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- PDB-5yco: Complex structure of PCNA with UHRF2 -

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Basic information

Entry
Database: PDB / ID: 5yco
TitleComplex structure of PCNA with UHRF2
Components
  • E3 ubiquitin-protein ligase UHRF2
  • Proliferating cell nuclear antigen
KeywordsDNA BINDING PROTEIN / Complex structure / PCNA / UHRF2
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 / positive regulation of DNA-directed DNA polymerase activity / Polymerase switching / Telomere C-strand (Lagging Strand) Synthesis / MutLalpha complex binding ...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 / positive regulation of DNA-directed DNA polymerase activity / Polymerase switching / Telomere C-strand (Lagging Strand) Synthesis / MutLalpha complex binding / Processive synthesis on the lagging strand / PCNA complex / Removal of the Flap Intermediate / Processive synthesis on the C-strand of the telomere / Polymerase switching on the C-strand of the telomere / Removal of the Flap Intermediate from the C-strand / Mismatch repair (MMR) directed by MSH2:MSH3 (MutSbeta) / Mismatch repair (MMR) directed by MSH2:MSH6 (MutSalpha) / Transcription of E2F targets under negative control by DREAM complex / SUMO transferase activity / replisome / response to L-glutamate / negative regulation of gene expression via chromosomal CpG island methylation / histone acetyltransferase binding / DNA polymerase processivity factor activity / leading strand elongation / G1/S-Specific Transcription / response to dexamethasone / replication fork processing / nuclear replication fork / protein sumoylation / SUMOylation of DNA replication proteins / PCNA-Dependent Long Patch Base Excision Repair / translesion synthesis / mismatch repair / heterochromatin / pericentric heterochromatin / response to cadmium ion / protein autoubiquitination / estrous cycle / cyclin-dependent protein kinase holoenzyme complex / base-excision repair, gap-filling / DNA polymerase binding / epithelial cell differentiation / SUMOylation of transcription cofactors / positive regulation of DNA repair / male germ cell nucleus / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / Translesion synthesis by REV1 / Translesion synthesis by POLK / liver regeneration / Translesion synthesis by POLI / replication fork / Gap-filling DNA repair synthesis and ligation in GG-NER / positive regulation of DNA replication / nuclear estrogen receptor binding / Termination of translesion DNA synthesis / Recognition of DNA damage by PCNA-containing replication complex / Translesion Synthesis by POLH / RING-type E3 ubiquitin transferase / receptor tyrosine kinase binding / HDR through Homologous Recombination (HRR) / Dual Incision in GG-NER / cellular response to hydrogen peroxide / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / ubiquitin-protein transferase activity / cellular response to UV / ubiquitin protein ligase activity / cellular response to xenobiotic stimulus / E3 ubiquitin ligases ubiquitinate target proteins / response to estradiol / heart development / RNA polymerase II-specific DNA-binding transcription factor binding / histone binding / damaged DNA binding / cell differentiation / chromosome, telomeric region / regulation of cell cycle / protein ubiquitination / nuclear body / centrosome / chromatin binding / protein-containing complex binding / chromatin / enzyme binding / negative regulation of transcription by RNA polymerase II / DNA binding / extracellular exosome / zinc ion binding / nucleoplasm / identical protein binding / nucleus
Similarity search - Function
: / : / : / : / UHRF1, tandem tudor domain / Tandem tudor domain within UHRF1 / UHRF1/2-like / SRA-YDG / SRA-YDG superfamily / SAD/SRA domain ...: / : / : / : / UHRF1, tandem tudor domain / Tandem tudor domain within UHRF1 / UHRF1/2-like / SRA-YDG / SRA-YDG superfamily / SAD/SRA domain / YDG domain profile. / SET and RING finger associated domain. Domain of unknown function in SET domain containing proteins and in Deinococcus radiodurans DRA1533. / 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 / PUA-like superfamily / : / PHD-finger / Zinc finger, RING-type, conserved site / Zinc finger RING-type signature. / Zinc finger PHD-type signature. / Ring finger / Zinc finger PHD-type profile. / Zinc finger, PHD-finger / Zinc finger, PHD-type / PHD zinc finger / Zinc finger, FYVE/PHD-type / Zinc finger RING-type profile. / Zinc finger, RING-type / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Zinc finger, RING/FYVE/PHD-type / Ubiquitin-like domain superfamily / Alpha Beta
Similarity search - Domain/homology
Proliferating cell nuclear antigen / E3 ubiquitin-protein ligase UHRF2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.199 Å
AuthorsWu, M. / Chen, W. / Hang, T. / Wang, C. / Zhang, X. / Zang, J.
Funding support China, 2items
OrganizationGrant numberCountry
National Key Research and Development Program of China2016YFA0400903, 2017YFA0503600 China
National Natural Science Foundation of ChinaU1532109, 31370756, and 31361163002 China
CitationJournal: Biochem. Biophys. Res. Commun. / Year: 2017
Title: Structure insights into the molecular mechanism of the interaction between UHRF2 and PCNA.
Authors: Chen, W. / Wu, M. / Hang, T. / Wang, C. / Zhang, X. / Zang, J.
History
DepositionSep 7, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 15, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 6, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Nov 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: Proliferating cell nuclear antigen
C: Proliferating cell nuclear antigen
D: Proliferating cell nuclear antigen
E: E3 ubiquitin-protein ligase UHRF2
F: E3 ubiquitin-protein ligase UHRF2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)124,60318
Polymers123,4666
Non-polymers1,13712
Water5,837324
1
A: Proliferating cell nuclear antigen
C: Proliferating cell nuclear antigen
D: Proliferating cell nuclear antigen
F: E3 ubiquitin-protein ligase UHRF2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,45313
Polymers91,6004
Non-polymers8539
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
E: E3 ubiquitin-protein ligase UHRF2

