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- PDB-3rn2: Structural Basis of Cytosolic DNA Recognition by Innate Immune Re... -

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Basic information

Entry
Database: PDB / ID: 3rn2
TitleStructural Basis of Cytosolic DNA Recognition by Innate Immune Receptors
Components
  • DNA (5'-D(*CP*CP*AP*TP*CP*AP*AP*AP*GP*AP*TP*CP*TP*TP*TP*GP*AP*TP*GP*G)-3')
  • Interferon-inducible protein AIM2
KeywordsImmune system/DNA / CYTOSOLIC DNA SENSOR / INFLAMMASOME / DNA BINDING / CYTOSOLIC / Immune system-DNA complex
Function / homology
Function and homology information


pyroptosome complex assembly / AIM2 inflammasome complex assembly / The AIM2 inflammasome / AIM2 inflammasome complex / regulation of behavior / cysteine-type endopeptidase activator activity / Cytosolic sensors of pathogen-associated DNA / pattern recognition receptor signaling pathway / negative regulation of NF-kappaB transcription factor activity / pattern recognition receptor activity ...pyroptosome complex assembly / AIM2 inflammasome complex assembly / The AIM2 inflammasome / AIM2 inflammasome complex / regulation of behavior / cysteine-type endopeptidase activator activity / Cytosolic sensors of pathogen-associated DNA / pattern recognition receptor signaling pathway / negative regulation of NF-kappaB transcription factor activity / pattern recognition receptor activity / pyroptotic inflammatory response / T cell homeostasis / cellular response to interferon-beta / positive regulation of defense response to virus by host / signaling adaptor activity / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / activation of innate immune response / positive regulation of interleukin-1 beta production / tumor necrosis factor-mediated signaling pathway / positive regulation of NF-kappaB transcription factor activity / brain development / neuron cellular homeostasis / cellular response to xenobiotic stimulus / positive regulation of inflammatory response / site of double-strand break / double-stranded DNA binding / defense response to virus / immune response / innate immune response / DNA damage response / mitochondrion / nucleoplasm / identical protein binding / cytoplasm / cytosol
Similarity search - Function
HIN-200/IF120x / HIN-200/IF120x domain / HIN-200 A and B domains profile. / HIN-200 family / DAPIN domain / DAPIN domain profile. / PAAD/DAPIN/Pyrin domain / PAAD/DAPIN/Pyrin domain / Death-like domain superfamily / Nucleic acid-binding proteins ...HIN-200/IF120x / HIN-200/IF120x domain / HIN-200 A and B domains profile. / HIN-200 family / DAPIN domain / DAPIN domain profile. / PAAD/DAPIN/Pyrin domain / PAAD/DAPIN/Pyrin domain / Death-like domain superfamily / Nucleic acid-binding proteins / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Nucleic acid-binding, OB-fold / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
DNA / DNA (> 10) / Interferon-inducible protein AIM2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.55 Å
AuthorsJin, T.C. / Xiao, T.
CitationJournal: Immunity / Year: 2012
Title: Structures of the HIN Domain:DNA Complexes Reveal Ligand Binding and Activation Mechanisms of the AIM2 Inflammasome and IFI16 Receptor.
Authors: Jin, T. / Perry, A. / Jiang, J. / Smith, P. / Curry, J.A. / Unterholzner, L. / Jiang, Z. / Horvath, G. / Rathinam, V.A. / Johnstone, R.W. / Hornung, V. / Latz, E. / Bowie, A.G. / Fitzgerald, K.A. / Xiao, T.S.
History
DepositionApr 21, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 25, 2012Provider: repository / Type: Initial release
Revision 1.1May 9, 2012Group: Database references
Revision 1.2Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Interferon-inducible protein AIM2
B: Interferon-inducible protein AIM2
K: DNA (5'-D(*CP*CP*AP*TP*CP*AP*AP*AP*GP*AP*TP*CP*TP*TP*TP*GP*AP*TP*GP*G)-3')
L: DNA (5'-D(*CP*CP*AP*TP*CP*AP*AP*AP*GP*AP*TP*CP*TP*TP*TP*GP*AP*TP*GP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,59910
Polymers59,2274
Non-polymers3726
Water81145
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5120 Å2
ΔGint-15 kcal/mol
Surface area28180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.560, 74.770, 65.520
Angle α, β, γ (deg.)90.00, 89.73, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Interferon-inducible protein AIM2 / Absent in melanoma 2


