obs: 0.062 / Net I/av σ(I): 8.2 / Net I/σ(I): 0
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.664 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 3366 / CC1/2: 0.705 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX(1.15.2_3472: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5MLO

5mlo


Resolution: 2.3→40.84 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 30.89
RfactorNum. reflection% reflection
Rfree0.2643 1783 5.19 %
Rwork0.2171 --
obs0.2195 34349 99.35 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.3→40.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5625 0 0 46 5671
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0055694
X-RAY DIFFRACTIONf_angle_d0.8527689
X-RAY DIFFRACTIONf_dihedral_angle_d6.3783462
X-RAY DIFFRACTIONf_chiral_restr0.05951
X-RAY DIFFRACTIONf_plane_restr0.005948
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3001-2.36220.40191030.31922565X-RAY DIFFRACTION100
2.3622-2.43170.35761600.3012459X-RAY DIFFRACTION100
2.4317-2.51020.32261500.28672437X-RAY DIFFRACTION100
2.5102-2.59990.36811320.2792545X-RAY DIFFRACTION100
2.5999-2.7040.31121360.27212498X-RAY DIFFRACTION100
2.704-2.8270.33031580.27322497X-RAY DIFFRACTION100
2.827-2.9760.35621490.27972473X-RAY DIFFRACTION100
2.976-3.16240.32651340.25892509X-RAY DIFFRACTION99
3.1624-3.40650.36251000.23852547X-RAY DIFFRACTION99
3.4065-3.74910.19741140.20992472X-RAY DIFFRACTION99
3.7491-4.29110.22741590.18142520X-RAY DIFFRACTION99
4.2911-5.40430.21951420.16272511X-RAY DIFFRACTION99
5.4043-40.85050.23061460.20692533X-RAY DIFFRACTION98

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