[English] 日本語
Yorodumi
- PDB-3qrf: Structure of a domain-swapped FOXP3 dimer -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3qrf
TitleStructure of a domain-swapped FOXP3 dimer
Components
  • (human hARRE2 DNA ...) x 2
  • Forkhead box protein P3
  • Nuclear factor of activated T-cells, cytoplasmic 2
KeywordsDNA BINDING PROTEIN/DNA / Beta Barrel / Domain Swap / Forkhead Domain / Immnoglobulin Fold / Protein-DNA Complex / Double Helix / Transcription Regulation / DNA Binding / Nucleus / DNA BINDING PROTEIN-DNA complex
Function / homology
Function and homology information


positive regulation of peripheral T cell tolerance induction / CD4-positive, CD25-positive, alpha-beta regulatory T cell lineage commitment / establishment of endothelial blood-brain barrier / lncRNA transcription / response to rapamycin / negative regulation of interleukin-4 production / negative regulation of CREB transcription factor activity / transcription factor AP-1 complex / negative regulation of chronic inflammatory response / transforming growth factor beta1 production ...positive regulation of peripheral T cell tolerance induction / CD4-positive, CD25-positive, alpha-beta regulatory T cell lineage commitment / establishment of endothelial blood-brain barrier / lncRNA transcription / response to rapamycin / negative regulation of interleukin-4 production / negative regulation of CREB transcription factor activity / transcription factor AP-1 complex / 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 / negative regulation of vascular associated smooth muscle cell differentiation / regulatory T cell differentiation / tolerance induction to self antigen / negative regulation of defense response to virus / negative regulation of T-helper 17 cell differentiation / T cell mediated immunity / myotube cell development / positive regulation of transforming growth factor beta1 production / negative regulation of immune response / T cell anergy / immature T cell proliferation in thymus / RUNX1 and FOXP3 control the development of regulatory T lymphocytes (Tregs) / positive regulation of T cell anergy / calcineurin-NFAT signaling cascade / 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 / cartilage development / positive regulation of regulatory T cell differentiation / negative regulation of cytokine production / myeloid cell homeostasis / positive regulation of myoblast fusion / negative regulation of interleukin-2 production / CLEC7A (Dectin-1) induces NFAT activation / RUNX1 regulates transcription of genes involved in WNT signaling / negative regulation of interleukin-10 production / histone acetyltransferase binding / NFAT protein binding / positive regulation of interleukin-4 production / negative regulation of NF-kappaB transcription factor activity / negative regulation of activated T cell proliferation / T cell homeostasis / negative regulation of interleukin-6 production / B cell homeostasis / negative regulation of type II interferon production / Calcineurin activates NFAT / negative regulation of tumor necrosis factor production / NF-kappaB binding / phosphatase binding / negative regulation of T cell proliferation / 14-3-3 protein binding / positive regulation of B cell proliferation / FCERI mediated Ca+2 mobilization / cellular response to calcium ion / T cell activation / negative regulation of DNA-binding transcription factor activity / B cell receptor signaling pathway / response to virus / DNA-binding transcription repressor activity, RNA polymerase II-specific / histone deacetylase binding / transcription corepressor activity / sequence-specific double-stranded DNA binding / cell migration / T cell receptor signaling pathway / DNA-binding transcription activator activity, RNA polymerase II-specific / molecular adaptor activity / transcription regulator complex / response to lipopolysaccharide / sequence-specific DNA binding / transcription by RNA polymerase II / DNA-binding transcription factor activity, RNA polymerase II-specific / chromatin remodeling / inflammatory response / RNA polymerase II cis-regulatory region sequence-specific DNA binding / response to xenobiotic stimulus / DNA-binding transcription factor activity / ribonucleoprotein complex / negative regulation of cell population proliferation / negative regulation of DNA-templated transcription / DNA damage response / chromatin binding / positive regulation of gene expression / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / chromatin / positive regulation of DNA-templated transcription / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / protein-containing complex / DNA binding / zinc ion binding / nucleoplasm
Similarity search - Function
: / FOXP, coiled-coil domain / : / FOXP coiled-coil domain / Nuclear factor of activated T cells (NFAT) / Rel homology domain (RHD), DNA-binding domain / Fork head domain / Forkhead domain / Fork head domain profile. / FORKHEAD ...: / FOXP, coiled-coil domain / : / FOXP coiled-coil domain / Nuclear factor of activated T cells (NFAT) / Rel homology domain (RHD), DNA-binding domain / Fork head domain / Forkhead domain / Fork head domain profile. / FORKHEAD / Fork head domain conserved site 2 / Fork head domain signature 2. / Rel homology domain (RHD), DNA-binding domain / Rel homology dimerisation domain / Rel homology DNA-binding domain / Rel homology dimerisation domain / NF-kappa-B/Rel/dorsal domain profile. / Rel homology domain (RHD), DNA-binding domain superfamily / ig-like, plexins, transcription factors / IPT domain / p53-like transcription factor, DNA-binding / Zinc finger C2H2 type domain signature. / Zinc finger C2H2-type / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Immunoglobulin E-set / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
DNA / DNA (> 10) / Nuclear factor of activated T-cells, cytoplasmic 2 / Forkhead box protein P3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsBandukwala, H.S. / Wu, Y. / Feurer, M. / Chen, Y. / Barbosa, B. / Ghosh, S. / Stroud, J.C. / Benoist, C. / Mathis, D. / Rao, A. / Chen, L.
CitationJournal: Immunity / Year: 2011
Title: Structure of a Domain-Swapped FOXP3 Dimer on DNA and Its Function in Regulatory T Cells.
Authors: Bandukwala, H.S. / Wu, Y. / Feuerer, M. / Chen, Y. / Barboza, B. / Ghosh, S. / Stroud, J.C. / Benoist, C. / Mathis, D. / Rao, A. / Chen, L.
History
DepositionFeb 17, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 20, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.3Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
N: Nuclear factor of activated T-cells, cytoplasmic 2
F: Forkhead box protein P3
G: Forkhead box protein P3
C: human hARRE2 DNA (Plus Strand)
D: human hARRE2 DNA (Minus Strand)
M: Nuclear factor of activated T-cells, cytoplasmic 2
H: Forkhead box protein P3
I: Forkhead box protein P3
A: human hARRE2 DNA (Plus Strand)
B: human hARRE2 DNA (Minus Strand)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)130,60814
Polymers130,51110
Non-polymers974
Water1267
1
N: Nuclear factor of activated T-cells, cytoplasmic 2
F: Forkhead box protein P3
G: Forkhead box protein P3
C: human hARRE2 DNA (Plus Strand)
D: human hARRE2 DNA (Minus Strand)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,3047
Polymers65,2565
Non-polymers492
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12130 Å2
ΔGint-101 kcal/mol
Surface area29440 Å2
MethodPISA
2
A: human hARRE2 DNA (Plus Strand)
B: human hARRE2 DNA (Minus Strand)

