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- PDB-7jm4: IRF Transcription Factor -

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Basic information

Entry
Database: PDB / ID: 7jm4
TitleIRF Transcription Factor
Components
  • (Interferon-Stimulated Response Elements) x 2
  • Interferon regulatory factor 4Interferon regulatory factors
KeywordsTRANSCRIPTION / DNA-bound transcription factor
Function / homology
Function and homology information


negative regulation of toll-like receptor signaling pathway / T-helper 17 cell lineage commitment / regulation of T-helper cell differentiation / myeloid dendritic cell differentiation / positive regulation of interleukin-13 production / immune system process / defense response to protozoan / positive regulation of interleukin-10 production / positive regulation of interleukin-4 production / positive regulation of interleukin-2 production ...negative regulation of toll-like receptor signaling pathway / T-helper 17 cell lineage commitment / regulation of T-helper cell differentiation / myeloid dendritic cell differentiation / positive regulation of interleukin-13 production / immune system process / defense response to protozoan / positive regulation of interleukin-10 production / positive regulation of interleukin-4 production / positive regulation of interleukin-2 production / T cell activation / Interferon gamma signaling / Interferon alpha/beta signaling / nucleosome / sequence-specific double-stranded DNA binding / positive regulation of cold-induced thermogenesis / DNA-binding transcription activator activity, RNA polymerase II-specific / Interleukin-4 and Interleukin-13 signaling / sequence-specific DNA binding / transcription coactivator activity / DNA-binding transcription factor activity, RNA polymerase II-specific / chromatin remodeling / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / chromatin / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / 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 / IRF tryptophan pentad repeat DNA-binding domain profile. / Interferon regulatory factor DNA-binding domain / 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 / IRF tryptophan pentad repeat DNA-binding domain profile. / Interferon regulatory factor DNA-binding domain / 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: 2.95 Å
AuthorsSundararaj, S. / Williams, S.J. / Casarotto, M.G.
Funding support Australia, 1items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia)APP1126201 Australia
CitationJournal: Nucleic Acids Res. / Year: 2021
Title: Structural determinants of the IRF4/DNA homodimeric complex.
Authors: Sundararaj, S. / Seneviratne, S. / Williams, S.J. / Enders, A. / Casarotto, M.G.
History
DepositionJul 31, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 24, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
D: Interferon-Stimulated Response Elements
E: Interferon-Stimulated Response Elements
B: Interferon regulatory factor 4
A: Interferon regulatory factor 4
C: Interferon-Stimulated Response Elements
F: Interferon-Stimulated Response Elements
G: Interferon regulatory factor 4
H: Interferon regulatory factor 4


Theoretical massNumber of molelcules
Total (without water)75,7188
Polymers75,7188
Non-polymers00
Water0
1
D: Interferon-Stimulated Response Elements
E: Interferon-Stimulated Response Elements
B: Interferon regulatory factor 4
A: Interferon regulatory factor 4


Theoretical massNumber of molelcules
Total (without water)37,8594
Polymers37,8594
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5860 Å2
ΔGint-43 kcal/mol
Surface area16870 Å2
MethodPISA
2
C: Interferon-Stimulated Response Elements
F: Interferon-Stimulated Response Elements
G: Interferon regulatory factor 4
H: Interferon regulatory factor 4


Theoretical massNumber of molelcules
Total (without water)37,8594
Polymers37,8594
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5820 Å2
ΔGint-43 kcal/mol
Surface area16860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)117.802, 117.802, 154.579
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: DNA chain Interferon-Stimulated Response Elements


Mass: 5840.830 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#2: DNA chain Interferon-Stimulated Response Elements


Mass: 5808.741 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: Protein
Interferon regulatory factor 4 / Interferon regulatory factors / IRF-4 / Lymphocyte-specific interferon regulatory factor / LSIRF / Multiple myeloma oncogene 1 / NF-EM5


