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- PDB-7oot: X-ray Structure of Interferon Regulatory Factor 4 DNA binding dom... -

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Basic information

Entry
Database: PDB / ID: 7oot
TitleX-ray Structure of Interferon Regulatory Factor 4 DNA binding domain bound to an interferon-stimulated response element
Components
  • DNA (5'-D(P*AP*GP*CP*TP*TP*TP*CP*TP*CP*GP*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*CP*GP*AP*GP*AP*AP*AP*GP*C)-3')
  • Interferon regulatory factor 4
KeywordsDNA BINDING PROTEIN / INTERFERON REGULATORY FACTORS / TRANSCRIPTION REGULATION / PROTEIN-DNA INTERACTION / TRANSCRIPTION
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 / 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 / immune system process / 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 / 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 / immune system process / 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 / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / regulation of transcription by RNA polymerase II / chromatin / positive regulation of DNA-templated transcription / positive regulation of transcription by RNA polymerase II / nucleoplasm / nucleus / membrane / 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
PHOSPHATE ION / DNA / DNA (> 10) / Interferon regulatory factor 4
Similarity search - Component
Biological speciesHomo sapiens (human)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsAgnarelli, A. / El Omari, K. / Alt, A.O. / Mancini, E.J.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Wellcome Trust204833/Z/16/Z United Kingdom
CitationJournal: To Be Published
Title: X-ray Structure of Interferon Regulatory Factor 4 DNA binding domain bound to interferon-stimulated response element
Authors: Agnarelli, A. / El Omari, K. / Alt, A.O. / Mancini, E.J.
History
DepositionMay 28, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 8, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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*CP*GP*AP*GP*AP*AP*AP*GP*C)-3')
E: DNA (5'-D(P*AP*GP*CP*TP*TP*TP*CP*TP*CP*GP*GP*TP*TP*TP*CP*AP*GP*TP*TP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,9755
Polymers44,8804
Non-polymers951
Water1,36976
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5660 Å2
ΔGint-51 kcal/mol
Surface area17750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.780, 83.250, 88.530
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 22 through 81 or resid 83...
d_2ens_1(chain "B" and (resid 22 through 81 or resid 83...

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1GLYPHEA1 - 60
d_12ens_1GLUASNA62 - 81
d_13ens_1SERTYRA83 - 104
d_14ens_1ILEALAA106 - 111
d_21ens_1GLYPHEB1 - 60
d_22ens_1GLUASNB62 - 81
d_23ens_1SERTYRB83 - 104
d_24ens_1ILEALAB106 - 111

NCS oper: (Code: givenMatrix: (0.991518549871, -0.0979031747484, 0.0854747543818), (-0.127240676114, -0.865214756999, 0.484987870583), (0.0264721665974, -0.491750335684, -0.870333747335)Vector: 16. ...NCS oper: (Code: given
Matrix: (0.991518549871, -0.0979031747484, 0.0854747543818), (-0.127240676114, -0.865214756999, 0.484987870583), (0.0264721665974, -0.491750335684, -0.870333747335)
Vector: 16.8957038683, -22.2757885736, 17.8098790205)

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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: 16306.470 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IRF4, MUM1 / Plasmid: pCDFDUET / 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*CP*GP*AP*GP*AP*AP*AP*GP*C)-3')


Mass: 6145.022 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Mus musculus (house mouse)
#3: DNA chain DNA (5'-D(P*AP*GP*CP*TP*TP*TP*CP*TP*CP*GP*GP*TP*TP*TP*CP*AP*GP*TP*TP*G)-3')


Mass: 6121.948 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Mus musculus (house mouse)
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 76 / 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: 2.29 Å3/Da / Density % sol: 46.24 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.1M Tris HCl pH 8.5, 30% PEG 4000, 0.2M lithium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9688 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Aug 1, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9688 Å / Relative weight: 1
ReflectionResolution: 2.25→44.3 Å / Num. obs: 23181 / % possible obs: 99.3 % / Redundancy: 6 % / Biso Wilson estimate: 45.62 Å2 / Rmerge(I) obs: 0.112 / Net I/σ(I): 11.1
Reflection shellResolution: 2.25→2.29 Å / Rmerge(I) obs: 1.136 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 1086

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Processing

Software
NameVersionClassification
xia2data reduction
xia2data scaling
PHASERphasing
PHENIX1.18.2_3874refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7O56

