[English] 日本語
Yorodumi
- PDB-8c8i: Human dUTPase in complex with a potent proteinaceous inhibitor (Stl) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8c8i
TitleHuman dUTPase in complex with a potent proteinaceous inhibitor (Stl)
Components
  • Deoxyuridine 5'-triphosphate nucleotidohydrolase, mitochondrial
  • Orf20
KeywordsHYDROLASE / Inhibitor / Complex / dUTPase
Function / homology
Function and homology information


pyrimidine deoxyribonucleotide binding / dUTP catabolic process / dUMP biosynthetic process / dUTP diphosphatase / dUTP diphosphatase activity / Interconversion of nucleotide di- and triphosphates / peroxisome proliferator activated receptor binding / nucleobase-containing compound metabolic process / signaling receptor inhibitor activity / dTMP biosynthetic process ...pyrimidine deoxyribonucleotide binding / dUTP catabolic process / dUMP biosynthetic process / dUTP diphosphatase / dUTP diphosphatase activity / Interconversion of nucleotide di- and triphosphates / peroxisome proliferator activated receptor binding / nucleobase-containing compound metabolic process / signaling receptor inhibitor activity / dTMP biosynthetic process / regulation of protein-containing complex assembly / liver development / DNA replication / magnesium ion binding / mitochondrion / DNA binding / RNA binding / extracellular exosome / nucleoplasm / identical protein binding / nucleus
Similarity search - Function
Deoxyuridine triphosphate nucleotidohydrolase / dUTPase-like / dUTPase / dUTPase, trimeric / dUTPase-like superfamily / Helix-turn-helix / Helix-turn-helix XRE-family like proteins / Cro/C1-type HTH domain profile. / Cro/C1-type helix-turn-helix domain / Lambda repressor-like, DNA-binding domain superfamily
Similarity search - Domain/homology
Deoxyuridine 5'-triphosphate nucleotidohydrolase, mitochondrial / Orf20
Similarity search - Component
Biological speciesHomo sapiens (human)
Staphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsKohegyi, B.K. / Nyiri, K. / Vertessy, B.G.
Funding support Hungary, 1items
OrganizationGrant numberCountry
Hungarian National Research, Development and Innovation OfficePD134324 Hungary
CitationJournal: Sci Rep / Year: 2025
Title: Full-length inhibitor protein is the most effective to perturb human dUTPase activity.
Authors: Kohegyi, B. / Toth, Z.S. / Gal, E. / Laczkovich, M. / Benedek, A. / Vertessy, B.G. / Nyiri, K.
History
DepositionJan 20, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 1, 2024Provider: repository / Type: Initial release
Revision 1.1Apr 16, 2025Group: Database references / Structure summary / Category: citation / citation_author / pdbx_entry_details
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Deoxyuridine 5'-triphosphate nucleotidohydrolase, mitochondrial
B: Deoxyuridine 5'-triphosphate nucleotidohydrolase, mitochondrial
C: Deoxyuridine 5'-triphosphate nucleotidohydrolase, mitochondrial
D: Orf20
E: Orf20
F: Orf20
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,1877
Polymers94,1636
Non-polymers241
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)78.450, 82.660, 139.600
Angle α, β, γ (deg.)90.00, 90.00, 90.00
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
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
d_1ens_1
d_2ens_1
d_3ens_1
d_1ens_2
d_2ens_2
d_3ens_2

NCS ensembles :
ID
ens_1
ens_2

NCS oper:
IDCodeMatrixVector
1given(-0.140034690694, 0.898545046119, 0.415941204376), (0.264957893786, 0.438766588366, -0.858650799484), (-0.954037525427, -0.0100339936699, -0.29951914638)11.1085615739, 9.26251166483, 34.9906048298
2given(-0.136692629585, 0.261217579129, -0.955552458723), (0.90025502466, 0.435252671726, -0.00979807787136), (0.413347330451, -0.861580227321, -0.294658270372)32.3750513231, -13.7041274144, 13.8695549527
3given(-0.135668353987, 0.276996457811, -0.951245005289), (0.89419766505, 0.447663442328, 0.0028245745787), (0.426620010718, -0.850217857236, -0.308423348162)32.1591077681, -13.9063838269, 13.855041465
4given(-0.14605442653, 0.91005222884, 0.387908552722), (0.232526613754, 0.412708347698, -0.880683367412), (-0.961560959267, -0.0384286419708, -0.271889244158)11.3312029569, 10.52337427, 34.8784911208

-
Components

#1: Protein Deoxyuridine 5'-triphosphate nucleotidohydrolase, mitochondrial / dUTPase / dUTP pyrophosphatase


Mass: 14178.108 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DUT / Production host: Escherichia coli (E. coli) / References: UniProt: P33316, dUTP diphosphatase
#2: Protein Orf20


Mass: 17209.420 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: Q9F0J8
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.42 Å3/Da / Density % sol: 49.08 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5 / Details: Ammonium sulfate, Sodium acetate

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 11.2C / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 16, 2021
RadiationMonochromator: Double Crystal Si111 with LN2 closed loop cooling
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.2→71.1 Å / Num. obs: 15601 / % possible obs: 100 % / Redundancy: 6.8 % / Biso Wilson estimate: 73.54 Å2 / CC1/2: 0.992 / Net I/σ(I): 9.6
Reflection shellResolution: 3.2→3.37 Å / Rmerge(I) obs: 1.077 / Num. unique obs: 2232 / % possible all: 100

-
Processing

Software
NameVersionClassification
PHENIX(1.19.2_4158: ???)refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.2→52.69 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.21 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2509 765 4.92 %
Rwork0.1932 --
obs0.196 15550 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.2→52.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6110 0 1 0 6111
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0046255
X-RAY DIFFRACTIONf_angle_d0.6948529
X-RAY DIFFRACTIONf_dihedral_angle_d4.871922
X-RAY DIFFRACTIONf_chiral_restr0.044955
X-RAY DIFFRACTIONf_plane_restr0.0051115
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2-3.450.28851500.21292900X-RAY DIFFRACTION100
3.45-3.790.26051630.20362888X-RAY DIFFRACTION100
3.79-4.340.24441340.1722963X-RAY DIFFRACTION100
4.34-5.470.21081580.16372940X-RAY DIFFRACTION100
5.47-52.690.26831600.21773094X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 20.1913 Å / Origin y: 8.7573 Å / Origin z: 11.2703 Å
111213212223313233
T0.3471 Å20.0256 Å20.0555 Å2-0.3196 Å2-0.02 Å2--0.3405 Å2
L1.4925 °2-0.0003 °20.6088 °2-1.5077 °20.6532 °2--2.213 °2
S0.17 Å °-0.0046 Å °0.2239 Å °-0.0018 Å °-0.071 Å °-0.1787 Å °0.3061 Å °-0.106 Å °-0.0668 Å °
Refinement TLS groupSelection details: all

+
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