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- PDB-6qc0: PCNA complex with Cdt2 C-terminal PIP-box peptide -

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Basic information

Entry
Database: PDB / ID: 6qc0
TitlePCNA complex with Cdt2 C-terminal PIP-box peptide
Components
  • Denticleless protein homolog
  • Proliferating cell nuclear antigen
KeywordsREPLICATION / complex / PIP
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 / MutLalpha complex binding / positive regulation of DNA-directed DNA polymerase activity / nuclear lamina / 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 / MutLalpha complex binding / positive regulation of DNA-directed DNA polymerase activity / nuclear lamina / 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) / replisome / Cul4-RING E3 ubiquitin ligase complex / Transcription of E2F targets under negative control by DREAM complex / Removal of the Flap Intermediate from the C-strand / Cul4A-RING E3 ubiquitin ligase complex / response to L-glutamate / Cul4B-RING E3 ubiquitin ligase complex / histone acetyltransferase binding / leading strand elongation / DNA polymerase processivity factor activity / G1/S-Specific Transcription / response to dexamethasone / replication fork processing / nuclear replication fork / mitotic G2 DNA damage checkpoint signaling / protein monoubiquitination / SUMOylation of DNA replication proteins / PCNA-Dependent Long Patch Base Excision Repair / estrous cycle / mismatch repair / translesion synthesis / response to cadmium ion / DNA polymerase binding / cyclin-dependent protein kinase holoenzyme complex / response to UV / epithelial cell differentiation / base-excision repair, gap-filling / positive regulation of G2/M transition of mitotic cell cycle / positive regulation of DNA repair / Translesion synthesis by REV1 / Translesion synthesis by POLK / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / Translesion synthesis by POLI / Gap-filling DNA repair synthesis and ligation in GG-NER / positive regulation of DNA replication / male germ cell nucleus / replication fork / nuclear estrogen receptor binding / liver regeneration / 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 / protein polyubiquitination / positive regulation of protein catabolic process / cellular response to UV / rhythmic process / cellular response to xenobiotic stimulus / E3 ubiquitin ligases ubiquitinate target proteins / response to estradiol / heart development / Neddylation / chromosome / protein-macromolecule adaptor activity / ubiquitin-dependent protein catabolic process / nuclear membrane / proteasome-mediated ubiquitin-dependent protein catabolic process / DNA replication / damaged DNA binding / chromosome, telomeric region / nuclear body / regulation of cell cycle / centrosome / DNA damage response / chromatin binding / protein-containing complex binding / chromatin / nucleolus / negative regulation of transcription by RNA polymerase II / enzyme binding / extracellular exosome / nucleoplasm / identical protein binding / nucleus / cytosol
Similarity search - Function
: / Box / Proliferating Cell Nuclear Antigen / Proliferating Cell Nuclear Antigen - #10 / 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 ...: / Box / Proliferating Cell Nuclear Antigen / Proliferating Cell Nuclear Antigen - #10 / 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 / : / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / Alpha Beta
Similarity search - Domain/homology
Proliferating cell nuclear antigen / Denticleless protein homolog
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.5 Å
AuthorsPerrakis, A.P. / von Castelmur, E.
CitationJournal: Life Sci Alliance / Year: 2018
Title: Direct binding of Cdt2 to PCNA is important for targeting the CRL4Cdt2E3 ligase activity to Cdt1.
Authors: Hayashi, A. / Giakoumakis, N.N. / Heidebrecht, T. / Ishii, T. / Panagopoulos, A. / Caillat, C. / Takahara, M. / Hibbert, R.G. / Suenaga, N. / Stadnik-Spiewak, M. / Takahashi, T. / Shiomi, Y. ...Authors: Hayashi, A. / Giakoumakis, N.N. / Heidebrecht, T. / Ishii, T. / Panagopoulos, A. / Caillat, C. / Takahara, M. / Hibbert, R.G. / Suenaga, N. / Stadnik-Spiewak, M. / Takahashi, T. / Shiomi, Y. / Taraviras, S. / von Castelmur, E. / Lygerou, Z. / Perrakis, A. / Nishitani, H.
History
DepositionDec 25, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 23, 2019Provider: repository / Type: Initial release
Revision 1.1May 15, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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
C: Proliferating cell nuclear antigen
E: Proliferating cell nuclear antigen
B: Denticleless protein homolog
D: Denticleless protein homolog
F: Denticleless protein homolog


Theoretical massNumber of molelcules
Total (without water)92,0976
Polymers92,0976
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8360 Å2
ΔGint-51 kcal/mol
Surface area34550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)151.369, 151.369, 91.489
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21C
12A
22E
13C
23E
14B
24D
15B
25F
16D
26F

