[English] 日本語
Yorodumi
- PDB-7kfp: Structure of human PARG complexed with PARG-119 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7kfp
TitleStructure of human PARG complexed with PARG-119
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 / poly(ADP-ribose) glycohydrolase activity / 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 / poly(ADP-ribose) glycohydrolase activity / 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 / cytosol / cytoplasm
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-WD7 / Poly(ADP-ribose) glycohydrolase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsBrosey, C.A. / Bommagani, S. / 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 14, 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: 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 1.3Nov 13, 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)62,0319
Polymers61,0201
Non-polymers1,0118
Water4,576254
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)66.532, 88.660, 94.426
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
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

-
Protein , 1 types, 1 molecules A

#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 (E. coli) / Strain (production host): Rosett2(DE3)
References: UniProt: Q86W56, poly(ADP-ribose) glycohydrolase

-
Non-polymers , 5 types, 262 molecules

#2: Chemical ChemComp-WD7 / N-{[2-(1,3-dimethyl-2-oxo-6-sulfanylidene-1,2,3,6-tetrahydro-7H-purin-7-yl)ethyl]carbamoyl}methanesulfonamide


Mass: 360.413 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H16N6O4S2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical
ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 254 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.33 Å3/Da / Density % sol: 47.3 %
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: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.9201 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Nov 26, 2019
RadiationMonochromator: Double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9201 Å / Relative weight: 1
ReflectionResolution: 1.9→29.58 Å / Num. obs: 44680 / % possible obs: 99.9 % / Redundancy: 5.9 % / Biso Wilson estimate: 31.12 Å2 / CC1/2: 0.997 / CC star: 0.999 / Rmerge(I) obs: 0.08665 / Rpim(I) all: 0.03888 / Rrim(I) all: 0.09518 / Net I/σ(I): 10.52
Reflection shellResolution: 1.9→1.968 Å / Redundancy: 6 % / Rmerge(I) obs: 0.6689 / Mean I/σ(I) obs: 2.25 / Num. unique obs: 4419 / CC1/2: 0.76 / CC star: 0.929 / Rpim(I) all: 0.2983 / Rrim(I) all: 0.7339 / % possible all: 99.98

-
Processing

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

4b1g


Resolution: 1.9→29.58 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 18.39 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1953 2260 5.06 %
Rwork0.1746 42414 -
obs0.1757 44674 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 91.89 Å2 / Biso mean: 37.574 Å2 / Biso min: 19.56 Å2
Refinement stepCycle: final / Resolution: 1.9→29.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3826 0 86 254 4166
Biso mean--46.84 39.21 -
Num. residues----497
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 16 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.9-1.940.27511320.237726172749
1.94-1.990.22451410.214525952736
1.99-2.040.24931490.203726002749
2.04-2.090.19091340.171626452779
2.09-2.150.18941290.170226182747
2.15-2.220.19421210.163726572778
2.22-2.30.20091430.153226182761
2.3-2.390.19081580.157426022760
2.39-2.50.21831360.15826392775
2.5-2.630.23061320.166126462778
2.63-2.80.20221330.165526572790
2.8-3.020.2081450.179226502795
3.02-3.320.17511500.1826622812
3.32-3.80.19131580.161126632821
3.8-4.780.15081400.158727172857
4.78-29.580.21761590.207328282987
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)
11.48540.9530.17751.26760.25330.4898-0.10130.21110.3074-0.12130.1260.4342-0.132-0.034-0.01690.27370.0012-0.03310.2710.07850.32652.4714-0.4764-10.3864
21.48350.29840.32032.9333-1.09332.0508-0.06920.3671-0.3314-0.48230.20620.00120.16760.0564-0.11870.3198-0.0365-0.03920.3022-0.09860.29598.5874-26.288-18.0935
31.6655-0.35020.40961.9226-0.541.4076-0.05960.0618-0.2204-0.05940.0916-0.03110.02260.0592-0.03540.197-0.02750.01440.2193-0.03210.221915.0888-20.301-5.9687
41.83721.2693-0.15962.45070.05690.2853-0.03910.09090.1766-0.03190.11820.0521-0.1247-0.0005-0.08220.2528-0.00670.0030.23090.0160.207518.45795.8628-8.3083
51.39680.43630.16122.1032-0.44961.2167-0.02560.0135-0.04510.02630.0475-0.0856-0.22860.1242-0.01120.2503-0.02330.00320.2525-0.00990.209117.7661-4.7021-4.6569
61.54290.9704-0.41631.9883-0.61080.3881-0.1995-0.0759-0.0405-0.03680.08730.00940.00850.03930.11730.28130.0032-0.01040.276-0.01270.180118.10043.7149-8.072
72.88780.3501-1.34381.94270.02132.8718-0.00470.32540.2038-0.24610.128-0.0261-0.0796-0.1586-0.14860.3197-0.0391-0.01050.26080.03310.254622.445310.6775-13.3417
82.83370.8751-0.32742.6605-0.47222.0639-0.03130.11790.3155-0.05870.0545-0.1673-0.11490.2097-0.02780.2616-0.0401-0.00830.2151-0.01220.266232.478919.6888-8.9049
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 451 through 508 )A451 - 508
2X-RAY DIFFRACTION2chain 'A' and (resid 509 through 543 )A509 - 543
3X-RAY DIFFRACTION3chain 'A' and (resid 544 through 688 )A544 - 688
4X-RAY DIFFRACTION4chain 'A' and (resid 689 through 753 )A689 - 753
5X-RAY DIFFRACTION5chain 'A' and (resid 754 through 804 )A754 - 804
6X-RAY DIFFRACTION6chain 'A' and (resid 805 through 837 )A805 - 837
7X-RAY DIFFRACTION7chain 'A' and (resid 838 through 878 )A838 - 878
8X-RAY DIFFRACTION8chain 'A' and (resid 879 through 961 )A879 - 961

+
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