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Basic information

Entry
Database: PDB / ID: 9toy
TitleInvestigating the binding mechanism of Interferon Regulatory Factor 4 to DNA in the context of Multiple Myeloma
Components
  • DNA (5'-D(P*AP*GP*CP*TP*TP*TP*CP*TP*CP*AP*GP*TP*TP*TP*CP*AP*GP*TP*TP*G)-3')
  • DNA (5'-D(P*TP*CP*AP*AP*CP*TP*GP*AP*AP*AP*CP*TP*GP*AP*GP*AP*AP*AP*GP*C)-3')
  • Interferon regulatory factor 4
KeywordsDNA BINDING PROTEIN / Transcription Factor
Function / homology
Function and homology information


T-helper 17 cell lineage commitment / regulation of T-helper cell differentiation / negative regulation of toll-like receptor signaling pathway / positive regulation of interleukin-13 production / myeloid dendritic cell differentiation / defense response to protozoan / positive regulation of interleukin-4 production / Regulation of MITF-M-dependent genes involved in pigmentation / positive regulation of interleukin-10 production / immune system process ...T-helper 17 cell lineage commitment / regulation of T-helper cell differentiation / negative regulation of toll-like receptor signaling pathway / positive regulation of interleukin-13 production / myeloid dendritic cell differentiation / defense response to protozoan / positive regulation of interleukin-4 production / Regulation of MITF-M-dependent genes involved in pigmentation / positive regulation of interleukin-10 production / immune system process / positive regulation of interleukin-2 production / Nuclear events stimulated by ALK signaling in cancer / T cell activation / Interferon gamma signaling / sequence-specific double-stranded DNA binding / Interferon alpha/beta signaling / nucleosome / positive regulation of cold-induced thermogenesis / Interleukin-4 and Interleukin-13 signaling / DNA-binding transcription activator activity, RNA polymerase II-specific / sequence-specific DNA binding / DNA-binding transcription factor activity, RNA polymerase II-specific / transcription coactivator activity / RNA polymerase II cis-regulatory region sequence-specific DNA binding / chromatin remodeling / DNA-binding transcription factor activity / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / chromatin / positive regulation of transcription by RNA polymerase II / nucleoplasm / membrane / nucleus / cytosol
Similarity search - Function
Interferon regulatory factor-3 / Interferon-regulatory factor 3 / Interferon-regulatory factor 3 / Interferon regulatory factor, conserved site / IRF tryptophan pentad repeat DNA-binding domain signature. / Interferon regulatory factor transcription factor / interferon regulatory factor / Interferon regulatory factor DNA-binding domain / IRF tryptophan pentad repeat DNA-binding domain profile. / SMAD-like domain superfamily ...Interferon regulatory factor-3 / Interferon-regulatory factor 3 / Interferon-regulatory factor 3 / Interferon regulatory factor, conserved site / IRF tryptophan pentad repeat DNA-binding domain signature. / Interferon regulatory factor transcription factor / interferon regulatory factor / Interferon regulatory factor DNA-binding domain / IRF tryptophan pentad repeat DNA-binding domain profile. / SMAD-like domain superfamily / SMAD/FHA domain superfamily / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
DNA / DNA (> 10) / Interferon regulatory factor 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsAlamaniotis, C. / Roe, M. / Mancini, E.J.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Acta Crystallogr F Struct Biol Commun / Year: 2021
Title: Phosphorus and sulfur SAD phasing of the nucleic acid-bound DNA-binding domain of interferon regulatory factor 4.
Authors: Agnarelli, A. / El Omari, K. / Duman, R. / Wagner, A. / Mancini, E.J.
History
DepositionDec 17, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 11, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Interferon regulatory factor 4
B: Interferon regulatory factor 4
C: DNA (5'-D(P*TP*CP*AP*AP*CP*TP*GP*AP*AP*AP*CP*TP*GP*AP*GP*AP*AP*AP*GP*C)-3')
E: DNA (5'-D(P*AP*GP*CP*TP*TP*TP*CP*TP*CP*AP*GP*TP*TP*TP*CP*AP*GP*TP*TP*G)-3')
D: Interferon regulatory factor 4
F: Interferon regulatory factor 4
G: DNA (5'-D(P*TP*CP*AP*AP*CP*TP*GP*AP*AP*AP*CP*TP*GP*AP*GP*AP*AP*AP*GP*C)-3')
H: DNA (5'-D(P*AP*GP*CP*TP*TP*TP*CP*TP*CP*AP*GP*TP*TP*TP*CP*AP*GP*TP*TP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,70513
Polymers81,5058
Non-polymers2005
Water1,928107
1
A: Interferon regulatory factor 4
B: Interferon regulatory factor 4
C: DNA (5'-D(P*TP*CP*AP*AP*CP*TP*GP*AP*AP*AP*CP*TP*GP*AP*GP*AP*AP*AP*GP*C)-3')
E: DNA (5'-D(P*AP*GP*CP*TP*TP*TP*CP*TP*CP*AP*GP*TP*TP*TP*CP*AP*GP*TP*TP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,9138
Polymers40,7524
Non-polymers1604
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6220 Å2
ΔGint-70 kcal/mol
Surface area17880 Å2
MethodPISA
2
D: Interferon regulatory factor 4
F: Interferon regulatory factor 4
G: DNA (5'-D(P*TP*CP*AP*AP*CP*TP*GP*AP*AP*AP*CP*TP*GP*AP*GP*AP*AP*AP*GP*C)-3')
H: DNA (5'-D(P*AP*GP*CP*TP*TP*TP*CP*TP*CP*AP*GP*TP*TP*TP*CP*AP*GP*TP*TP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,7925
Polymers40,7524
Non-polymers401
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6120 Å2
ΔGint-53 kcal/mol
Surface area17880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.512, 65.116, 70.694
Angle α, β, γ (deg.)89.859, 75.316, 66.791
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
32A
42D
53A
63F
74B
84D
95B
105F
116C
126G
137E
147H
158D
168F

