[English] 日本語
Yorodumi
- PDB-7kg7: Structure of human PARG complexed with PARG-292 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7kg7
TitleStructure of human PARG complexed with PARG-292
ComponentsPoly(ADP-ribose) glycohydrolase
KeywordsHYDROLASE/HYDROLASE inhibitor / HYDROLASE / hydrolase inhibitor complex / methyl xanthine / HYDROLASE-HYDROLASE inhibitor complex
Function / homology
Function and homology information


nucleotide-sugar metabolic process / poly(ADP-ribose) glycohydrolase activity / poly(ADP-ribose) glycohydrolase / ATP generation from poly-ADP-D-ribose / POLB-Dependent Long Patch Base Excision Repair / regulation of DNA repair / base-excision repair, gap-filling / carbohydrate metabolic process / nuclear body / mitochondrial matrix ...nucleotide-sugar metabolic process / poly(ADP-ribose) glycohydrolase activity / poly(ADP-ribose) glycohydrolase / ATP generation from poly-ADP-D-ribose / POLB-Dependent Long Patch Base Excision Repair / regulation of DNA repair / base-excision repair, gap-filling / carbohydrate metabolic process / nuclear body / mitochondrial matrix / nucleoplasm / nucleus / cytoplasm / cytosol
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
Similarity search - Domain/homology
Chem-WDJ / Poly(ADP-ribose) glycohydrolase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsBrosey, C.A. / Balapiti-Modarage, L.P.F. / Warden, L.S. / Jones, D.E. / Ahmed, Z. / Tainer, J.A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)R01 CA200231 United States
CitationJournal: Prog.Biophys.Mol.Biol. / Year: 2021
Title: Targeting SARS-CoV-2 Nsp3 macrodomain structure with insights from human poly(ADP-ribose) glycohydrolase (PARG) structures with inhibitors.
Authors: Brosey, C.A. / Houl, J.H. / Katsonis, P. / Balapiti-Modarage, L.P.F. / Bommagani, S. / Arvai, A. / Moiani, D. / Bacolla, A. / Link, T. / Warden, L.S. / Lichtarge, O. / Jones, D.E. / Ahmed, Z. / Tainer, J.A.
History
DepositionOct 16, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 10, 2021Provider: repository / Type: Initial release
Revision 1.1Jun 16, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Oct 18, 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
Revision 1.3Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Poly(ADP-ribose) glycohydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,18711
Polymers61,0201
Non-polymers1,16610
Water5,188288
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)66.607, 89.038, 94.799
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

-
Components

#1: Protein Poly(ADP-ribose) glycohydrolase


Mass: 61020.375 Da / Num. of mol.: 1 / Mutation: K616A, Q617A, K618A, E688A, K689A, K690A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PARG / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta2
References: UniProt: Q86W56, poly(ADP-ribose) glycohydrolase
#2: Chemical ChemComp-WDJ / 8-{[2-(1,1-dioxo-1lambda~6~,4-thiazinan-4-yl)ethyl]sulfanyl}-1,3-dimethyl-3,7-dihydro-1H-purine-2,6-dione


Mass: 373.451 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H19N5O4S2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#4: Chemical
ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 288 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.35 Å3/Da / Density % sol: 47.8 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 0.1 M PCTP, pH 7.5, 0.2 M AmSO4, 18-23% PEG3350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Jun 19, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.85→64.9 Å / Num. obs: 48514 / % possible obs: 99.33 % / Redundancy: 10.5 % / Biso Wilson estimate: 30.46 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.09191 / Rpim(I) all: 0.02945 / Rrim(I) all: 0.09667 / Net I/σ(I): 14.26
Reflection shellResolution: 1.85→1.916 Å / Redundancy: 10.3 % / Rmerge(I) obs: 1.356 / Mean I/σ(I) obs: 1.83 / Num. unique obs: 4759 / CC1/2: 0.697 / CC star: 0.906 / Rpim(I) all: 0.4401 / Rrim(I) all: 1.428 / % possible all: 99.31