Mass: 23480.465 Da / Num. of mol.: 2 / Fragment: unp residues 144-343
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: AIM2 / Plasmid: pET30a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O14862
#2: DNA chain DNA (5'-D(*CP*CP*AP*TP*CP*AP*AP*AP*GP*AP*TP*CP*TP*TP*TP*GP*AP*TP*GP*G)-3')


Mass: 6132.991 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: DNA 20-mer
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 45 / 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: 2.42 Å3/Da / Density % sol: 49.21 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 8% PEG1000, 0.1 M KCl, 10 mM MgCl2, 0.1 M MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.0332 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 13, 2010
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.55→50 Å / Num. all: 18573 / Num. obs: 18538 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.16 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 25.49
Reflection shellResolution: 2.55→2.59 Å / Redundancy: 4.25 % / Rmerge(I) obs: 0.617 / Mean I/σ(I) obs: 3.11 / % possible all: 99.8

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Processing

Software
NameVersionClassification
Blu-Icedata collection
PHASERphasing
PHENIX(phenix.refine: dev_723)refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry code 3RLO

3rlo


Resolution: 2.55→43.765 Å / σ(F): 1.36 / Phase error: 35.14 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.2525 955 5.15 %
Rwork0.2084 --
obs0.2103 18538 99.83 %
all-18573 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 30.543 Å2 / ksol: 0.325 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--5.5273 Å2-0 Å21.5054 Å2
2---1.3701 Å20 Å2
3---6.8974 Å2
Refinement stepCycle: LAST / Resolution: 2.55→43.765 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3095 814 24 45 3978
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0054121
X-RAY DIFFRACTIONf_angle_d0.5445631
X-RAY DIFFRACTIONf_dihedral_angle_d17.6241611
X-RAY DIFFRACTIONf_chiral_restr0.032649
X-RAY DIFFRACTIONf_plane_restr0.002569
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5502-2.68450.35871410.33332492X-RAY DIFFRACTION95
2.6845-2.85260.37861220.32052498X-RAY DIFFRACTION95
2.8526-3.07260.37751430.29322490X-RAY DIFFRACTION94
3.0726-3.38130.26071310.23912489X-RAY DIFFRACTION95
3.3813-3.86960.25761260.21952532X-RAY DIFFRACTION95
3.8696-4.87130.21541330.15872521X-RAY DIFFRACTION95
4.8713-28.42770.20631540.16082552X-RAY DIFFRACTION94
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)
18.1605-0.3829-0.60844.0010.77545.0083-0.15840.1487-0.1186-0.03450.2671-0.0555-0.07760.2315-0.0110.2278-0.0345-0.11580.262-0.00550.1603-19.0573-6.038-30.2437
25.32532.0177-1.21644.98042.72826.34040.1570.04030.2547-0.0375-0.13170.50470.0077-0.64910.09470.1906-0.0915-0.16110.4337-0.04620.4518-27.3475-8.207-28.861
34.41160.07151.31284.51650.73561.75430.2055-0.17720.22830.4279-0.2605-0.2906-0.0328-0.0390.0880.2212-0.0739-0.0770.4711-0.10620.4528-5.4112-1.4806-15.2435
43.3956-0.25711.3362.4879-1.60121.43710.18920.628-0.0885-0.0612-0.4355-0.67990.1730.9180.1770.28030.0532-0.10880.555-0.05430.48211.68512.4348-20.6676
55.53261.7049-1.2634.4895-2.70663.0885-0.1050.2375-0.25730.4639-0.0417-0.46-0.06170.32470.19280.24630.0277-0.10850.3327-0.14490.3185-2.9532-3.9024-19.3695