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111GLYGLYGLUGLUAA19 - 1303 - 114
211GLYGLYGLUGLUBB19 - 1303 - 114
322GLYGLYPROPROAA19 - 1293 - 113
422GLYGLYPROPRODE19 - 1293 - 113
533ASNASNGLUGLUAA21 - 1305 - 114
633ASNASNGLUGLUFF21 - 1305 - 114
744GLYGLYPROPROBB19 - 1293 - 113
844GLYGLYPROPRODE19 - 1293 - 113
955ASNASNGLUGLUBB21 - 1305 - 114
1055ASNASNGLUGLUFF21 - 1305 - 114
1166DTDTDCDCCC1 - 201 - 20
1266DTDTDCDCGG1 - 201 - 20
1377DADADGDGED1 - 201 - 20
1477DADADGDGHH1 - 201 - 20
1588ASNASNPROPRODE21 - 1295 - 113
1688ASNASNPROPROFF21 - 1295 - 113

NCS ensembles :
IDDetails
1Local NCS retraints between domains: 1 2
2Local NCS retraints between domains: 3 4
3Local NCS retraints between domains: 5 6
4Local NCS retraints between domains: 7 8
5Local NCS retraints between domains: 9 10
6Local NCS retraints between domains: 11 12
7Local NCS retraints between domains: 13 14
8Local NCS retraints between domains: 15 16

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Components

#1: Protein
Interferon regulatory factor 4 / IRF-4 / Lymphocyte-specific interferon regulatory factor / LSIRF / Multiple myeloma oncogene 1 / NF-EM5


Mass: 14243.163 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: His-tagged protein for purification. Tag removed via HRV 3C Protease.
Source: (gene. exp.) Homo sapiens (human) / Gene: IRF4, MUM1 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: Q15306
#2: DNA chain DNA (5'-D(P*TP*CP*AP*AP*CP*TP*GP*AP*AP*AP*CP*TP*GP*AP*GP*AP*AP*AP*GP*C)-3')


Mass: 6160.034 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: DNA chain DNA (5'-D(P*AP*GP*CP*TP*TP*TP*CP*TP*CP*AP*GP*TP*TP*TP*CP*AP*GP*TP*TP*G)-3')


Mass: 6105.949 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#4: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 107 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

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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: 2.77 Å3/Da / Density % sol: 55.54 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: 0.2M Calcium Acetate, 0.1M MES pH 6, 20% PEG 8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9762 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Jul 23, 2025
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 1.86→59.556 Å / Num. obs: 70231 / % possible obs: 95.52 % / Redundancy: 3.6 % / CC1/2: 0.9757 / Net I/σ(I): 11.14
Reflection shellResolution: 1.86→1.89 Å / Num. unique obs: 2415 / CC1/2: 0.363

