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- PDB-4i1l: Structural and Biological Features of FOXP3 Dimerization Relevant... -

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Basic information

Entry
Database: PDB / ID: 4i1l
TitleStructural and Biological Features of FOXP3 Dimerization Relevant to Regulatory T Cell Function
ComponentsForkhead box protein P3
KeywordsTRANSCRIPTION REGULATOR / FOXP3 / DIMERIZATION / COMPLEX ENSEMBLE / STABILITY / REGULATORY ACTIVITY / ACETYATION / DNA-BINDING / METAL-BINDING / NUCLEUS / TRANSCRIPTION / ZINC-FINGER
Function / homology
Function and homology information


T cell tolerance induction / positive regulation of peripheral T cell tolerance induction / CD4-positive, CD25-positive, alpha-beta regulatory T cell lineage commitment / tolerance induction / 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 / CD4-positive, CD25-positive, alpha-beta regulatory T cell lineage commitment / tolerance induction / 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 T cell cytokine production / transforming growth factor beta1 production / negative regulation of chronic inflammatory response / 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 / T cell mediated immunity / negative regulation of lymphocyte proliferation / negative regulation of T-helper 17 cell differentiation / positive regulation of transforming growth factor beta1 production / T cell anergy / positive regulation of T cell anergy / lymphocyte proliferation / immature T cell proliferation in thymus / positive regulation of T cell tolerance induction / negative regulation of isotype switching to IgE isotypes / isotype switching to IgE isotypes / CD4-positive, alpha-beta T cell differentiation / positive regulation of immature T cell proliferation in thymus / CD4-positive, alpha-beta T cell proliferation / positive regulation of CD4-positive, CD25-positive, alpha-beta regulatory T cell differentiation / regulation of immunoglobulin production / negative regulation of immune response / negative regulation of CD4-positive, alpha-beta T cell proliferation / positive regulation of regulatory T cell differentiation / negative regulation of interleukin-17 production / regulation of T cell anergy / myeloid cell homeostasis / negative regulation of cytokine production / negative regulation of NF-kappaB transcription factor activity / negative regulation of interleukin-2 production / histone acetyltransferase binding / negative regulation of interleukin-10 production / NFAT protein binding / positive regulation of interleukin-4 production / B cell homeostasis / negative regulation of interleukin-6 production / negative regulation of type II interferon production / negative regulation of tumor necrosis factor production / negative regulation of T cell proliferation / T cell proliferation / T cell activation / response to virus / negative regulation of DNA-binding transcription factor activity / DNA-binding transcription repressor activity, RNA polymerase II-specific / negative regulation of inflammatory response / histone deacetylase binding / transcription corepressor activity / T cell receptor signaling pathway / gene expression / DNA-binding transcription activator activity, RNA polymerase II-specific / sequence-specific DNA binding / response to lipopolysaccharide / transcription by RNA polymerase II / DNA-binding transcription factor activity, RNA polymerase II-specific / inflammatory response / chromatin remodeling / DNA-binding transcription factor activity / RNA polymerase II cis-regulatory region sequence-specific DNA binding / 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 / nucleoplasm / identical protein binding / nucleus / metal ion binding / cytosol / cytoplasm
Similarity search - Function
: / FOXP, coiled-coil domain / : / FOXP coiled-coil domain / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #340 / Fork head domain / Forkhead domain / Fork head domain profile. / FORKHEAD / Fork head domain conserved site 2 ...: / FOXP, coiled-coil domain / : / FOXP coiled-coil domain / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #340 / 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 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
ACETATE ION / Forkhead box protein P3
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.1 Å
AuthorsSong, X.M. / Greene, M.I. / Zhou, Z.C.
CitationJournal: Cell Rep / Year: 2012
Title: Structural and biological features of FOXP3 dimerization relevant to regulatory T cell function.
Authors: Song, X. / Li, B. / Xiao, Y. / Chen, C. / Wang, Q. / Liu, Y. / Berezov, A. / Xu, C. / Gao, Y. / Li, Z. / Wu, S.L. / Cai, Z. / Zhang, H. / Karger, B.L. / Hancock, W.W. / Wells, A.D. / Zhou, Z. / Greene, M.I.
History
DepositionNov 21, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 5, 2012Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_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_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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.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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Forkhead box protein P3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,7589
Polymers10,2791
Non-polymers4798
Water34219
1
A: Forkhead box protein P3
hetero molecules

A: Forkhead box protein P3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,51618
Polymers20,5582
Non-polymers95816
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_554-y,-x,-z-1/41
Buried area3160 Å2
ΔGint-88 kcal/mol
Surface area10190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.130, 37.130, 135.672
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number95
Space group name H-MP4322
Components on special symmetry positions
IDModelComponents
11A-401-

HOH

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Components

#1: Protein Forkhead box protein P3 / Scurfin


Mass: 10278.895 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 189-276
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Foxp3 / Plasmid: PET51B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q99JB6
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 19 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.27 Å3/Da / Density % sol: 45.92 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.3
Details: 20MM HEPES, PH 7.3, 1MM TCEP, 0.5% CHAPS, 100MM NACL, 100MM NAAC PH 4.5, ~1.8M MGSO4, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12B / Wavelength: 1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Feb 26, 2008 / Details: MIRRORS
RadiationMonochromator: Si 111 CHANNEL / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
111
211
ReflectionResolution: 2.1→50 Å / Num. all: 6154 / Num. obs: 6111 / % possible obs: 99.3 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 5.2 % / Biso Wilson estimate: 50 Å2 / Rmerge(I) obs: 0.064 / Rsym value: 0.064 / Net I/σ(I): 30.86
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.511 / Mean I/σ(I) obs: 3.75 / Rsym value: 0.511 / % possible all: 100

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
SOLVEphasing
REFMAC5.4.0069refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MAD / Resolution: 2.1→35.81 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.9 / SU B: 6.561 / SU ML: 0.086 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.187 / ESU R Free: 0.183 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.289 280 4.6 %RANDOM
Rwork0.236 ---
obs0.238 5811 100 %-
all-5811 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 49.457 Å2
Baniso -1Baniso -2Baniso -3
1-2.37 Å20 Å20 Å2
2--2.37 Å20 Å2
3----4.75 Å2
Refinement stepCycle: LAST / Resolution: 2.1→35.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms471 0 26 19 516
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0250.021495
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.8892.01663
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.488561
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.15627.08324
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.5671588
X-RAY DIFFRACTIONr_dihedral_angle_4_deg6.664151
X-RAY DIFFRACTIONr_chiral_restr0.1410.270
X-RAY DIFFRACTIONr_gen_planes_refined0.010.02365
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.3991.5312
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.6492481
X-RAY DIFFRACTIONr_scbond_it4.9773183
X-RAY DIFFRACTIONr_scangle_it7.8434.5182
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.15 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.197 18 -
Rwork0.218 406 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: 3.327 Å / Origin y: 14.482 Å / Origin z: 27.05 Å
111213212223313233
T-0.0897 Å2-0.0114 Å20.0036 Å2-0.0908 Å2-0.0117 Å2---0.0106 Å2
L1.5231 °2-0.0685 °23.8315 °2-0.1505 °2-0.2202 °2--9.6538 °2
S0.0065 Å °-0.1632 Å °0.0889 Å °-0.085 Å °-0.095 Å °-0.0216 Å °0.1682 Å °-0.0979 Å °0.0884 Å °

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