[English] 日本語
Yorodumi
- EMDB-46499: FoxP3 multimers bridge four T2G repeat DNAs -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-46499
TitleFoxP3 multimers bridge four T2G repeat DNAs
Map data
Sample
  • Complex: FoxP3-T4G repeats complex
    • Protein or peptide: Forkhead box protein P3
    • DNA: DNA (48-MER)
    • DNA: DNA (47-MER)
KeywordsFoxP3 / STRs / transcriptional factor / FKH / DNA bridging / TRANSCRIPTION / TRANSCRIPTION-DNA complex
Function / homology
Function and homology information


T cell tolerance induction / positive regulation of peripheral T cell tolerance induction / tolerance induction / CD4-positive, CD25-positive, alpha-beta regulatory T cell lineage commitment / establishment of endothelial blood-brain barrier / positive regulation of CD4-positive, alpha-beta T cell differentiation / negative regulation of alpha-beta T cell proliferation / response to rapamycin / alpha-beta T cell proliferation / negative regulation of interleukin-4 production ...T cell tolerance induction / positive regulation of peripheral T cell tolerance induction / tolerance induction / CD4-positive, CD25-positive, alpha-beta regulatory T cell lineage commitment / establishment of endothelial blood-brain barrier / positive regulation of CD4-positive, alpha-beta T cell differentiation / negative regulation of alpha-beta T cell proliferation / response to rapamycin / alpha-beta T cell proliferation / negative regulation of interleukin-4 production / negative regulation of CREB transcription factor activity / RUNX1 and FOXP3 control the development of regulatory T lymphocytes (Tregs) / CD4-positive, CD25-positive, alpha-beta regulatory T cell differentiation / negative regulation of chronic inflammatory response / transforming growth factor beta1 production / negative regulation of T cell cytokine production / negative regulation of interleukin-5 production / regulation of isotype switching to IgG isotypes / regulatory T cell differentiation / tolerance induction to self antigen / negative regulation of defense response to virus / negative regulation of lymphocyte proliferation / negative regulation of T-helper 17 cell differentiation / T cell mediated immunity / positive regulation of transforming growth factor beta1 production / negative regulation of immune response / T cell anergy / immature T cell proliferation in thymus / positive regulation of T cell tolerance induction / lymphocyte proliferation / positive regulation of T cell anergy / CD4-positive, alpha-beta T cell differentiation / positive regulation of CD4-positive, CD25-positive, alpha-beta regulatory T cell differentiation / positive regulation of immature T cell proliferation in thymus / CD4-positive, alpha-beta T cell proliferation / negative regulation of CD4-positive, alpha-beta T cell proliferation / negative regulation of isotype switching to IgE isotypes / isotype switching to IgE isotypes / negative regulation of interleukin-17 production / regulation of T cell anergy / regulation of immunoglobulin production / myeloid cell homeostasis / positive regulation of regulatory T cell differentiation / negative regulation of cytokine production / negative regulation of interleukin-2 production / negative regulation of NF-kappaB transcription factor activity / negative regulation of interleukin-10 production / NFAT protein binding / histone acetyltransferase binding / positive regulation of interleukin-4 production / negative regulation of interleukin-6 production / negative regulation of type II interferon production / B cell homeostasis / negative regulation of tumor necrosis factor production / T cell proliferation / negative regulation of DNA-binding transcription factor activity / negative regulation of T cell proliferation / T cell activation / negative regulation of inflammatory response / response to virus / histone deacetylase binding / transcription corepressor activity / T cell receptor signaling pathway / DNA-binding transcription activator activity, RNA polymerase II-specific / response to lipopolysaccharide / gene expression / sequence-specific DNA binding / transcription by RNA polymerase II / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / chromatin remodeling / inflammatory response / DNA-binding transcription factor activity / negative regulation of cell population proliferation / negative regulation of gene expression / negative regulation of DNA-templated transcription / DNA-templated transcription / positive regulation of gene expression / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / zinc ion binding / nucleoplasm / identical protein binding / nucleus / cytoplasm / cytosol
Similarity search - Function
: / FOXP, coiled-coil domain / : / FOXP coiled-coil domain / Fork head domain / Forkhead domain / Fork head domain profile. / FORKHEAD / Fork head domain conserved site 2 / Fork head domain signature 2. ...: / FOXP, coiled-coil domain / : / FOXP coiled-coil domain / Fork head domain / Forkhead domain / Fork head domain profile. / FORKHEAD / Fork head domain conserved site 2 / Fork head domain signature 2. / Zinc finger C2H2 type domain signature. / Zinc finger C2H2-type / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
Forkhead box protein P3
Similarity search - Component
Biological speciesMus musculus (house mouse) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.0 Å
AuthorsLeng F / Hur S
Funding support United States, 1 items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: To Be Published
Title: FoxP3 multimers bridge three T4G repeat DNAs
Authors: Leng F / Hur S
History
DepositionAug 8, 2024-
Header (metadata) releaseOct 29, 2025-
Map releaseOct 29, 2025-
UpdateOct 29, 2025-
Current statusOct 29, 2025Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_46499.png