-
Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4B1G

4b1g


Resolution: 1.85→64.9 Å / SU ML: 0.2102 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 20.3146
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1955 2316 4.78 %
Rwork0.1774 46180 -
obs0.1783 48496 99.34 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 36.36 Å2
Refinement stepCycle: LAST / Resolution: 1.85→64.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3869 0 65 288 4222
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00464024
X-RAY DIFFRACTIONf_angle_d0.71485480
X-RAY DIFFRACTIONf_chiral_restr0.0457605
X-RAY DIFFRACTIONf_plane_restr0.0044692
X-RAY DIFFRACTIONf_dihedral_angle_d13.54931410
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.85-1.890.35591360.30592651X-RAY DIFFRACTION99.22
1.89-1.930.30351320.26382691X-RAY DIFFRACTION99.37
1.93-1.970.23881260.23232655X-RAY DIFFRACTION97.92
1.97-2.020.25051490.19872672X-RAY DIFFRACTION99.65
2.02-2.080.23381430.18112661X-RAY DIFFRACTION99.61
2.08-2.140.1891370.16892709X-RAY DIFFRACTION99.51
2.14-2.210.17951270.16322709X-RAY DIFFRACTION99.72
2.21-2.290.20311330.15972687X-RAY DIFFRACTION99.26
2.29-2.380.19691410.15612691X-RAY DIFFRACTION99.37
2.38-2.490.19011120.15522725X-RAY DIFFRACTION99.54
2.49-2.620.17961230.16212718X-RAY DIFFRACTION99.23
2.62-2.780.19811070.16862752X-RAY DIFFRACTION98.79
2.78-30.21741090.18092732X-RAY DIFFRACTION99.44
3-3.30.21620.1782719X-RAY DIFFRACTION99.86
3.3-3.780.19521550.1642749X-RAY DIFFRACTION99.86
3.78-4.760.14861710.15482767X-RAY DIFFRACTION99.49
4.76-64.90.20711530.20942892X-RAY DIFFRACTION98.99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.21151753723-1.126400997790.2571820031182.49841391407-0.4452750316110.410420702233-0.0565352287385-0.02799832426080.004089820573750.04990229590550.0631406737056-0.05617003146230.08637415005060.0468350872443-0.002000759676930.2467955373860.009389505109470.00147143805680.260180543379-0.02045347285780.17901692501118.14220615461.617464642585.93326200034
23.96310914088-1.350397297150.6052546515382.83366648665-0.5312080283861.98916922056-0.0490349207452-0.191785084329-0.3810584167250.1362422826540.114718376769-0.08643711122390.09599025308770.091249850641-0.0575107779820.2772367605080.0236930908381-0.006065794292550.2129242563260.01893120450630.24962130897729.2194449955-17.14669011279.92983595773
31.83672448938-2.1363727966-0.08041803918922.80664531270.2957393717840.161384342825-0.0575590496878-0.169740295482-0.6645956842570.08042477758990.07818123244570.6996728098770.0890929590087-0.019451007235-0.02984122360190.276537173555-0.02621170157440.008290232296140.290282734240.06526418057050.4446754097654.03456590355-6.739057196646.48451636408
42.059494965050.196272761148-0.3267617540411.95766813886-0.5549771654271.13822396811-0.0787545421045-0.1982473897980.3375243941240.1837733678480.1178322634650.0263270180292-0.06047570148950.0511049318493-0.03903070080990.2253158089520.0281426905009-0.007094097935660.242438478425-0.04683098151160.26027360423913.208811220620.80036082528.8774643152
52.05586705347-1.31770522560.1378379987792.541242960520.0460022067780.324177165099-0.0161146516207-0.225841257419-0.1922658538990.1228556117480.1200861797430.02529894093550.0705044772538-0.0101972095001-0.09980444598350.2635692596530.0035610529567-0.0113585762520.2551653006560.02505977621950.21106431075518.6122644604-5.872958235818.52184821102
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 754 through 837 )754 - 837299 - 383
22chain 'A' and (resid 838 through 962 )838 - 962384 - 511
33chain 'A' and (resid 451 through 493 )451 - 4931 - 43
44chain 'A' and (resid 494 through 688 )494 - 68844 - 233
55chain 'A' and (resid 689 through 753 )689 - 753234 - 298

+
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