[English] 日本語
Yorodumi
- PDB-2n7d: Solution structure of the UBL domain of human Ddi2 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2n7d
TitleSolution structure of the UBL domain of human Ddi2
ComponentsProtein DDI1 homolog 2
KeywordsUNKNOWN FUNCTION / DDI2
Function / homology
Function and homology information


regulation of DNA stability / cellular response to hydroxyurea / Hydrolases; Acting on peptide bonds (peptidases); Aspartic endopeptidases / proteasomal protein catabolic process / ubiquitin binding / regulation of protein stability / protein processing / chromosome / aspartic-type endopeptidase activity / nucleoplasm ...regulation of DNA stability / cellular response to hydroxyurea / Hydrolases; Acting on peptide bonds (peptidases); Aspartic endopeptidases / proteasomal protein catabolic process / ubiquitin binding / regulation of protein stability / protein processing / chromosome / aspartic-type endopeptidase activity / nucleoplasm / identical protein binding / cytosol
Similarity search - Function
DNA damage inducible protein 1 ubiquitin-like domain / Aspartic peptidase, DDI1-type / Aspartyl protease / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Ubiquitin-like (UB roll) / Ubiquitin family / Ubiquitin domain profile. / Ubiquitin-like domain / Aspartic peptidase domain superfamily / Ubiquitin-like domain superfamily ...DNA damage inducible protein 1 ubiquitin-like domain / Aspartic peptidase, DDI1-type / Aspartyl protease / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Ubiquitin-like (UB roll) / Ubiquitin family / Ubiquitin domain profile. / Ubiquitin-like domain / Aspartic peptidase domain superfamily / Ubiquitin-like domain superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
Protein DDI1 homolog 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / torsion angle dynamics, molecular dynamics
AuthorsSiva, M. / Grantz Saskova, K. / Veverka, V.
CitationJournal: Sci Rep / Year: 2016
Title: Human DNA-Damage-Inducible 2 Protein Is Structurally and Functionally Distinct from Its Yeast Ortholog.
Authors: Siva, M. / Svoboda, M. / Veverka, V. / Trempe, J.F. / Hofmann, K. / Kozisek, M. / Hexnerova, R. / Sedlak, F. / Belza, J. / Brynda, J. / Sacha, P. / Hubalek, M. / Starkova, J. / Flaisigova, I. ...Authors: Siva, M. / Svoboda, M. / Veverka, V. / Trempe, J.F. / Hofmann, K. / Kozisek, M. / Hexnerova, R. / Sedlak, F. / Belza, J. / Brynda, J. / Sacha, P. / Hubalek, M. / Starkova, J. / Flaisigova, I. / Konvalinka, J. / Saskova, K.G.
History
DepositionSep 8, 2015Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jul 20, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 3, 2016Group: Database references
Revision 1.2Aug 10, 2016Group: Structure summary
Revision 1.3Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_spectrometer / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.4May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Protein DDI1 homolog 2


Theoretical massNumber of molelcules
Total (without water)11,1421
Polymers11,1421
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)40 / 100structures with the least restraint violations
RepresentativeModel #1lowest energy

-
Components

#1: Protein Protein DDI1 homolog 2


Mass: 11142.463 Da / Num. of mol.: 1 / Fragment: UBL domain (UNP residues 1-76)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DDI2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5TDH0

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1213D HN(CA)CB
1313D CBCA(CO)NH
1413D (H)CCH-TOCSY
1513D 1H-13C NOESY
1613D 1H-15N NOESY
1713D HNCO

-
Sample preparation

DetailsContents: 25 mM sodium phosphate, 100 mM sodium chloride, 95% H2O/5% D2O
Solvent system: 95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentSolution-ID
25 mMsodium phosphate-11
100 mMsodium chloride-21
Sample conditionsIonic strength: 0.1 / pH: 6.5 / Pressure: ambient / Temperature: 298 K

-
NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE8501
Bruker AvanceBrukerAVANCE6002

-
Processing

NMR software
NameDeveloperClassification
YASARAYASARArefinement
CYANAGuntert, Mumenthaler and Wuthrichrefinement
RefinementMethod: torsion angle dynamics, molecular dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 100 / Conformers submitted total number: 40

+
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://pdbjlvh1.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