[English] 日本語
Yorodumi
- PDB-2kw3: Heterotrimeric interaction between RFX5 and RFXAP -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2kw3
TitleHeterotrimeric interaction between RFX5 and RFXAP
Components
  • DNA-binding protein RFX5
  • Regulatory factor X-associated protein
KeywordsDNA BINDING PROTEIN / MHCII / RFX5 / RFXAP / Enhanceosome
Function / homology
Function and homology information


positive regulation of MHC class II biosynthetic process / RNA polymerase II transcription regulatory region sequence-specific DNA binding / RNA polymerase II transcription regulator complex / sequence-specific double-stranded DNA binding / DNA-binding transcription activator activity, RNA polymerase II-specific / sequence-specific DNA binding / DNA-binding transcription factor activity, RNA polymerase II-specific / nuclear speck / RNA polymerase II cis-regulatory region sequence-specific DNA binding / intracellular membrane-bounded organelle ...positive regulation of MHC class II biosynthetic process / RNA polymerase II transcription regulatory region sequence-specific DNA binding / RNA polymerase II transcription regulator complex / sequence-specific double-stranded DNA binding / DNA-binding transcription activator activity, RNA polymerase II-specific / sequence-specific DNA binding / DNA-binding transcription factor activity, RNA polymerase II-specific / nuclear speck / RNA polymerase II cis-regulatory region sequence-specific DNA binding / intracellular membrane-bounded organelle / chromatin / regulation of transcription by RNA polymerase II / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / DNA binding / nucleoplasm / nucleus
Similarity search - Function
Helix Hairpins - #1290 / Regulatory factor X-associated C-terminal binding domain / Regulatory factor X-associated protein, RFXANK-binding domain / RFXAP, C-terminal domain superfamily / Regulatory factor X-associated C-terminal binding domain / RFX5, C-terminal / RFX5, N-terminal / : / RFX5 DNA-binding domain / RFX5 N-terminal domain ...Helix Hairpins - #1290 / Regulatory factor X-associated C-terminal binding domain / Regulatory factor X-associated protein, RFXANK-binding domain / RFXAP, C-terminal domain superfamily / Regulatory factor X-associated C-terminal binding domain / RFX5, C-terminal / RFX5, N-terminal / : / RFX5 DNA-binding domain / RFX5 N-terminal domain / RFX5 DNA-binding domain / Four Helix Bundle (Hemerythrin (Met), subunit A) / RFX-like DNA-binding protein / RFX DNA-binding domain / DNA-binding RFX-type winged-helix domain / RFX-type winged-helix DNA-binding domain profile. / Helix Hairpins / Helix non-globular / Special / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
Regulatory factor X-associated protein / DNA-binding protein RFX5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / distance geometry
AuthorsLaird, K.M. / Briggs, L.L. / Boss, J.M. / Summers, M.F. / Garvie, C.W.
CitationJournal: To be Published
Title: Solution structure of the heterotrimeric complex between RFX5 and RFXAP reveals molecular details associated with MHCII gene expression
Authors: Laird, K.M. / Briggs, L.L. / Boss, J.M. / Summers, M.F. / Garvie, C.W.
History
DepositionMar 30, 2010Deposition site: BMRB / Processing site: RCSB
Revision 1.0Aug 25, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2May 1, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: DNA-binding protein RFX5
B: DNA-binding protein RFX5
C: Regulatory factor X-associated protein


Theoretical massNumber of molelcules
Total (without water)22,0273
Polymers22,0273
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)20 / 600structures with the lowest energy
RepresentativeModel #1lowest energy

-
Components

#1: Protein DNA-binding protein RFX5 / Regulatory factor X 5


Mass: 7466.284 Da / Num. of mol.: 2 / Fragment: UNP residues 24-90
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RFX5 / References: UniProt: P48382
#2: Protein Regulatory factor X-associated protein / RFX-associated protein / RFX DNA-binding complex 36 kDa subunit


Mass: 7094.037 Da / Num. of mol.: 1 / Fragment: UNP residues 214-271
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RFXAP / References: UniProt: O00287

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-1H NOESY
1313D CBCA(CO)NH
1413D HNCA
1513D HN(CO)CA

-
Sample preparation

DetailsContents: 1 mM [U-98% 15N] RFX5 and RFXAP-1, 1 mM [U-98% 13C; U-98% 15N] RFX5 and RFXAP-2, 95% H2O/5% D2O
Solvent system: 95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMRFX5 and RFXAP-1[U-98% 15N]1
1 mMRFX5 and RFXAP-2[U-98% 13C; U-98% 15N]1
Sample conditionsIonic strength: 150 / pH: 7.0 / Pressure: ambient / Temperature: 308 K

-
NMR measurement

NMR spectrometerType: Bruker DMX / Manufacturer: Bruker / Model: DMX / Field strength: 600 MHz

-
Processing

NMR software
NameDeveloperClassification
CYANAGuntert, Mumenthaler and Wuthrichrefinement
CYANAGuntert, Mumenthaler and Wuthrichstructure solution
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
TopSpinBruker Biospincollection
ProcheckNMRLaskowski and MacArthurdata analysis
NMRViewJohnson, One Moon Scientificchemical shift assignment
NMRViewJohnson, One Moon Scientificdata analysis
NMRDrawDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
RefinementMethod: distance geometry / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 600 / Conformers submitted total number: 20

+
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