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- PDB-6td4: IRF4 DNA-binding domain surface entropy mutant apo structure -

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Basic information

Entry
Database: PDB / ID: 6td4
TitleIRF4 DNA-binding domain surface entropy mutant apo structure
ComponentsInterferon regulatory factor 4
KeywordsDNA BINDING PROTEIN / DNA BINDING DOMAIN / SURFACE ENTROPY MUTANT / APO
Function / homology
Function and homology information


T-helper 17 cell lineage commitment / negative regulation of toll-like receptor signaling pathway / regulation of T-helper cell differentiation / myeloid dendritic cell differentiation / positive regulation of interleukin-13 production / immune system process / positive regulation of interleukin-4 production / defense response to protozoan / Regulation of MITF-M-dependent genes involved in pigmentation / positive regulation of interleukin-10 production ...T-helper 17 cell lineage commitment / negative regulation of toll-like receptor signaling pathway / regulation of T-helper cell differentiation / myeloid dendritic cell differentiation / positive regulation of interleukin-13 production / immune system process / positive regulation of interleukin-4 production / defense response to protozoan / Regulation of MITF-M-dependent genes involved in pigmentation / positive regulation of interleukin-10 production / Nuclear events stimulated by ALK signaling in cancer / positive regulation of interleukin-2 production / T cell activation / Interferon gamma signaling / sequence-specific double-stranded DNA binding / Interferon alpha/beta signaling / nucleosome / 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 / DNA-binding transcription factor activity / RNA polymerase II cis-regulatory region sequence-specific DNA binding / 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 / 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
Interferon regulatory factor 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.71 Å
AuthorsTucker, J.A. / Martin, M.P. / Wang, L.Z. / Jennings, C. / Heath, R.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Cancer Research UKC2115/A21421 United Kingdom
CitationJournal: To Be Published
Title: Cancer-associated mutations in the IRF4 DNA-binding domain confer no disadvantage in DNA-binding affinity and may increase transcriptional activity
Authors: Tatum, N.J. / Scott, R. / Doody, G.M. / Hickson, I. / Jennings, C. / Martin, M.P. / Tooze, R.M. / Tucker, J.A. / Wittner, A. / Wang, L.Z. / Wright, E.K. / Wedge, S.R. / Noble, M.E.M.
History
DepositionNov 7, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 18, 2020Provider: repository / Type: Initial release
Revision 1.1Feb 17, 2021Group: Database references / Source and taxonomy / Structure summary
Category: entity / entity_name_com ...entity / entity_name_com / entity_src_gen / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _entity.pdbx_description / _entity_src_gen.pdbx_gene_src_gene ..._entity.pdbx_description / _entity_src_gen.pdbx_gene_src_gene / _struct_ref.db_code / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_db_accession / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_ref_seq.pdbx_db_accession / _struct_ref_seq_dif.details / _struct_ref_seq_dif.pdbx_seq_db_accession_code / _struct_ref_seq_dif.pdbx_seq_db_seq_num
Revision 1.2Jun 23, 2021Group: Refinement description / Source and taxonomy / Category: entity_src_gen / pdbx_refine_tls_group
Item: _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _pdbx_refine_tls_group.selection_details
Revision 1.3May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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
A: Interferon regulatory factor 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,9742
Polymers13,9391
Non-polymers351
Water2,414134
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area80 Å2
ΔGint-4 kcal/mol
Surface area6860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.874, 67.457, 69.884
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11A-378-

HOH

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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: 13938.777 Da / Num. of mol.: 1 / Mutation: E45A E46A K47A C99A
Source method: isolated from a genetically manipulated source
Details: Additional residues at N- and C-termini from cloning
Source: (gene. exp.) Homo sapiens (human) / Gene: IRF4, MUM1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta (DE3) pLysS / References: UniProt: Q15306
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 134 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.83 Å3/Da / Density % sol: 56.49 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 25 % PEG 3350, 0.1 M HEPES pH 7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 14, 2016
RadiationMonochromator: single bounce monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 1.71→39.28 Å / Num. obs: 17568 / % possible obs: 100 % / Redundancy: 6.5 % / Biso Wilson estimate: 33.56 Å2 / CC1/2: 0.994 / Rrim(I) all: 0.041 / Net I/σ(I): 16.9
Reflection shellResolution: 1.71→1.78 Å / Redundancy: 5.7 % / Mean I/σ(I) obs: 1.7 / Num. unique obs: 2774 / CC1/2: 0.839 / Rrim(I) all: 1.12 / % possible all: 100

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Processing

Software
NameVersionClassification
BUSTERrefinement
REFMACrefinement
PHENIX1.17.1_3660refinement
xia2data reduction
AutoSolphasing
Cootmodel building
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: personal communication