M: Nuclear factor of activated T-cells, cytoplasmic 2
H: Forkhead box protein P3
I: Forkhead box protein P3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,3047
Polymers65,2565
Non-polymers492
Water181
TypeNameSymmetry operationNumber
crystal symmetry operation2_646-x+1,y-1/2,-z+11
identity operation1_555x,y,z1
Buried area12080 Å2
ΔGint-101 kcal/mol
Surface area29480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.667, 131.234, 68.665
Angle α, β, γ (deg.)90.00, 89.95, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

-
Protein , 2 types, 6 molecules NMFGHI

#1: Protein Nuclear factor of activated T-cells, cytoplasmic 2 / NF-ATc2 / NFATc2 / NFAT pre-existing subunit / NF-ATp / T-cell transcription factor NFAT1


Mass: 32209.703 Da / Num. of mol.: 2 / Fragment: human NFAT1 DNA Binding Domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NFATC2, NFAT1, NFATP / Production host: Escherichia coli (E. coli) / References: UniProt: Q13469
#2: Protein
Forkhead box protein P3 / Scurfin


Mass: 10082.725 Da / Num. of mol.: 4 / Fragment: human FOXP3 DNA Binding Domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FOXP3, IPEX, JM2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9BZS1

-
Human hARRE2 DNA ... , 2 types, 4 molecules CADB

#3: DNA chain human hARRE2 DNA (Plus Strand)


Mass: 6491.230 Da / Num. of mol.: 2 / Fragment: human IL-2 promoter ARRE2 site (plus strand) / Source method: obtained synthetically / Details: The core hARRE2 site occurs naturally in humans.
#4: DNA chain human hARRE2 DNA (Minus Strand)


Mass: 6389.186 Da / Num. of mol.: 2 / Fragment: human IL-2 promoter ARRE2 site (minus strand) / Source method: obtained synthetically / Details: The core hARRE2 site occurs naturally in humans.

-
Non-polymers , 2 types, 11 molecules

#5: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 7 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.89 Å3/Da / Density % sol: 57.42 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.63
Details: 5 mM HEPES, pH 7.63, 2 mM dithiothreitol (DTT), 0.5 mM EDTA, and 150 mM NaCl, VAPOR DIFFUSION, HANGING DROP, temperature 291K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 0.97625 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jan 22, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. all: 36536 / Num. obs: 35150 / % possible obs: 96.2 % / Observed criterion σ(F): 0
Reflection shellResolution: 2.8→2.93 Å / Rmerge(I) obs: 1.021 / Mean I/σ(I) obs: 4.15 / Num. unique all: 4468 / % possible all: 99.3

-
Processing

Software
NameVersionClassification
ADSCQuantumdata collection
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1a02 - NFAT + DNA only

1a02


Resolution: 2.8→50 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.2828 3413 Random
Rwork0.2478 --
all-36536 -
obs-35150 -
Refinement stepCycle: LAST / Resolution: 2.8→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7384 1710 4 7 9105

+
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