Downloads & links

-
Map

FileDownload / File: emd_46499.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 512 pix.
= 423.424 Å		0.83 Å/pix.
x 512 pix.
= 423.424 Å		0.83 Å/pix.
x 512 pix.
= 423.424 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.827 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.35
Minimum - Maximum-3.212635 - 4.9898067
Average (Standard dev.)0.0032841994 (±0.059228636)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 423.424 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: #1

Fileemd_46499_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_46499_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : FoxP3-T4G repeats complex

EntireName: FoxP3-T4G repeats complex
Components
  • Complex: FoxP3-T4G repeats complex
    • Protein or peptide: Forkhead box protein P3
    • DNA: DNA (48-MER)
    • DNA: DNA (47-MER)

-
Supramolecule #1: FoxP3-T4G repeats complex

SupramoleculeName: FoxP3-T4G repeats complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Mus musculus (house mouse)

-
Macromolecule #1: Forkhead box protein P3

MacromoleculeName: Forkhead box protein P3 / type: protein_or_peptide / ID: 1 / Number of copies: 28 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 27.282246 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: GSYPLLANGV CKWPGCEKVF EEPEEFLKHC QADHLLDEKG KAQCLLQREV VQSLEQQLEL EKEKLGAMQA HLAGKMALAK APSVASMDK SSCCIVATST QGSVLPAWSA PREAPDGGLF AVRRHLWGSH GNSSFPEFFH NMDYFKYHNM RPPFTYATLI R WAILEAPE ...String:
GSYPLLANGV CKWPGCEKVF EEPEEFLKHC QADHLLDEKG KAQCLLQREV VQSLEQQLEL EKEKLGAMQA HLAGKMALAK APSVASMDK SSCCIVATST QGSVLPAWSA PREAPDGGLF AVRRHLWGSH GNSSFPEFFH NMDYFKYHNM RPPFTYATLI R WAILEAPE RQRTLNEIYH WFTRMFAYFR NHPATWKNAI RHNLSLHKCF VRVESEKGAV WTVDEFEFRK KRSQRPNK

UniProtKB: Forkhead box protein P3

-
Macromolecule #2: DNA (48-MER)

MacromoleculeName: DNA (48-MER) / type: dna / ID: 2 / Number of copies: 4 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 21.92934 KDa
SequenceString: (DC)(DA)(DA)(DC)(DA)(DA)(DC)(DA)(DA)(DC) (DA)(DA)(DC)(DA)(DA)(DC)(DA)(DA)(DC)(DA) (DA)(DC)(DA)(DA)(DC)(DA)(DA)(DC)(DA) (DA)(DC)(DA)(DA)(DC)(DA)(DA)(DC)(DA)(DA) (DC) (DA)(DA)(DC)(DA)(DA)(DC) ...String:
(DC)(DA)(DA)(DC)(DA)(DA)(DC)(DA)(DA)(DC) (DA)(DA)(DC)(DA)(DA)(DC)(DA)(DA)(DC)(DA) (DA)(DC)(DA)(DA)(DC)(DA)(DA)(DC)(DA) (DA)(DC)(DA)(DA)(DC)(DA)(DA)(DC)(DA)(DA) (DC) (DA)(DA)(DC)(DA)(DA)(DC)(DA)(DA) (DC)(DA)(DA)(DC)(DA)(DA)(DC)(DA)(DA)(DC) (DA)(DA) (DC)(DA)(DA)(DC)(DA)(DA)(DC) (DA)(DA)(DC)(DA)(DA)

-
Macromolecule #3: DNA (47-MER)

MacromoleculeName: DNA (47-MER) / type: dna / ID: 3 / Number of copies: 4 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 22.457217 KDa
SequenceString: (DT)(DT)(DG)(DT)(DT)(DG)(DT)(DT)(DG)(DT) (DT)(DG)(DT)(DT)(DG)(DT)(DT)(DG)(DT)(DT) (DG)(DT)(DT)(DG)(DT)(DT)(DG)(DT)(DT) (DG)(DT)(DT)(DG)(DT)(DT)(DG)(DT)(DT)(DG) (DT) (DT)(DG)(DT)(DT)(DG)(DT) ...String:
(DT)(DT)(DG)(DT)(DT)(DG)(DT)(DT)(DG)(DT) (DT)(DG)(DT)(DT)(DG)(DT)(DT)(DG)(DT)(DT) (DG)(DT)(DT)(DG)(DT)(DT)(DG)(DT)(DT) (DG)(DT)(DT)(DG)(DT)(DT)(DG)(DT)(DT)(DG) (DT) (DT)(DG)(DT)(DT)(DG)(DT)(DT)(DG) (DT)(DT)(DG)(DT)(DT)(DG)(DT)(DT)(DG)(DT) (DT)(DG) (DT)(DT)(DG)(DT)(DT)(DG)(DT) (DT)(DG)(DT)(DT)(DG)

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration1 mg/mL
BufferpH: 7.5
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.2 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

7tdx

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 1340131
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION

-
Atomic model buiding 1

RefinementProtocol: BACKBONE TRACE
Output model

PDB-9d2l:
FoxP3 multimers bridge four T2G repeat DNAs

+
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