Mass: 13104.822 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IRF4, MUM1 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: Q15306

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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: 4.09 Å3/Da / Density % sol: 69.92 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: 10 % PEG 4000, 0.1 M Na acetate pH 4.6

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Apr 17, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.95→48.44 Å / Num. obs: 26659 / % possible obs: 99 % / Redundancy: 11.1 % / Biso Wilson estimate: 76.67 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.1054 / Rrim(I) all: 0.1106 / Net I/σ(I): 19.23
Reflection shellResolution: 2.95→3.055 Å / Rmerge(I) obs: 1.251 / Num. unique obs: 2492 / CC1/2: 0.692 / CC star: 0.904 / Rpim(I) all: 1.318 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2IRF

2irf


Resolution: 2.95→48.44 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.08 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2055 1320 4.98 %
Rwork0.1848 --
obs0.1859 26532 99.52 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.95→48.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3649 1555 0 0 5204
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0035493
X-RAY DIFFRACTIONf_angle_d0.6217742
X-RAY DIFFRACTIONf_dihedral_angle_d19.6853007
X-RAY DIFFRACTIONf_chiral_restr0.041801
X-RAY DIFFRACTIONf_plane_restr0.003731
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.95-3.06810.32941410.33172635X-RAY DIFFRACTION96
3.0681-3.20770.28161450.27142784X-RAY DIFFRACTION100
3.2077-3.37680.311460.24642801X-RAY DIFFRACTION100
3.3768-3.58830.25691450.23232770X-RAY DIFFRACTION100
3.5883-3.86520.23231460.20882796X-RAY DIFFRACTION100
3.8652-4.2540.16341450.16812789X-RAY DIFFRACTION100
4.254-4.86910.20371450.16092843X-RAY DIFFRACTION100
4.8691-6.13260.17671510.15452840X-RAY DIFFRACTION100
6.1326-48.440.16371560.14732954X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
14.3004-3.6224.77543.7338-3.01359.5205-0.44121.2119-1.1593-1.26321.04930.080.04890.4798-0.53370.5965-0.10230.03070.6034-0.06290.541125.1627-28.1457-38.1472
25.29452.20231.34622.0643-0.66325.0259-0.6716-0.04020.3116-0.13850.2301-0.48610.10580.70230.38750.56490.1185-0.02480.66260.07180.796454.6459-26.7844-38.9787
37.85145.55877.87989.67017.20528.3633-1.72571.40152.1222-0.89221.7361-0.7707-0.31050.9308-0.04080.54420.0681-0.00351.10690.28341.151768.8468-26.5556-47.8292
43.0042-1.9797-1.61552.26420.49111.6803-0.4611-0.549-0.28140.07710.01380.04540.40360.11110.42620.54980.04050.03760.55750.07090.524740.0366-28.5786-35.5864
59.6027-6.7759-3.94127.63174.21363.67730.0859-0.1510.48790.2434-0.0141-0.7371-0.1838-0.4398-0.13030.7266-0.0663-0.08020.52530.06470.515241.1545-7.1114-30.589
65.9003-0.12411.43096.18150.68445.21610.1023-0.4186-0.46820.83280.0627-0.3671-0.3493-0.4683-0.17520.79790.0789-0.06150.51280.02080.552334.0672-7.0055-23.0441
