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- PDB-8hcm: zebrafish IRF-11 DBD complex with DNA -

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Basic information

Entry
Database: PDB / ID: 8hcm
Titlezebrafish IRF-11 DBD complex with DNA
Components
  • DNA (5'-D(P*GP*CP*TP*TP*TP*CP*AP*CP*TP*TP*TP*CP*TP*A)-3')
  • DNA (5'-D(P*TP*AP*GP*AP*AP*AP*GP*TP*GP*AP*AP*AP*GP*C)-3')
  • Interferon regulatory factor
KeywordsDNA BINDING PROTEIN/DNA / zebrafish / IRF / DBD / DNA BINDING PROTEIN / DNA BINDING PROTEIN-DNA complex
Function / homology
Function and homology information


immune system process / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / regulation of transcription by RNA polymerase II / nucleus
Similarity search - Function
Interferon regulatory factor-1/2 / 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. / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
DNA / DNA (> 10) / Interferon regulatory factor
Similarity search - Component
Biological speciesDanio rerio (zebrafish)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.59 Å
AuthorsWang, Z.X. / Zhang, Y.A. / Ouyang, S.Y.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31725026; 82225028; 82172287 China
CitationJournal: J Immunol. / Year: 2024
Title: Crystal Structures of DNA-bound Fish IRF10 and IRF11 Reveal the Determinants of IFN Regulation.
Authors: Wang, Z.X. / Liu, B. / Xie, H. / Liu, X. / Li, X. / Shi, F. / Ouyang, S. / Zhang, Y.A.
History
DepositionNov 2, 2022Deposition site: PDBJ / Processing site: RCSB
Revision 1.0May 15, 2024Provider: repository / Type: Initial release
Revision 1.1Aug 7, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Sep 4, 2024Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Interferon regulatory factor
B: DNA (5'-D(P*TP*AP*GP*AP*AP*AP*GP*TP*GP*AP*AP*AP*GP*C)-3')
C: DNA (5'-D(P*GP*CP*TP*TP*TP*CP*AP*CP*TP*TP*TP*CP*TP*A)-3')


Theoretical massNumber of molelcules
Total (without water)21,3373
Polymers21,3373
Non-polymers00
Water1086
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3250 Å2
ΔGint-27 kcal/mol
Surface area9990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.118, 61.118, 220.054
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122
Space group name HallP612(x,y,z+5/12)
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/6
#3: y,-x+y,z+5/6
#4: -y,x-y,z+1/3
#5: -x+y,-x,z+2/3
#6: x-y,-y,-z
#7: -x,-x+y,-z+2/3
#8: -x,-y,z+1/2
#9: y,x,-z+1/3
#10: -y,-x,-z+5/6
#11: -x+y,y,-z+1/2
#12: x,x-y,-z+1/6

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Components

#1: Protein Interferon regulatory factor


Mass: 12778.608 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Danio rerio (zebrafish) / Gene: irf1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q1RLP9
#2: DNA chain DNA (5'-D(P*TP*AP*GP*AP*AP*AP*GP*TP*GP*AP*AP*AP*GP*C)-3')


Mass: 4361.880 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (5'-D(P*GP*CP*TP*TP*TP*CP*AP*CP*TP*TP*TP*CP*TP*A)-3')


Mass: 4196.739 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 6 / 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: 2.94 Å3/Da / Density % sol: 58.12 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, sitting drop / Details: 1.6 M sodium/potassium phosphate pH 6.5

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Data collection

DiffractionMean temperature: 298.15 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9791 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 26, 2020
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.59→30.27 Å / Num. obs: 12847 / % possible obs: 94.81 % / Redundancy: 1.6 % / Biso Wilson estimate: 42.74 Å2 / CC1/2: 0.996 / Net I/σ(I): 18.29
Reflection shellResolution: 2.59→2.69 Å / Num. unique obs: 614 / CC1/2: 0.926

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Processing

Software
NameVersionClassification
HKL-2000data reduction
HKL-2000data scaling
PHENIX1.19.2_4158phasing
PHENIX1.19.2_4158refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2IRF

