[English] 日本語
Yorodumi
- PDB-5yco: Complex structure of PCNA with UHRF2 -

+
Open data


ID or keywords:

Loading...

-
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 / 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 / SUMO transferase activity / 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 / protein sumoylation / estrous cycle / PCNA-Dependent Long Patch Base Excision Repair / cyclin-dependent protein kinase holoenzyme complex / protein autoubiquitination / heterochromatin / pericentric heterochromatin / 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 / SUMOylation of transcription cofactors / 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 / RING-type E3 ubiquitin transferase / 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 / 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 / histone binding / RNA polymerase II-specific DNA-binding transcription factor binding / chromosome, telomeric region / damaged DNA binding / cell differentiation / nuclear body / regulation of cell cycle / protein ubiquitination / cell cycle / centrosome / chromatin binding / protein-containing complex binding / chromatin / enzyme binding / negative regulation of transcription by RNA polymerase II / DNA binding / extracellular exosome / nucleoplasm / identical protein binding / nucleus / metal ion binding
Similarity search - Function
: / : / : / : / UHRF1, tandem tudor domain / UHRF1/2-like / Tandem tudor domain within UHRF1 / SRA-YDG / SRA-YDG superfamily / SAD/SRA domain ...: / : / : / : / UHRF1, tandem tudor domain / UHRF1/2-like / Tandem tudor domain within UHRF1 / 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 / Zinc finger, RING-type, conserved site / Zinc finger RING-type signature. / PHD-finger / Ring finger / Zinc finger PHD-type signature. / Zinc finger PHD-type profile. / Zinc finger, PHD-finger / Zinc finger, PHD-type / PHD zinc finger / Zinc finger RING-type profile. / Zinc finger, RING-type / Zinc finger, FYVE/PHD-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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
Phasing

PhasingMethod: molecular replacement

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more