[English] 日本語
Yorodumi
- PDB-5mav: Crystal structure of human PCNA in complex with PARG (poly(ADP-ri... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5mav
TitleCrystal structure of human PCNA in complex with PARG (poly(ADP-ribose) glycohydrolase) peptide.
Components
  • Poly (ADP-ribose) glycohydrolase
  • Proliferating cell nuclear antigen
KeywordsTRANSCRIPTION / PCNA / PARG / interactions
Function / homology
Function and homology information


poly(ADP-ribose) glycohydrolase activity / poly(ADP-ribose) glycohydrolase / 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 ...poly(ADP-ribose) glycohydrolase activity / poly(ADP-ribose) glycohydrolase / 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 / replisome / response to L-glutamate / histone acetyltransferase binding / DNA polymerase processivity factor activity / leading strand elongation / G1/S-Specific Transcription / response to dexamethasone / replication fork processing / nuclear replication fork / SUMOylation of DNA replication proteins / PCNA-Dependent Long Patch Base Excision Repair / translesion synthesis / mismatch repair / regulation of DNA repair / response to cadmium ion / estrous cycle / cyclin-dependent protein kinase holoenzyme complex / base-excision repair, gap-filling / DNA polymerase binding / epithelial cell differentiation / male germ cell nucleus / positive regulation of DNA repair / 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 / 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 / cellular response to UV / cellular response to xenobiotic stimulus / E3 ubiquitin ligases ubiquitinate target proteins / response to estradiol / heart development / carbohydrate metabolic process / damaged DNA binding / chromosome, telomeric region / 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
Poly(ADP-ribose) glycohydrolase / Poly (ADP-ribose) glycohydrolase (PARG), catalytic domain / : / Poly (ADP-ribose) glycohydrolase (PARG), Macro domain fold / Poly (ADP-ribose) glycohydrolase (PARG), helical domain / Box / Proliferating Cell Nuclear Antigen / Proliferating Cell Nuclear Antigen - #10 / Proliferating cell nuclear antigen signature 2. / Proliferating cell nuclear antigen, PCNA, conserved site ...Poly(ADP-ribose) glycohydrolase / Poly (ADP-ribose) glycohydrolase (PARG), catalytic domain / : / Poly (ADP-ribose) glycohydrolase (PARG), Macro domain fold / Poly (ADP-ribose) glycohydrolase (PARG), helical domain / 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 / : / Alpha Beta
Similarity search - Domain/homology
Proliferating cell nuclear antigen / poly(ADP-ribose) glycohydrolase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.575 Å
AuthorsGrishkovskaya, I. / Djinovic-Carugo, K. / Slade, D.
CitationJournal: Nucleic Acids Res. / Year: 2017
Title: A novel non-canonical PIP-box mediates PARG interaction with PCNA.
Authors: Kaufmann, T. / Grishkovskaya, I. / Polyansky, A.A. / Kostrhon, S. / Kukolj, E. / Olek, K.M. / Herbert, S. / Beltzung, E. / Mechtler, K. / Peterbauer, T. / Gotzmann, J. / Zhang, L. / Hartl, M. ...Authors: Kaufmann, T. / Grishkovskaya, I. / Polyansky, A.A. / Kostrhon, S. / Kukolj, E. / Olek, K.M. / Herbert, S. / Beltzung, E. / Mechtler, K. / Peterbauer, T. / Gotzmann, J. / Zhang, L. / Hartl, M. / Zagrovic, B. / Elsayad, K. / Djinovic-Carugo, K. / Slade, D.
History
DepositionNov 6, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 2, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 6, 2017Group: 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_PubMed / _citation.title / _citation_author.name
Revision 1.2Oct 16, 2019Group: Data collection / Category: reflns_shell
Revision 1.3Jan 17, 2024Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Proliferating cell nuclear antigen
C: Proliferating cell nuclear antigen
E: Proliferating cell nuclear antigen
B: Proliferating cell nuclear antigen
D: Proliferating cell nuclear antigen
F: Proliferating cell nuclear antigen
G: Poly (ADP-ribose) glycohydrolase
H: Poly (ADP-ribose) glycohydrolase
K: Poly (ADP-ribose) glycohydrolase
L: Poly (ADP-ribose) glycohydrolase
N: Poly (ADP-ribose) glycohydrolase
M: Poly (ADP-ribose) glycohydrolase