76.9863-3.68340.79483.39310.41162.5515-0.8534-1.44490.41010.00170.32390.55380.3734-1.05670.24660.7699-0.00310.07230.7428-0.04930.586120.3421-17.1315-32.5385
82.1259-2.157-2.20196.8287-1.73896.80790.0170.2146-0.17990.0361-0.19120.0239-1.1273-0.7150.1060.6489-0.0075-0.02810.5604-0.09980.387132.1119-11.2835-38.4576
93.7791-0.9121-2.73434.45970.13312.3835-0.0992-0.1341-0.37630.10750.0131-0.20240.2431-0.24350.09420.6085-0.022-0.04240.45580.05210.48736.0649-17.9811-37.8157
106.2572-2.92015.66073.2866-1.97975.7293-0.8313-2.8072-1.78050.31070.8580.6399-0.1701-1.6833-0.08530.991-0.09910.12930.85140.13060.708726.4529-18.5185-19.7611
119.49113.0308-1.098.29610.26487.8417-0.6933-1.2976-0.54611.35860.3724-0.4116-0.33481.10280.27590.86070.1419-0.0480.78670.09370.45937.4251-15.1564-21.1885
122.9073-1.69170.28164.7926-1.62364.72070.0057-0.4223-0.51390.8374-0.32670.07590.1561-0.12420.23490.783-0.13970.00470.58120.07760.6825-6.8264-50.3952-26.2778
134.33921.34061.54087.49763.77518.61180.21410.3832-0.52340.52570.1984-1.43760.72561.2116-0.47520.7455-0.0027-0.11490.91020.02630.868610.9036-46.7485-33.6309
145.6724-1.13070.33434.10781.22214.3199-0.0161-0.4491-0.29940.0711-0.21650.34360.4461-0.5486-0.05470.679-0.02550.0880.55170.06220.5833-3.1873-46.9928-38.5601
152.5891-1.9595-3.24.81552.59955.01990.06420.12870.1053-0.1941-0.3094-0.1107-0.2318-0.30370.03610.4979-0.02130.01840.4975-0.0010.4474-1.4845-41.0734-41.1275
169.0457-3.27091.7476.2923-0.10362.467-0.3295-2.1744-0.00291.0910.38311.0282-0.3276-0.6890.04291.18730.05310.32750.82280.05950.8209-9.3738-38.4699-23.9636
179.1832-2.6523-2.04255.2724-0.26976.4579-0.62-1.57340.64361.06290.5852-1.09380.31490.26410.27621.014-0.1462-0.22720.9484-0.03380.70096.235-41.9224-19.5188
186.8051-2.0719-0.14715.8058-0.256.6519-0.5425-0.6756-0.29481.34250.16660.234-0.2127-1.00460.22230.9124-0.11370.00750.9970.12760.5612-5.1673-42.8098-21.1333
194.7241-2.17572.79331.5945-0.25034.3553-0.3921-0.1126-0.28790.34780.10130.1142-0.3968-0.1870.24130.6813-0.06840.07660.6603-0.04020.5956-5.3464-30.5785-38.2118
203.61173.325-2.0888.30924.76289.7369-0.07980.88510.83680.09080.11621.4471-1.3299-1.7874-0.02180.89090.25940.15381.33730.16241.1377-34.2089-24.3126-39.9791
215.51620.8921-5.38959.4194-3.84816.2231-1.20710.6568-1.6883-0.26421.18891.32970.1343-0.9890.03320.73570.06990.18951.26220.04971.0763-32.5596-24.9906-48.0232
222.6677-1.5424-0.55943.107-1.58282.0235-0.2247-0.8971-0.35610.45810.04060.0273-0.6816-0.23270.15150.71350.07740.00220.8496-0.07580.4982-10.4359-29.8587-37.4436
233.34163.55410.15264.8948-3.02479.1147-1.16050.39940.95410.529-0.2906-0.9572-0.27490.8211.48060.7207-0.0506-0.0530.85230.05960.781812.5761-27.8759-31.8495
243.60971.18310.21753.0287-0.25436.29730.27440.5454-0.065-0.5957-0.2701-0.740.54961.12020.03580.8080.22790.2020.87590.05420.90158.9501-40.9209-59.0999