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Processing

Software
NameVersionClassification
REFMAC5.8.0430 (refmacat 0.4.105)refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→59.556 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.94 / WRfactor Rfree: 0.241 / WRfactor Rwork: 0.196 / SU B: 8.774 / SU ML: 0.204 / Average fsc free: 0.9316 / Average fsc work: 0.9519 / Cross valid method: FREE R-VALUE / ESU R: 0.204 / ESU R Free: 0.185
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2578 1471 2.934 %
Rwork0.2107 48664 -
all0.212 --
obs-50135 98.192 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 55.671 Å2
Baniso -1Baniso -2Baniso -3
1-6.724 Å20.12 Å2-4.069 Å2
2---4.995 Å20.131 Å2
3----2.002 Å2
Refinement stepCycle: LAST / Resolution: 2.1→59.556 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3749 1640 5 107 5501
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0125690
X-RAY DIFFRACTIONr_bond_other_d0.0010.0164459
X-RAY DIFFRACTIONr_angle_refined_deg2.8771.8268023
X-RAY DIFFRACTIONr_angle_other_deg0.8451.76610393
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4695447
X-RAY DIFFRACTIONr_dihedral_angle_2_deg10.681532
X-RAY DIFFRACTIONr_dihedral_angle_other_2_deg0.815556
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.87710691
X-RAY DIFFRACTIONr_dihedral_angle_6_deg15.05210203
X-RAY DIFFRACTIONr_chiral_restr0.1260.2822
X-RAY DIFFRACTIONr_gen_planes_refined0.0180.025587
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021213
X-RAY DIFFRACTIONr_nbd_refined0.2240.21036
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2170.24173
X-RAY DIFFRACTIONr_nbtor_refined0.2170.22574
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0980.22698
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.190.2179
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0430.24
X-RAY DIFFRACTIONr_metal_ion_refined0.0840.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.220.234
X-RAY DIFFRACTIONr_nbd_other0.2440.256
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.340.28
X-RAY DIFFRACTIONr_mcbond_it8.0115.451800
X-RAY DIFFRACTIONr_mcbond_other7.995.4481799
X-RAY DIFFRACTIONr_mcangle_it9.8539.7612243
X-RAY DIFFRACTIONr_mcangle_other9.8519.7632244
X-RAY DIFFRACTIONr_scbond_it9.6345.583890
X-RAY DIFFRACTIONr_scbond_other9.6345.583890
X-RAY DIFFRACTIONr_scangle_it11.9629.9645780
X-RAY DIFFRACTIONr_scangle_other11.9619.9645781
X-RAY DIFFRACTIONr_lrange_it15.57562.5537001
X-RAY DIFFRACTIONr_lrange_other15.58662.4326988
X-RAY DIFFRACTIONr_ncsr_local_group_10.1230.053567
X-RAY DIFFRACTIONr_ncsr_local_group_20.0640.053667
X-RAY DIFFRACTIONr_ncsr_local_group_30.1140.053548
X-RAY DIFFRACTIONr_ncsr_local_group_40.1190.053553
X-RAY DIFFRACTIONr_ncsr_local_group_50.0950.053609
X-RAY DIFFRACTIONr_ncsr_local_group_60.050.051912
X-RAY DIFFRACTIONr_ncsr_local_group_70.0490.051756
X-RAY DIFFRACTIONr_ncsr_local_group_80.1110.053537
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AX-RAY DIFFRACTIONLocal ncs0.123270.05008
12BX-RAY DIFFRACTIONLocal ncs0.123270.05008
23AX-RAY DIFFRACTIONLocal ncs0.063970.05009
24DX-RAY DIFFRACTIONLocal ncs0.063970.05009
35AX-RAY DIFFRACTIONLocal ncs0.114060.05008
36FX-RAY DIFFRACTIONLocal ncs0.114060.05008
47BX-RAY DIFFRACTIONLocal ncs0.118940.05008
48DX-RAY DIFFRACTIONLocal ncs0.118940.05008
59BX-RAY DIFFRACTIONLocal ncs0.094710.05009
510FX-RAY DIFFRACTIONLocal ncs0.094710.05009
611CX-RAY DIFFRACTIONLocal ncs0.049950.0501
612GX-RAY DIFFRACTIONLocal ncs0.049950.0501
713EX-RAY DIFFRACTIONLocal ncs0.04890.05008
714HX-RAY DIFFRACTIONLocal ncs0.04890.05008
815DX-RAY DIFFRACTIONLocal ncs0.110550.05008
816FX-RAY DIFFRACTIONLocal ncs0.110550.05008
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
2.1-2.1540.3461030.33535270.33537340.8960.89897.21480.332
2.154-2.2130.338970.31434680.31536550.8930.9197.53760.306
2.213-2.2770.3851110.30834050.3136040.8770.91697.55830.291
2.277-2.3470.3681020.31232940.31334830.890.92197.50220.299
2.347-2.4240.33910.31132210.31233820.9090.92997.93020.283
2.424-2.5090.354920.28430940.28632560.9180.94397.85010.255
2.509-2.6040.348790.26730080.26931520.9230.95297.93780.243
2.604-2.710.307860.24528580.24729990.9220.96498.16610.22
2.71-2.830.296930.23427620.23629040.9440.96898.31270.208
2.83-2.9680.29780.21126520.21327730.9560.97398.44930.186
2.968-3.1280.304750.21325290.21626400.9470.97398.63640.193
3.128-3.3170.28690.20323860.20524900.9510.98298.59440.197
3.317-3.5450.256760.21122590.21223640.9630.97998.77330.202
3.545-3.8280.242600.19620790.19821590.970.98299.07360.191
3.828-4.1920.171610.15819500.15820260.9840.98999.25960.157
4.192-4.6840.194620.14717280.14918050.9770.98899.1690.15
4.684-5.4030.181490.14915490.1516070.9790.9999.43990.155
5.403-6.6040.226430.17413090.17613580.9830.98799.55820.184
6.604-9.2820.211280.17110200.17210590.9740.98798.96130.191
9.282-59.5560.302160.2375660.2395820.9770.9541000.271

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