2irf


Resolution: 2.59→30.27 Å / SU ML: 0.344 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 29.8553
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2742 1295 10.09 %
Rwork0.2312 11543 -
obs0.2356 12838 90.08 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 63.46 Å2
Refinement stepCycle: LAST / Resolution: 2.59→30.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms839 574 0 6 1419
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0111506
X-RAY DIFFRACTIONf_angle_d1.30022155
X-RAY DIFFRACTIONf_chiral_restr0.0773229
X-RAY DIFFRACTIONf_plane_restr0.0227178
X-RAY DIFFRACTIONf_dihedral_angle_d33.3591381
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.59-2.70.3955750.2914632X-RAY DIFFRACTION44
2.7-2.820.39581190.38461058X-RAY DIFFRACTION75
2.82-2.970.35191460.30611345X-RAY DIFFRACTION94
2.97-3.160.38461610.28511412X-RAY DIFFRACTION100
3.16-3.40.31281600.24081442X-RAY DIFFRACTION100
3.4-3.740.2391560.21271405X-RAY DIFFRACTION100
3.74-4.280.22541660.19491423X-RAY DIFFRACTION100
4.28-5.390.21741590.19941427X-RAY DIFFRACTION100
5.39-30.270.27591530.21511399X-RAY DIFFRACTION98
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)
18.362371007350.3497449921861.628830704964.22345525206-1.369726122875.878559342220.410444641858-0.148169157981-0.843140541812-1.039560932790.173488259930.3476806001641.300507406060.00979095306315-0.4556035437130.7803838711670.0491808224841-0.09117923612240.1938243162610.06511370362960.3721414840497.125284403925.368585107698.92947865654
29.37257648706-4.898762295887.298116339817.476882503080.6059519366429.660516190120.446276178842-0.175829819097-0.541361582898-0.3710596971960.3942789812970.8534321732280.983692689986-1.49727692842-0.80917627010.7364704447680.00889403334154-0.2501461415710.5587051178450.3612661136810.565224136045-3.174610855110.82940947835.92079975421
33.233698065762.226057847740.3888417661942.58135031478-2.65161330069.170980155860.1902136506150.741599387169-1.44825977328-1.4697914551-0.281427220197-0.351010290941.940487321970.3945619805-0.1949875127971.377265497220.158523146743-0.05830248261210.493231748636-0.01694818527520.6436360418695.449967049454.80911390589-4.31241571606
40.1420981146290.421591301425-0.1960969797271.34805587262-1.02428333351.495584484780.3969430141630.3154237897770.328248048373-0.5106510818970.2793150999380.816899554731-0.414296183164-0.947586848149-0.1965395585290.8329137048810.4403522553570.05438776386070.2498912042640.3305596411030.5020561206380.21162074438319.51007292647.73576063703
50.354561036244-0.0469537601315-0.279496707930.631010308485-0.5383092049850.8408605477210.268696933894-0.1624643401780.2767080078280.02961899187440.154901277522-0.0414914434687-0.4279938962960.05035832634340.07991137975630.7445295053030.3801733372670.320265597075-0.0119893734463-0.02369967274460.4630250828886.5179158178919.92085198316.1894779144
63.403025770970.109909137657-0.7429371747915.071296804450.8956873819250.3323224690910.2277264775570.3229909074910.477369973747-1.308052345040.22456356673-0.3604179422040.02607857152960.30194219694-0.3987605536911.008108443870.3546490576920.2062601813330.271519903589-0.06489225193210.36673982566314.072567788314.2801568966-1.33566150728
77.06661641682-1.664574853880.4369197975035.19778260982.039888673986.63257777093-0.04295010087080.263808196678-0.259162103831-0.665591410450.31290073005-0.0152332889965-0.01078931742550.0455392113002-0.2533570886660.8420886689250.2411699205490.1343607719540.5422230455740.06835378576480.3210281232089.3352225878913.6338199196-1.32992301264
81.34863530653-0.221661192713-0.1778120728924.36520838098-1.807225144252.894036349690.2372245918710.01469748992771.08789353032-0.0653772025369-0.142320619472-0.512388757722-1.323753125280.3724843293350.2678106054281.18964209901-0.02660155798120.3719042253750.272090846796-0.0515051779170.82829305807512.609376834531.8546995628.8365650227
92.05284803154-2.487833687342.634351789244.22826187688-3.204501727743.689394450040.3489657877890.206163098710.793116793689-0.300518441238-0.101369317788-0.521408084682-1.293503055730.2766907332270.1130814463861.232990880190.01662868867480.3793520680990.3994257141790.0595747780050.66690237640713.383863260628.38493454899.49525080314
100.761627007574-0.927993559038-0.2654103598751.130665918130.3233050816090.0924646031650.137410022917-0.05789730159050.00526992712194-0.2537591518250.1604656026370.280831220524-0.0762826187131-0.102647463744-0.2685192523422.089590441380.6601551727190.6226212031250.9880439939970.4193420872281.75413445218-6.0753760497841.38667238060.838345477187
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 1 through 14 )AA1 - 141 - 14
22chain 'A' and (resid 15 through 20 )AA15 - 2015 - 20
33chain 'A' and (resid 21 through 28 )AA21 - 2821 - 28
44chain 'A' and (resid 29 through 57 )AA29 - 5729 - 57
55chain 'A' and (resid 58 through 83 )AA58 - 8358 - 83
66chain 'A' and (resid 84 through 101 )AA84 - 10184 - 93
77chain 'A' and (resid 102 through 108 )AA102 - 10894 - 100
88chain 'B' and (resid 1 through 14 )BB1 - 14
99chain 'C' and (resid 1 through 13 )CC1 - 13
1010chain 'C' and (resid 14 through 14 )CD14

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