7o56


Resolution: 2.25→44.27 Å / SU ML: 0.3297 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.039
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2383 1116 4.82 %
Rwork0.202 22017 -
obs0.2038 23133 99.14 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 54.73 Å2
Refinement stepCycle: LAST / Resolution: 2.25→44.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1854 820 5 76 2755
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00862828
X-RAY DIFFRACTIONf_angle_d1.04173990
X-RAY DIFFRACTIONf_chiral_restr0.0522412
X-RAY DIFFRACTIONf_plane_restr0.0075374
X-RAY DIFFRACTIONf_dihedral_angle_d29.02431124
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 0.549032188968 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.25-2.350.31411340.30882611X-RAY DIFFRACTION96.76
2.35-2.480.33841170.28992745X-RAY DIFFRACTION99.55
2.48-2.630.30421220.27612749X-RAY DIFFRACTION99.93
2.63-2.830.32271380.27022752X-RAY DIFFRACTION99.83
2.83-3.120.30061500.25542736X-RAY DIFFRACTION99.55
3.12-3.570.24311400.20792715X-RAY DIFFRACTION97.74
3.57-4.50.20831690.15932771X-RAY DIFFRACTION99.83
4.5-44.270.18651460.15622938X-RAY DIFFRACTION99.84
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)
10.434234759528-0.804122008456-0.2741559754071.56761953790.730946899220.861940077465-0.3515694188550.9863672004240.4696407897240.123259502266-0.2341914280251.00330012067-0.36314408218-0.7923653355120.5117779733490.3716091595430.0900763662848-0.08261591408570.9086192378350.06184413974951.26565118412-22.0930652952-6.7324026062316.7249932144
20.7977345620591.36847340605-0.1925036873622.53482739737-0.3492903880611.651040093450.336536319283-0.111934664841-0.3286117400330.114461489478-0.174107652642-0.6559002865470.08436389531140.0553411678135-0.00346232812350.389171493723-0.0994773357588-0.04483711776140.4836991450180.03679053836070.58568634281410.685525116-9.61447881110.7394644237
38.95557478288-3.697588093124.157885214952.75539008026-1.897026564062.526470039490.0486183677634-1.13178671218-0.4923632985520.3519518294820.3067937237861.148604402630.517161688362-1.08498224231-0.0660998728430.455513202956-0.1769800568710.04457930683730.5661228943510.02011763952670.458375434932-12.4207051426-18.887484540329.5595554087
44.528395830410.233520642868-0.3482402780594.878750214792.833353164839.232628893130.185024788714-1.24190930780.2658859446051.10055951715-0.1061427653410.7036717546690.0957900037698-0.1888581795980.1251417852340.558855454645-0.1459587638370.009605961690830.627008946752-0.005685541934480.415530329351-4.04060053668-16.750455884435.7647173076
59.58023812517-2.19760324802-3.818087901847.428586743653.92071773516.01401993536-0.108175848652-0.940745540278-1.225269809610.557908769351-0.388096551868-1.102038793330.9732575984270.751645772083-0.09703794342230.5831050670670.03132962592690.0002466901778840.5257889779560.1425096650720.6446938689437.47013419901-21.891872858421.7962251838
62.95772728187-0.280445231514-0.5800288288232.94225972497-0.08669620740652.31657594274-0.3094280282410.171073995179-0.140068379007-0.6489080353250.08368715675170.1270357260290.224231338354-0.166578305357-0.03393093201680.457978587318-0.1316363959080.0003066725150240.4673607776160.0207605807410.375706030105-5.87855537323-20.503117066516.3862899331
78.58931714153-0.2893544367822.006108031053.625196727950.8691535686164.386213222950.0225365056337-0.8053005385480.8633655711550.322659926983-0.06174448332810.0565985209645-0.0749868647505-0.3121696447430.04818669654990.481239384103-0.0780986135456-0.04736751565540.434883351604-0.03452541713580.470177867053-0.180237452337-8.8479226849930.2364196429
80.8507633675590.498382833985-0.02765453684121.321621316170.3006766086510.7937236386050.260739299766-0.411569455437-0.532347068856-0.03804404327611.301784334761.07893919165-0.1396019406640.250272526315-0.8261621948080.6000707574890.2216012980150.1525948431271.17061886123-0.1966330644261.11180558414-17.1706563701-5.2731310255733.5487583298
