[English] 日本語
Yorodumi
- SASDC77: Deoxyuridine 5'-triphosphate nucleotidohydrolase complex with SaP... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: SASBDB / ID: SASDC77
SampleDeoxyuridine 5'-triphosphate nucleotidohydrolase complex with SaPIbov1 pathogenicity island repressor [3:3] (SEC-SAXS)
  • Deoxyuridine 5'-triphosphate nucleotidohydrolase (protein), hDUT, Homo sapiens
  • SaPIbov1 pathogenicity island repressor (protein), Stl, Staphylococcus aureus
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
Stl / Deoxyuridine 5'-triphosphate nucleotidohydrolase, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
Staphylococcus aureus (bacteria)
CitationDate: 2018 Mar 12
Title: Structural model of human dUTPase in complex with a novel proteinaceous inhibitor
Authors: Nyíri K / Mertens H / Tihanyi B / Nagy G / Kőhegyi B / Matejka J / Harris M / Szabó J / Papp-Kádár V / Németh-Pongrácz V / Ozohanics O / Vékey K / Svergun D / Borysik A
Contact author
  • Haydyn Mertens (EMBL-Hamburg, European Molecular Biology Laboratory (EMBL) - Hamburg outstation, Notkestraße 85, Geb. 25A, 22607 Hamburg, Deutschland, Germany)

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Models

Model #1491
Type: dummy / Software: (2.9.0) / Radius of dummy atoms: 3.40 A / Symmetry: P3 / Chi-square value: 1.066
Search similar-shape structures of this assembly by Omokage search (details)
Model #1492
Type: mix / Software: (2.9.0) / Radius of dummy atoms: 1.90 A / Symmetry: P3 / Chi-square value: 1.41
Search similar-shape structures of this assembly by Omokage search (details)

-
Sample

SampleName: Deoxyuridine 5'-triphosphate nucleotidohydrolase complex with SaPIbov1 pathogenicity island repressor [3:3] (SEC-SAXS)
Dry vol: 188384 / Entity id: 775 / 776
BufferName: 50 mM HEPES 300 mM NaCl 5 mM MgCl2 / pH: 7.5 / Comment: Buffer B
Entity #775Name: hDUT / Type: protein
Description: Deoxyuridine 5'-triphosphate nucleotidohydrolase
Formula weight: 18.029 / Num. of mol.: 3 / Source: Homo sapiens / References: UniProt: P33316
Sequence:
GSHMPCSEET PAISPSKRAR PAEVGGMQLR FARLSEHATA PTRGSARAAG YDLYSAYDYT IPPMEKAVVK TDIQIALPSG CYGRVAPRSG LAAKHFIDVG AGVIDEDYRG NVGVVLFNFG KEKFEVKKGD RIAQLICERI FYPEIEEVQA LDDTERGSGG FGSTGKN
Entity #776Name: Stl / Type: protein / Description: SaPIbov1 pathogenicity island repressor / Formula weight: 32.016 / Num. of mol.: 2 / Source: Staphylococcus aureus / References: UniProt: E2FZP6
Sequence: GSPEFSMEGA GQMAELPTHY GTIIKTLRKY MKLTQSKLSE RTGFSQNTIS NHENGNRNIG VNEIEIYGKG LGIPSYILHR ISDEFKEKGY SPTLNDFGKF DKMYSYVNKA YYNDGDIYYS SYDLYDETIK LLELLKESKI NVNDIDYDYV LKLYKQILST DTEKSIINYE ...Sequence:
GSPEFSMEGA GQMAELPTHY GTIIKTLRKY MKLTQSKLSE RTGFSQNTIS NHENGNRNIG VNEIEIYGKG LGIPSYILHR ISDEFKEKGY SPTLNDFGKF DKMYSYVNKA YYNDGDIYYS SYDLYDETIK LLELLKESKI NVNDIDYDYV LKLYKQILST DTEKSIINYE TLANTRKSSD KKREVTIEEI GEFHEKYLKL LFTNLETHND RKKALAEIEK LKEESIYLGE KLRLVPNHHY DAIKGKPMYK LYLYEYPDRL EHQKKIILEK DTN

-
Experimental information

BeamInstrument name: PETRA III EMBL P12 / City: Hamburg / 国: Germany / Type of source: X-ray synchrotron / Wavelength: 0.124 Å / Dist. spec. to detc.: 3.1 mm
DetectorName: Pilatus 2M
Scan
Title: hDUTstl_SEC_1 / Measurement date: Jul 10, 2016 / Storage temperature: 10 °C / Cell temperature: 10 °C / Exposure time: 1 sec. / Number of frames: 3600 / Unit: 1/nm /
MinMax
Q0.0771 5.0307
Distance distribution function P(R)
Sofotware P(R): GNOM 5.0 / Number of points: 1200 /
MinMax
Q0.0771412 3.38043
P(R) point1 1200
R0 17
Result
Type of curve: single_conc / Standard: water
ExperimentalExperimental errorStandardStandard errorPorodPorod errorEstimatedEstimated errorEstimated method
MW145 kDa10 145 kDa10 134 kDa9 ---
Volume----227 nm310 290 20 DAM volume

P(R)P(R) errorGuinierGuinier error
Forward scattering, I00.041 0.002 0.041 0.001
Radius of gyration, Rg4.47 nm0.1 4.36 nm0.1

MinMaxError
D-17 0.5
Guinier point1 64 -

+
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