252.3992-2.2916-0.13953.4796-1.04373.72-0.15270.0933-0.56530.0132-0.2014-0.11950.63040.07860.39460.74430.05940.13730.63380.02260.787250.54-40.6375-47.1066
263.19690.98430.45123.9167-3.87694.52540.82770.508-0.35730.119-0.5470.17450.0613-0.0093-0.17110.86440.1121-0.0210.84480.17440.773160.4286-43.7135-34.9671
272.4246-1.18312.42054.47010.20792.9668-0.2053-0.00380.2890.16360.0557-0.449-0.26930.4007-0.00630.58970.10480.10270.66050.18340.766556.5299-31.6965-48.3909
284.5021.5848-4.09561.4143-3.10726.89220.26770.0668-0.0996-0.38250.0145-0.01050.04410.2752-0.1960.53080.12260.03830.651-0.05310.605147.9004-32.2691-58.8627
298.2234-0.1508-2.18735.4457-0.87234.7997-0.05870.21440.49940.06290.18820.6039-0.4479-0.359-0.19640.8170.1474-0.04780.56920.01590.6512-18.4083-13.8033-59.2009
302.9808-0.26810.17132.3940.6553.63030.079-0.25810.16960.435-0.03520.0063-0.6335-0.34150.02370.95650.12250.04330.6103-0.00920.6253-16.0003-16.4657-44.2531
317.77430.02523.05634.34941.43327.34730.13360.7034-1.0566-0.22220.0287-0.0774-0.17860.281-0.14320.57030.1050.02550.4968-0.06240.4563-9.9721-23.78-58.4162
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'D' and (resid 1 through 5 )
2X-RAY DIFFRACTION2chain 'D' and (resid 6 through 19 )
3X-RAY DIFFRACTION3chain 'E' and (resid 1 through 5 )
4X-RAY DIFFRACTION4chain 'E' and (resid 6 through 19 )
5X-RAY DIFFRACTION5chain 'B' and (resid 23 through 34 )
6X-RAY DIFFRACTION6chain 'B' and (resid 35 through 53 )
7X-RAY DIFFRACTION7chain 'B' and (resid 54 through 63 )
8X-RAY DIFFRACTION8chain 'B' and (resid 64 through 78 )
9X-RAY DIFFRACTION9chain 'B' and (resid 79 through 109 )
10X-RAY DIFFRACTION10chain 'B' and (resid 110 through 121 )
11X-RAY DIFFRACTION11chain 'B' and (resid 122 through 129 )
12X-RAY DIFFRACTION12chain 'G' and (resid 21 through 53 )
13X-RAY DIFFRACTION13chain 'G' and (resid 54 through 67 )
14X-RAY DIFFRACTION14chain 'G' and (resid 68 through 77 )
15X-RAY DIFFRACTION15chain 'G' and (resid 78 through 103 )
16X-RAY DIFFRACTION16chain 'G' and (resid 104 through 109 )
17X-RAY DIFFRACTION17chain 'G' and (resid 110 through 121 )
18X-RAY DIFFRACTION18chain 'G' and (resid 122 through 129 )
19X-RAY DIFFRACTION19chain 'C' and (resid 1 through 15 )
20X-RAY DIFFRACTION20chain 'C' and (resid 16 through 19 )
21X-RAY DIFFRACTION21chain 'F' and (resid 1 through 5 )
22X-RAY DIFFRACTION22chain 'F' and (resid 6 through 15 )
23X-RAY DIFFRACTION23chain 'F' and (resid 16 through 19 )
24X-RAY DIFFRACTION24chain 'A' and (resid 21 through 48 )
25X-RAY DIFFRACTION25chain 'A' and (resid 49 through 78 )
26X-RAY DIFFRACTION26chain 'A' and (resid 79 through 89 )
27X-RAY DIFFRACTION27chain 'A' and (resid 90 through 109 )
28X-RAY DIFFRACTION28chain 'A' and (resid 110 through 129 )
29X-RAY DIFFRACTION29chain 'H' and (resid 21 through 53 )
30X-RAY DIFFRACTION30chain 'H' and (resid 54 through 109 )
31X-RAY DIFFRACTION31chain 'H' and (resid 110 through 128 )

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