99.078021331953.722131754140.4538267542371.91259578427-0.2053510605340.4164563373820.2481244659710.2764350966881.575700228290.03013986238160.1694945497431.08239574179-1.08466931064-0.305111878795-0.02029139034680.4803534661660.03821064683150.09116070786680.433587688810.04986280136560.4978974639018.9661328731910.04009939371.05438708306
106.36100702074-0.330102882633-0.6874161495843.55786590644-0.7028844425724.558272414680.2406561169550.5390032435660.587570869513-0.386887136519-0.191032134761-0.311530667656-0.745654887311-0.5331749104530.4124614968450.4626820987670.0009404070674650.1140074596550.4809779418560.03139853675090.49351794627116.899699046511.6647717044-5.68344071807
117.65145764268-1.396979987876.406269637733.02444855512-0.5380117589788.78378953188-0.1703815547950.133482780120.7913466883750.191523609774-0.302197399063-0.773640492771-0.4645468482190.292064653697-0.09069255642470.43677047688-0.07027017380410.05990079167560.5032763065330.07341828165460.5462709082926.48362845444.696938308914.68056254985
127.97872838313-0.4647276784061.144003603264.250554292591.876094179363.5557184252-0.240352573772-0.4356006596360.8254137862050.7064233402620.0717458929225-0.15758149574-0.513463446160.521434902084-0.1880268338970.549659071849-0.0468842334330.04475483075470.498071836256-0.001538271819170.45800334021917.77820117289.1807535732710.9899393516
131.62270970381-0.4180198864721.164842490822.88715884106-1.170133854322.48218278462-0.286739930328-0.7356173835830.08675023747310.728137821969-0.00915229314250.0547269006957-0.783053883404-0.4908951900470.1153108700730.5866345345150.02493648100310.02200167528790.504211693184-0.02744296946170.4336569989514.65253562842.8733319145314.3516790406
147.03819730075-0.242268929413-1.650340548883.21528871464-1.202916083743.697835014550.2467604161870.78283465536-0.221945974754-0.236148271223-0.465776081558-0.2899050922830.4452688433050.111621751568-0.1167758099490.56046822710.0713921676730.1198153099420.45501504068-0.02432575119560.46409291128320.0651264458-0.0328836019303-4.12910248016
152.42231774047-1.464993114241.78854110461.13831084587-1.627707693412.73435895999-0.3445749232230.05200746021830.349975620087-0.5724154002450.7090986204131.42002139855-0.573775732511-0.291710110894-0.4223821450570.513936692714-0.119799636049-0.1747772930411.26057342158-0.05269759692230.7926935342043.197912606120.655961409299-9.00872001627
160.8482542520881.00932268206-1.293774882142.63479989963-0.2315584968493.14353865046-0.1119398397340.146239174648-0.308002403230.0284946814385-0.0251918382332-0.6390705965810.07462816651990.332549548022-0.05965011275350.291163841705-0.0428577890035-0.04933385016850.402261366130.03551871236630.57815114565914.0087613134-8.3457910678413.0174633654
170.02395273694250.147759339867-0.2745364197863.10912954645-0.9981648421623.48010073365-0.0833076271195-0.239012691456-0.06113465901-0.178862316967-0.03726740441981.09409845621-0.234479648058-0.9034043292170.2097282978820.410534933463-0.132124160292-0.223634890880.8462993993930.239483901940.873663930828-17.3701717031-9.399144711039.32547385089
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'E' and (resid 1 through 5 )EE1 - 5
22chain 'E' and (resid 6 through 20 )EE6 - 20
33chain 'A' and (resid 22 through 34 )AA22 - 341 - 13
44chain 'A' and (resid 35 through 53 )AA35 - 5314 - 32
55chain 'A' and (resid 54 through 68 )AA54 - 6833 - 47
66chain 'A' and (resid 69 through 103 )AA69 - 10348 - 82
77chain 'A' and (resid 104 through 127 )AA104 - 12783 - 106
88chain 'A' and (resid 128 through 132 )AA128 - 132107 - 111
99chain 'B' and (resid 22 through 34 )BB22 - 341 - 13
1010chain 'B' and (resid 35 through 48 )BB35 - 4814 - 27
1111chain 'B' and (resid 49 through 63 )BB49 - 6328 - 42
1212chain 'B' and (resid 64 through 77 )BB64 - 7743 - 56
1313chain 'B' and (resid 78 through 103 )BB78 - 10357 - 82
1414chain 'B' and (resid 104 through 127 )BB104 - 12783 - 106
1515chain 'B' and (resid 128 through 132 )BB128 - 132107 - 111
1616chain 'C' and (resid 1 through 15 )CD1 - 15
1717chain 'C' and (resid 16 through 20 )CD16 - 20

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