[English] 日本語
Yorodumi
- PDB-6emp: Solution structure of the LEDGF/p75 IBD - POGZ (aa 1370-1404) complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6emp
TitleSolution structure of the LEDGF/p75 IBD - POGZ (aa 1370-1404) complex
ComponentsPC4 and SFRS1-interacting protein,Pogo transposable element with ZNF domain
KeywordsTRANSCRIPTION / protein-protein complex / epigenetics / leukemia
Function / homology
Function and homology information


kinetochore assembly / supercoiled DNA binding / Integration of viral DNA into host genomic DNA / Autointegration results in viral DNA circles / mitotic sister chromatid cohesion / 2-LTR circle formation / Formation of WDR5-containing histone-modifying complexes / Vpr-mediated nuclear import of PICs / Integration of provirus / APOBEC3G mediated resistance to HIV-1 infection ...kinetochore assembly / supercoiled DNA binding / Integration of viral DNA into host genomic DNA / Autointegration results in viral DNA circles / mitotic sister chromatid cohesion / 2-LTR circle formation / Formation of WDR5-containing histone-modifying complexes / Vpr-mediated nuclear import of PICs / Integration of provirus / APOBEC3G mediated resistance to HIV-1 infection / mRNA 5'-splice site recognition / heterochromatin / nuclear periphery / double-strand break repair via homologous recombination / euchromatin / response to heat / DNA-binding transcription factor binding / response to oxidative stress / transcription coactivator activity / chromatin remodeling / cell division / chromatin binding / chromatin / positive regulation of transcription by RNA polymerase II / DNA binding / RNA binding / nucleoplasm / nucleus / metal ion binding / cytosol / cytoplasm
Similarity search - Function
DDE superfamily endonuclease domain / HTH CenpB-type DNA-binding domain / DDE superfamily endonuclease / Tc5 transposase DNA-binding domain / CENPB-type HTH domain profile. / Putative DNA-binding domain in centromere protein B, mouse jerky and transposases. / : / Lens epithelium-derived growth factor, integrase-binding domain / HIV integrase-binding domain superfamily / Lens epithelium-derived growth factor (LEDGF) ...DDE superfamily endonuclease domain / HTH CenpB-type DNA-binding domain / DDE superfamily endonuclease / Tc5 transposase DNA-binding domain / CENPB-type HTH domain profile. / Putative DNA-binding domain in centromere protein B, mouse jerky and transposases. / : / Lens epithelium-derived growth factor, integrase-binding domain / HIV integrase-binding domain superfamily / Lens epithelium-derived growth factor (LEDGF) / TFIIS/LEDGF domain superfamily / domain with conserved PWWP motif / PWWP domain / PWWP domain profile. / PWWP domain / zinc finger / Zinc finger C2H2 type domain profile. / Zinc finger C2H2 superfamily / Zinc finger C2H2 type domain signature. / Zinc finger C2H2-type / Homeobox-like domain superfamily
Similarity search - Domain/homology
PC4 and SFRS1-interacting protein / Pogo transposable element with ZNF domain
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsVeverka, V.
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2018
Title: Affinity switching of the LEDGF/p75 IBD interactome is governed by kinase-dependent phosphorylation.
Authors: Sharma, S. / Cermakova, K. / De Rijck, J. / Demeulemeester, J. / Fabry, M. / El Ashkar, S. / Van Belle, S. / Lepsik, M. / Tesina, P. / Duchoslav, V. / Novak, P. / Hubalek, M. / Srb, P. / ...Authors: Sharma, S. / Cermakova, K. / De Rijck, J. / Demeulemeester, J. / Fabry, M. / El Ashkar, S. / Van Belle, S. / Lepsik, M. / Tesina, P. / Duchoslav, V. / Novak, P. / Hubalek, M. / Srb, P. / Christ, F. / Rezacova, P. / Hodges, H.C. / Debyser, Z. / Veverka, V.
History
DepositionOct 3, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 25, 2018Provider: repository / Type: Initial release
Revision 1.1Aug 1, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2May 8, 2019Group: Data collection / Category: pdbx_nmr_software / Item: _pdbx_nmr_software.name
Revision 1.3Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status / pdbx_nmr_spectrometer
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
Revision 1.4Jun 19, 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: PC4 and SFRS1-interacting protein,Pogo transposable element with ZNF domain


Theoretical massNumber of molelcules
Total (without water)16,0361
Polymers16,0361
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area10290 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)40 / 100structures with the least restraint violations
RepresentativeModel #1lowest energy

-
Components

#1: Protein PC4 and SFRS1-interacting protein,Pogo transposable element with ZNF domain / CLL-associated antigen KW-7 / Dense fine speckles 70 kDa protein / DFS 70 / Lens epithelium-derived ...CLL-associated antigen KW-7 / Dense fine speckles 70 kDa protein / DFS 70 / Lens epithelium-derived growth factor / Transcriptional coactivator p75/p52 / Suppressor of hairy wing homolog 5 / Zinc finger protein 280E / Zinc finger protein 635


Mass: 16036.094 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Gene: PSIP1, DFS70, LEDGF, PSIP2, POGZ, KIAA0461, SUHW5, ZNF280E, ZNF635, Nbla00003
Production host: Escherichia coli (E. coli) / References: UniProt: O75475, UniProt: Q7Z3K3

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic13D HN(CA)CB
121isotropic13D HNCO
131isotropic13D (H)CCH-TOCSY

-
Sample preparation

DetailsType: solution
Contents: 0.5 mM [U-13C; U-15N] LEDGF/p75 IBD-POGZ, 50 mM TRIS, 150 mM sodium chloride, 95% H2O/5% D2O
Label: s1 / Solvent system: 95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.5 mMLEDGF/p75 IBD-POGZ[U-13C; U-15N]1
50 mMTRISnatural abundance1
150 mMsodium chloridenatural abundance1
Sample conditionsIonic strength: 200 mM / Label: c1 / pH: 7 / Pressure: arbitraty Pa / Temperature: 298 K

-
NMR measurement

NMR spectrometerType: Bruker AVANCE III / Manufacturer: Bruker / Model: AVANCE III / Field strength: 850 MHz

-
Processing

NMR software
NameDeveloperClassification
TopSpinBruker Biospincollection
SparkyGoddardchemical shift assignment
CYANAGuntert, Mumenthaler and Wuthrichstructure calculation
YASARAKriegerrefinement
RefinementMethod: simulated annealing / Software ordinal: 4
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://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