B: Proliferating cell nuclear antigen
hetero molecules

B: Proliferating cell nuclear antigen
hetero molecules

B: Proliferating cell nuclear antigen
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,45313
Polymers91,6004
Non-polymers8539
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z2
crystal symmetry operation2_675-y+1,x-y+2,z1
crystal symmetry operation3_465-x+y-1,-x+1,z1
Unit cell
Length a, b, c (Å)202.514, 202.514, 123.937
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3

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Components

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


Mass: 29866.891 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PCNA / Production host: Escherichia coli K-12 (bacteria) / Strain (production host): K-12 / References: UniProt: P12004
#2: Protein/peptide E3 ubiquitin-protein ligase UHRF2


Mass: 1999.287 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 784-800 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
References: UniProt: Q96PU4, RING-type E3 ubiquitin transferase
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 324 / 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: 4.27 Å3/Da / Density % sol: 71.18 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / Details: 2 M ammonium sulfate, 0.1 M Tris pH 8.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9791 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 20, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 94479 / % possible obs: 98.1 % / Redundancy: 2.1 % / Biso Wilson estimate: 41.15 Å2 / Rmerge(I) obs: 0.051 / Rpim(I) all: 0.043 / Rrim(I) all: 0.067 / Χ2: 1.201 / Net I/σ(I): 12.1 / Num. measured all: 199263
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.2-2.282.10.46795580.640.4050.6211.10999.2
2.28-2.372.10.37395850.7440.3220.4951.11899.5
2.37-2.482.10.26996210.8510.2320.3571.18999.5
2.48-2.612.10.18395500.9180.1570.2421.21399.5
2.61-2.772.10.13295420.960.1130.1741.2699.5
2.77-2.992.10.08695910.9810.0740.1141.38199.2
2.99-3.292.10.05694990.9920.0480.0741.36598.6
3.29-3.762.10.0494250.9950.0340.0531.20897.3
3.76-4.742.10.03691090.9950.030.0471.09294.7
4.74-502.20.02889990.9970.0230.0371.06393.6

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
HKL-2000data collection
HKL-2000data scaling
PHASERphasing
PDB_EXTRACT3.22data extraction
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3VKX

3vkx


Resolution: 2.199→41.312 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 23.24 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2201 4857 5.14 %
Rwork0.2039 89607 -
obs0.2048 94464 98.06 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 104.85 Å2 / Biso mean: 48.4451 Å2 / Biso min: 23.71 Å2
Refinement stepCycle: final / Resolution: 2.199→41.312 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7806 0 64 324 8194
Biso mean--62.09 47.58 -
Num. residues----1014
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.017998
X-RAY DIFFRACTIONf_angle_d1.29810795
X-RAY DIFFRACTIONf_chiral_restr0.0611274
X-RAY DIFFRACTIONf_plane_restr0.0081369
X-RAY DIFFRACTIONf_dihedral_angle_d7.7295816
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.1991-2.2240.3411040.26543093319799
2.224-2.25020.29721950.271330013196100
2.2502-2.27760.29491750.24672990316599
2.2776-2.30650.27681710.247330323203100
2.3065-2.33680.28651990.2632994319399
2.3368-2.36880.28761640.247230293193100
2.3688-2.40270.25611760.245330413217100
2.4027-2.43850.28191700.23362997316799
2.4385-2.47660.25231950.235330383233100
2.4766-2.51720.22241190.21783038315799
2.5172-2.56060.31071910.229530273218100
2.5606-2.60720.23171640.216130113175100
2.6072-2.65730.27931400.223430573197100
2.6573-2.71160.25181260.223930583184100
2.7116-2.77050.24361300.22013030316099
2.7705-2.83490.20731600.22863068322899
2.8349-2.90580.25851730.2213004317799
2.9058-2.98440.24851680.2193018318699
2.9844-3.07210.23361530.2083043319699
3.0721-3.17130.24971510.22023017316899
3.1713-3.28460.18321630.21472972313598
3.2846-3.4160.24141620.20162991315398
3.416-3.57140.25331270.18812993312098
3.5714-3.75960.20031210.19493029315097
3.7596-3.9950.19471560.18982939309596
3.995-4.30310.16611420.1812803294594
4.3031-4.73560.17671920.15032858305094
4.7356-5.41950.19042220.17012823304595
5.4195-6.82310.21941800.22162861304195
6.8231-41.31960.21761680.20292752292091

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