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11METMETILEILEAA1 - 2553 - 257
21METMETILEILECB1 - 2553 - 257
12METMETILEILEAA1 - 2553 - 257
22METMETILEILEEC1 - 2553 - 257
13METMETILEILECB1 - 2553 - 257
23METMETILEILEEC1 - 2553 - 257
14SERSERARGARGBD705 - 7152 - 12
24SERSERARGARGDE705 - 7152 - 12
15SERSERARGARGBD705 - 7152 - 12
25SERSERARGARGFF705 - 7152 - 12
16SERSERARGARGDE705 - 7152 - 12
26SERSERARGARGFF705 - 7152 - 12

NCS ensembles :
ID
1
2
3
4
5
6

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Components

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


Mass: 28949.912 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 Denticleless protein homolog / DDB1- and CUL4-associated factor 2 / Lethal(2) denticleless protein homolog / Retinoic acid- ...DDB1- and CUL4-associated factor 2 / Lethal(2) denticleless protein homolog / Retinoic acid-regulated nuclear matrix-associated protein


Mass: 1749.090 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q9NZJ0

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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: 3.38 Å3/Da / Density % sol: 63.64 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: 10% (w/v) PEG 6000 100 mM MES/HCl

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.8726 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Apr 12, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 3.5→45.7 Å / Num. obs: 14850 / % possible obs: 97.1 % / Redundancy: 8 % / Net I/σ(I): 7.1
Reflection shellResolution: 3.5→3.83 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.5→43.73 Å / Cor.coef. Fo:Fc: 0.922 / Cor.coef. Fo:Fc free: 0.856 / SU B: 82.844 / SU ML: 0.513 / Cross valid method: THROUGHOUT / ESU R Free: 0.598 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25164 748 5 %RANDOM
Rwork0.1956 ---
obs0.19836 14082 97.22 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 68.691 Å2
Baniso -1Baniso -2Baniso -3
1--0.83 Å2-0.42 Å20 Å2
2---0.83 Å20 Å2
3---2.71 Å2
Refinement stepCycle: 1 / Resolution: 3.5→43.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6173 0 0 0 6173
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0136256
X-RAY DIFFRACTIONr_bond_other_d0.0070.0175923
X-RAY DIFFRACTIONr_angle_refined_deg1.8061.6328438
X-RAY DIFFRACTIONr_angle_other_deg1.2721.57713782
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.3575790
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.69723.716296
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.156151170
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.3551530
X-RAY DIFFRACTIONr_chiral_restr0.2330.2842
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.026894
X-RAY DIFFRACTIONr_gen_planes_other0.0050.021192
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.0694.0813181
X-RAY DIFFRACTIONr_mcbond_other2.0694.0813180
X-RAY DIFFRACTIONr_mcangle_it3.6156.1183964
X-RAY DIFFRACTIONr_mcangle_other3.6156.1183965
X-RAY DIFFRACTIONr_scbond_it1.7624.2783075
X-RAY DIFFRACTIONr_scbond_other1.7624.2783076
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.1816.3314475
X-RAY DIFFRACTIONr_long_range_B_refined6.02946.6756492
X-RAY DIFFRACTIONr_long_range_B_other6.02846.6756493
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A69830.14
12C69830.14
21A69480.14
22E69480.14
31C70780.13
32E70780.13
41B2430.15
42D2430.15
51B2710.17
52F2710.17
61D2440.19
62F2440.19
LS refinement shellResolution: 3.497→3.587 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.381 30 -
Rwork0.325 659 -
obs--62.35 %
Refinement TLS params.Method: refined / Origin x: 41.292 Å / Origin y: 15.988 Å / Origin z: -4.624 Å
111213212223313233
T0.0477 Å2-0.0328 Å20.008 Å2-0.0369 Å2-0.0584 Å2--0.4358 Å2
L1.6129 °2-0.4666 °2-0.1369 °2-0.8321 °2-0.2674 °2--1.4987 °2
S0.0748 Å °-0.1151 Å °-0.0966 Å °-0.0888 Å °0.0457 Å °0.0656 Å °-0.1413 Å °0.0757 Å °-0.1204 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 999
2X-RAY DIFFRACTION1C0 - 999
3X-RAY DIFFRACTION1E0 - 999
4X-RAY DIFFRACTION1B0 - 999
5X-RAY DIFFRACTION1D0 - 999
6X-RAY DIFFRACTION1F0 - 999

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