Resolution: 1.71→39.28 Å / SU ML: 0.2108 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 37.9394
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2453 839 4.83 %
Rwork0.2168 16542 -
obs0.2182 17381 99.64 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 52.64 Å2
Refinement stepCycle: LAST / Resolution: 1.71→39.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms865 0 1 135 1001
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0042912
X-RAY DIFFRACTIONf_angle_d0.59141236
X-RAY DIFFRACTIONf_chiral_restr0.0447125
X-RAY DIFFRACTIONf_plane_restr0.0046161
X-RAY DIFFRACTIONf_dihedral_angle_d20.7829343
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.71-1.820.39721360.39722724X-RAY DIFFRACTION99.79
1.82-1.960.33921460.30692695X-RAY DIFFRACTION99.3
1.96-2.150.28761180.23762754X-RAY DIFFRACTION99.62
2.15-2.470.25171300.23462727X-RAY DIFFRACTION99.24
2.47-3.110.26851600.23872763X-RAY DIFFRACTION99.9
3.11-39.280.21671490.18712879X-RAY DIFFRACTION99.97
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)
18.46539917936-0.498174179114-0.283948697932.89770955363.597281995438.668539137650.2596655185360.8619144694720.281067499677-0.105397698721-0.440431849270.7798221315730.565577726385-1.081891417950.005754500830570.3344207219280.1362870742230.01526061707680.6182738007720.03284738078440.392222913969-14.7304637087-18.3047757903-5.17892743364
26.77105158822-1.2655498284-0.821377740514.801476772060.4058847113646.16604673070.3276667865971.438671104580.918680165875-0.337531276509-0.0133784246559-0.104956780285-0.344096356749-0.705661607502-0.07333967905050.282297442710.06522999365840.01350211865880.4874977256630.2127020193990.449557206248-5.04829891266-16.3853348467-10.2014406247
34.75957628438-4.374264623190.4325232130894.348010128390.9615795021969.12449293781-0.374377735615-1.29339860532.131080591651.57546344474-0.496311993791-0.493909869869-1.003301759451.148050750340.6209214438420.662246554686-0.0412557552516-0.0939756488130.996122954019-0.2432643954490.832520169132.11985282413-15.76896108524.22584616621
45.465664465370.696268135971-1.70480465845.040713249140.1489184107779.78011953153-0.133889079907-0.3937429013680.8595586484780.3769570315810.332725023404-0.186685917954-0.533092503225-0.0792748482895-0.1839628836590.3755131596250.0783351411824-0.002523918068010.428257116384-0.06101951576230.318259639552-11.7475780499-15.57112639944.93004009496
51.94614287692-1.3690877465-2.025822167012.347129928383.482878832585.73715159805-0.365172493434-2.403290204871.017908316350.130769091114-0.3217201308740.2955966592620.463306515132-0.4250314713760.4010381472850.5963366431210.0347595054111-0.03122491415821.05782427325-0.3128547429930.555591311652-14.2311136393-14.439065284914.5834794665
62.978379601440.047087609324-0.1455014101387.757755587274.440130080964.58361230037-0.089342829625-0.7191332229630.2788448320160.8038669972090.149002215442-0.008095086489810.7353820717920.250729794379-0.1444087161430.416666032040.0682529630940.005395186648580.471028529462-0.01090704412440.254352648778-6.86333293774-23.25414318236.17448781166
74.043587042-0.583367824977-3.969830301814.28203072836-0.1904717698084.14089744671-0.7566376360250.83987716055-1.381546835220.09321088000120.491885551436-0.215873759511.05957059310.3988776065390.2241922135330.4629219867840.0329908419865-0.03445034198220.575808425145-0.1327651084880.365040030704-3.78605120475-28.4742609561-9.74696501547
84.072070325093.257771727081.493452235296.871516949763.003347458564.15556337508-0.2544450824161.04407880212-0.0154805863579-0.1256108229670.1355694446-0.3534939802990.1162427900580.6643190624530.06451346152170.330512185722-0.0121036179948-0.01925330424490.4310854976060.07308454078020.3205771981362.79039470864-22.1299684906-6.82655856815
96.299671618174.595341031584.681375574984.155516013733.13842773284.12703486342-0.2589233969890.295205576005-1.345558320382.16184678511-0.2505306433361.48818939352.11736905727-3.136305402870.509182368390.740399980078-0.1252528263520.04667011446671.02017263708-0.1703558527330.77402304699-16.4341342643-30.8801508657-13.6861539533
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|21-34 }
2X-RAY DIFFRACTION2{ A|35-53 }
3X-RAY DIFFRACTION3{ A|54-68 }
4X-RAY DIFFRACTION4{ A|69-77 }
5X-RAY DIFFRACTION5{ A|78-89 }
6X-RAY DIFFRACTION6{ A|90-103 }
7X-RAY DIFFRACTION7{ A|104-113 }
8X-RAY DIFFRACTION8{ A|114-127 }
9X-RAY DIFFRACTION9{ A|128-133 }

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