65.81131.61331.25933.53050.85032.6661-0.18360.41140.1776-0.26310.26640.0423-0.22250.3144-0.06380.111-0.0449-0.03460.3149-0.01070.2147-11.108440.7633-17.2445
72.6547-1.56321.46965.9445-1.26392.79090.08030.8706-0.8399-0.2875-0.2133-0.44790.25410.49330.16050.14230.00220.06170.564-0.12680.5022-1.855734.9976-18.5826
85.87813.52832.61046.11731.41294.7773-0.21350.08660.9236-0.12510.0956-0.1087-0.42870.21940.09130.2084-0.0653-0.18830.33070.00290.5414-7.320846.7358-17.0622
95.63491.78740.29692.2096-0.36892.80530.1043-1.09410.3930.2633-0.1401-0.22320.12990.1930.03020.1766-0.0046-0.11930.4315-0.07910.3146-10.065935.1959-3.5238
102.5533-0.25510.84962.74521.18931.82030.1796-0.7110.71960.2251-0.03190.48950.0369-0.59610.07580.1505-0.07860.04050.64360.02050.3932-34.584832.8631-7.369
118.1698-1.80262.35885.06150.78794.10330.3261-0.3570.05330.0431-0.30720.40360.1608-0.5486-0.17150.11320.00480.02340.52260.06170.3991-33.426330.8479-9.7914
126.1784-0.8709-1.67761.3745-0.92091.55070.1082-0.42220.29880.22080.18350.2466-0.02720.0659-0.27680.2599-0.0194-0.01840.5551-0.0350.4083-24.622836.3518-8.2851
135.2229-0.2794-1.03495.1791-1.77121.80420.0633-0.48810.36780.10010.23670.68820.0373-0.06-0.2880.09930.0041-0.0860.5851-0.01130.4119-27.892936.4275-8.4899
141.0508-0.2469-0.24631.0920.09031.93110.257-0.0664-0.03720.00780.1229-0.09060.01010.0565-0.08980.59060.0185-0.02390.5912-0.06290.1122-14.524619.1873-40.8618
153.611-0.40630.22030.4646-0.99424.01080.2104-0.057-0.08180.08310.2333-0.0997-0.21520.1642-0.21770.6045-0.0133-0.09290.5596-0.03020.1468-11.360416.8212-16.7652
162.8855-0.22232.15970.0324-0.4296.11330.184-0.3967-0.37040.04130.11880.10260.7551-0.1673-0.23530.7958-0.0513-0.05820.57010.11520.2105-16.476115.05223.1709
172.9603-0.44520.31292.3191.6026.20970.09880.0779-0.07360.02350.2815-0.25080.16530.3431-0.17970.7539-0.0076-0.02430.7411-0.11830.1907-8.502215.94763.8658
181.5698-0.46270.7111.52560.07872.23890.0422-0.1809-0.06250.11860.08640.04850.1607-0.0445-0.01110.61250.00090.00850.60640.01920.0865-15.906219.6111-14.5682
191.89960.0502-0.0011.04870.09132.86220.16330.10280.0113-0.15420.1296-0.0115-0.1115-0.06330.10570.61470.0155-0.08240.5002-0.09140.1106-15.194316.9199-38.9394
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resseq 147:204)
2X-RAY DIFFRACTION2chain 'A' and (resseq 205:239)
3X-RAY DIFFRACTION3chain 'A' and (resseq 240:286)
4X-RAY DIFFRACTION4chain 'A' and (resseq 287:313)
5X-RAY DIFFRACTION5chain 'A' and (resseq 314:340)
6X-RAY DIFFRACTION6chain 'B' and (resseq 147:198)
7X-RAY DIFFRACTION7chain 'B' and (resseq 199:210)
8X-RAY DIFFRACTION8chain 'B' and (resseq 211:229)
9X-RAY DIFFRACTION9chain 'B' and (resseq 230:265)
10X-RAY DIFFRACTION10chain 'B' and (resseq 266:286)
11X-RAY DIFFRACTION11chain 'B' and (resseq 287:308)
12X-RAY DIFFRACTION12chain 'B' and (resseq 309:319)
13X-RAY DIFFRACTION13chain 'B' and (resseq 320:339)
14X-RAY DIFFRACTION14chain 'K' and (resseq 1:8)
15X-RAY DIFFRACTION15chain 'K' and (resseq 9:15)
16X-RAY DIFFRACTION16chain 'K' and (resseq 16:20)
17X-RAY DIFFRACTION17chain 'L' and (resseq 1:5)
18X-RAY DIFFRACTION18chain 'L' and (resseq 6:11)
19X-RAY DIFFRACTION19chain 'L' and (resseq 12:20)

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