Theoretical massNumber of molelcules
Total (without water)187,59412
Polymers187,59412
Non-polymers00
Water57632
1
A: Proliferating cell nuclear antigen
C: Proliferating cell nuclear antigen
E: Proliferating cell nuclear antigen
G: Poly (ADP-ribose) glycohydrolase
H: Poly (ADP-ribose) glycohydrolase
M: Poly (ADP-ribose) glycohydrolase


Theoretical massNumber of molelcules
Total (without water)93,7976
Polymers93,7976
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8270 Å2
ΔGint-45 kcal/mol
Surface area35880 Å2
MethodPISA
2
B: Proliferating cell nuclear antigen
D: Proliferating cell nuclear antigen
F: Proliferating cell nuclear antigen
K: Poly (ADP-ribose) glycohydrolase
L: Poly (ADP-ribose) glycohydrolase
N: Poly (ADP-ribose) glycohydrolase


Theoretical massNumber of molelcules
Total (without water)93,7976
Polymers93,7976
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8190 Å2
ΔGint-37 kcal/mol
Surface area35190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.597, 153.604, 85.512
Angle α, β, γ (deg.)90.00, 96.90, 90.00
Int Tables number4
Space group name H-MP1211
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

-
Components

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


Mass: 29020.990 Da / Num. of mol.: 6
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
Poly (ADP-ribose) glycohydrolase


Mass: 2244.637 Da / Num. of mol.: 6 / Fragment: UNP residues 402-420 / Source method: obtained synthetically / Details: peptide / Source: (synth.) Homo sapiens (human) / References: UniProt: Q0MQR4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 32 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.9 Å3/Da / Density % sol: 57.62 %
Crystal growTemperature: 295.15 K / Method: vapor diffusion, sitting drop
Details: 0.1 M Tris-HCl pH 7.5, 20% PEG 3350, 0.2 M ammonium acetate

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.968 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 29, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.968 Å / Relative weight: 1
ReflectionResolution: 2.57→47.671 Å / Num. obs: 62473 / % possible obs: 99.1 % / Redundancy: 4.8 % / Biso Wilson estimate: 58.38713131 Å2 / Rmerge(I) obs: 0.26 / Rpim(I) all: 0.132 / Rrim(I) all: 0.293 / Net I/σ(I): 5.6

-
Processing

Software
NameVersionClassification
PHENIX(1.10_2155: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1VYM

1vym


Resolution: 2.575→47.671 Å / SU ML: 0.53 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 37.7
RfactorNum. reflection% reflection
Rfree0.2909 3032 4.88 %
Rwork0.2387 --
obs0.2412 62098 98.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.575→47.671 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12149 0 0 32 12181
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00712321
X-RAY DIFFRACTIONf_angle_d1.04116617
X-RAY DIFFRACTIONf_dihedral_angle_d16.3517615
X-RAY DIFFRACTIONf_chiral_restr0.0561962
X-RAY DIFFRACTIONf_plane_restr0.0062119
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5751-2.61530.43531110.41592140X-RAY DIFFRACTION79
2.6153-2.65820.40641360.4072694X-RAY DIFFRACTION99
2.6582-2.7040.39921620.39252662X-RAY DIFFRACTION99
2.704-2.75320.42711520.3892680X-RAY DIFFRACTION99
2.7532-2.80610.38791310.37112697X-RAY DIFFRACTION100
2.8061-2.86340.42391110.36782727X-RAY DIFFRACTION100
2.8634-2.92570.33831480.35452686X-RAY DIFFRACTION100
2.9257-2.99370.39231230.34322728X-RAY DIFFRACTION100
2.9937-3.06860.38791380.32732719X-RAY DIFFRACTION100
3.0686-3.15150.36781620.32262661X-RAY DIFFRACTION100
3.1515-3.24420.43961290.3172718X-RAY DIFFRACTION100
3.2442-3.34890.40191370.28852697X-RAY DIFFRACTION100
3.3489-3.46860.34341480.26612687X-RAY DIFFRACTION100
3.4686-3.60740.32141520.24012719X-RAY DIFFRACTION100
3.6074-3.77150.29371310.2312721X-RAY DIFFRACTION100
3.7715-3.97030.2931340.21272711X-RAY DIFFRACTION100
3.9703-4.21890.21231340.18972729X-RAY DIFFRACTION100
4.2189-4.54440.23981280.17622756X-RAY DIFFRACTION100
4.5444-5.00130.22221360.16442700X-RAY DIFFRACTION100
5.0013-5.72390.25371210.1872754X-RAY DIFFRACTION100
5.7239-7.20760.25251540.22082731X-RAY DIFFRACTION100
7.2076-47.67890.20241540.1792749X-RAY DIFFRACTION100

+
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://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