[English] 日本語
Yorodumi
- PDB-2kzs: DAXX helical bundle (DHB) domain -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2kzs
TitleDAXX helical bundle (DHB) domain
ComponentsDeath-associated protein 6
KeywordsAPOPTOSIS / helical bundle / DHB domain / Fas death-domain associated protein / DAXX / Rassf1C interacting domain
Function / homology
Function and homology information


cellular response to diamide / Defective Inhibition of DNA Recombination at Telomere Due to DAXX Mutations / Defective Inhibition of DNA Recombination at Telomere Due to ATRX Mutations / SUMO-modified protein reader activity / neuron intrinsic apoptotic signaling pathway in response to oxidative stress / cellular response to sodium arsenite / transcription regulator inhibitor activity / nuclear androgen receptor binding / protein kinase activator activity / androgen receptor signaling pathway ...cellular response to diamide / Defective Inhibition of DNA Recombination at Telomere Due to DAXX Mutations / Defective Inhibition of DNA Recombination at Telomere Due to ATRX Mutations / SUMO-modified protein reader activity / neuron intrinsic apoptotic signaling pathway in response to oxidative stress / cellular response to sodium arsenite / transcription regulator inhibitor activity / nuclear androgen receptor binding / protein kinase activator activity / androgen receptor signaling pathway / chromosome, centromeric region / regulation of protein ubiquitination / extrinsic apoptotic signaling pathway via death domain receptors / positive regulation of protein kinase activity / cellular response to unfolded protein / JNK cascade / cellular response to copper ion / Inhibition of DNA recombination at telomere / heat shock protein binding / cellular response to cadmium ion / SUMOylation of transcription cofactors / molecular condensate scaffold activity / PML body / HCMV Early Events / transcription corepressor activity / nucleosome assembly / Regulation of TP53 Degradation / p53 binding / cellular response to heat / histone binding / regulation of gene expression / regulation of apoptotic process / RNA polymerase II-specific DNA-binding transcription factor binding / transcription coactivator activity / nuclear body / chromatin remodeling / positive regulation of protein phosphorylation / negative regulation of gene expression / negative regulation of DNA-templated transcription / ubiquitin protein ligase binding / regulation of DNA-templated transcription / nucleolus / protein kinase binding / enzyme binding / protein homodimerization activity / nucleoplasm / nucleus / cytosol
Similarity search - Function
Daxx helical bundle domain / Daxx, N-terminal Rassf1C-interacting domain / Daxx, N-terminal domain superfamily / Daxx, histone-binding domain / Daxx, histone-binding domain superfamily / Daxx N-terminal Rassf1C-interacting domain / Death domain-associated protein 6, histone binding domain / Helicase, Ruva Protein; domain 3 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Death domain associated protein / Death domain-associated protein 6
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model 2
AuthorsEscobar-Cabrera, E. / Lau, D.K.W. / Giovinazzi, S. / Ishov, A.M. / McIntosh, L.P.
CitationJournal: Structure / Year: 2010
Title: Structural Characterization of the DAXX N-Terminal Helical Bundle Domain and Its Complex with Rassf1C.
Authors: Escobar-Cabrera, E. / Lau, D.K. / Giovinazzi, S. / Ishov, A.M. / McIntosh, L.P.
History
DepositionJun 23, 2010Deposition site: BMRB / Processing site: RCSB
Revision 1.0Dec 15, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 5, 2020Group: Database references / Other
Category: database_2 / pdbx_database_status / struct_ref_seq_dif
Item: _pdbx_database_status.status_code_cs / _struct_ref_seq_dif.details
Revision 1.3Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data
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: Death-associated protein 6


Theoretical massNumber of molelcules
Total (without water)10,9511
Polymers10,9511
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)25 / 120structures with the lowest energy
RepresentativeModel #1lowest energy

-
Components

#1: Protein Death-associated protein 6 /


Mass: 10950.833 Da / Num. of mol.: 1 / Fragment: UNP residues 55 to 144
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Description: Cloned into pET28a from a human cDNA library, using NdeI and XhoI
Gene: DAXX, DADB-159G18.9-007, DAMC-227D19.15-007, DAQB-126H3.2-007, XXbac-BCX165D10.3-007, XXbac-BPG185D15.6-007
Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q4VX54, UniProt: Q9UER7*PLUS

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1213D HN(CA)CB
1312D 1H-13C HSQC
1413D CBCA(CO)NH
1513D HBHA(CO)NH
1613D (H)CCH-TOCSY
1713D 1H-15N NOESY
1813D 1H-15N TOCSY
1913D 1H-13C NOESY
11013D H(CC)(CO)NH-TOCSY
11112D (HB)CB(CGCD)HD
11212D (HB)CBCGCDCE)HE
11312D HMBC
11422D 1H-13C HSQC
1151CT methyl-methyl-HSQC
1161CT amide-methyl-HSQC

-
Sample preparation

Details
Solution-IDContentsSolvent system
11.2 mM [U-100% 13C; U-100% 15N] DAXX-1, 10 mM potassium phosphate-2, 100 mM KCl-3, 0.1 mM EDTA-4, 95% H2O/5% D2O95% H2O/5% D2O
20.8 mM [U-10% 13C] DAXX-5, 95% H2O/5% D2O95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.2 mMDAXX-1[U-100% 13C; U-100% 15N]1
10 mMpotassium phosphate-21
100 mMKCl-31
0.1 mMEDTA-41
0.8 mMDAXX-5[U-10% 13C]2
Sample conditionsIonic strength: 0.16 / pH: 6.5 / Pressure: ambient / Temperature: 298 K

-
NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA6001
Varian UnityVarianUNITY5002

-
Processing

NMR software
NameVersionDeveloperClassification
ARIA2.2Linge, O'Donoghue and Nilgesstructure solution
ARIA2.2Linge, O'Donoghue and Nilgessemi-automatic peak assignment
ARIA2.2Linge, O'Donoghue and Nilgesrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR constraintsNOE constraints total: 3585 / NOE intraresidue total count: 1153 / NOE long range total count: 761 / NOE medium range total count: 962 / NOE sequential total count: 709 / Protein chi angle constraints total count: 0 / Protein other angle constraints total count: 0 / Protein phi angle constraints total count: 69 / Protein psi angle constraints total count: 69
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 120 / Conformers submitted total number: 25 / Maximum lower distance constraint violation: 0.02 Å / Maximum upper distance constraint violation: 0.28 Å

+
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