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- PDB-3rn5: Structural basis of cytosolic DNA recognition by innate immune re... -

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Basic information

Entry
Database: PDB / ID: 3rn5
TitleStructural basis of cytosolic DNA recognition by innate immune receptors
Components
  • DNA (5'-D(*CP*CP*AP*TP*CP*AP*AP*AP*GP*AP*GP*AP*GP*AP*AP*AP*GP*AP*G)-3')
  • DNA (5'-D(*GP*CP*TP*CP*TP*TP*TP*CP*TP*CP*TP*CP*TP*TP*TP*GP*AP*TP*G)-3')
  • Interferon-inducible protein AIM2
KeywordsImmune system/DNA / OB FOLD / 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 / positive regulation of cysteine-type endopeptidase activity / pattern recognition receptor activity / pattern recognition receptor signaling pathway ...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 / positive regulation of cysteine-type endopeptidase activity / pattern recognition receptor activity / pattern recognition receptor signaling pathway / negative regulation of NF-kappaB transcription factor activity / pyroptosis / T cell homeostasis / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / cellular response to interferon-beta / signaling adaptor activity / positive regulation of defense response to virus by host / tumor necrosis factor-mediated signaling pathway / activation of innate immune response / positive regulation of interleukin-1 beta production / brain development / positive regulation of inflammatory response / neuron cellular homeostasis / cellular response to xenobiotic stimulus / site of double-strand break / positive regulation of NF-kappaB transcription factor activity / double-stranded DNA binding / defense response to virus / immune response / inflammatory response / innate immune response / DNA damage response / mitochondrion / nucleoplasm / identical protein binding / cytosol / cytoplasm
Similarity search - Function
HIN-200/IF120x / HIN-200 family / HIN-200/IF120x domain / HIN-200 A and B domains profile. / 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 family / HIN-200/IF120x domain / HIN-200 A and B domains profile. / 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: 2.5 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
C: Interferon-inducible protein AIM2
D: Interferon-inducible protein AIM2
K: DNA (5'-D(*CP*CP*AP*TP*CP*AP*AP*AP*GP*AP*GP*AP*GP*AP*AP*AP*GP*AP*G)-3')
L: DNA (5'-D(*GP*CP*TP*CP*TP*TP*TP*CP*TP*CP*TP*CP*TP*TP*TP*GP*AP*TP*G)-3')
M: DNA (5'-D(*CP*CP*AP*TP*CP*AP*AP*AP*GP*AP*GP*AP*GP*AP*AP*AP*GP*AP*G)-3')
N: DNA (5'-D(*GP*CP*TP*CP*TP*TP*TP*CP*TP*CP*TP*CP*TP*TP*TP*GP*AP*TP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)117,77817
Polymers117,2198
Non-polymers5599
Water2,936163
1
A: Interferon-inducible protein AIM2
B: Interferon-inducible protein AIM2
K: DNA (5'-D(*CP*CP*AP*TP*CP*AP*AP*AP*GP*AP*GP*AP*GP*AP*AP*AP*GP*AP*G)-3')
L: DNA (5'-D(*GP*CP*TP*CP*TP*TP*TP*CP*TP*CP*TP*CP*TP*TP*TP*GP*AP*TP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,8588
Polymers58,6104
Non-polymers2484
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4360 Å2
ΔGint-23 kcal/mol
Surface area27850 Å2
MethodPISA
2
C: Interferon-inducible protein AIM2
D: Interferon-inducible protein AIM2
M: DNA (5'-D(*CP*CP*AP*TP*CP*AP*AP*AP*GP*AP*GP*AP*GP*AP*AP*AP*GP*AP*G)-3')
N: DNA (5'-D(*GP*CP*TP*CP*TP*TP*TP*CP*TP*CP*TP*CP*TP*TP*TP*GP*AP*TP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,9209
Polymers58,6104
Non-polymers3105
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4490 Å2
ΔGint-4 kcal/mol
Surface area28500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.360, 136.360, 77.040
Angle α, β, γ (deg.)90.00, 89.98, 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.: 4 / 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*GP*AP*GP*AP*AP*AP*GP*AP*G)-3')


Mass: 5904.879 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: DNA 19mer
#3: DNA chain DNA (5'-D(*GP*CP*TP*CP*TP*TP*TP*CP*TP*CP*TP*CP*TP*TP*TP*GP*AP*TP*G)-3')


Mass: 5743.705 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: DNA 19mer
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 163 / 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: 2.79 Å3/Da / Density % sol: 55.98 %
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: Jul 16, 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: 2.5→50 Å / Num. all: 44491 / Num. obs: 44323 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.42 % / Rmerge(I) obs: 0.053 / Net I/σ(I): 19.26
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 4.45 % / Rmerge(I) obs: 0.621 / Mean I/σ(I) obs: 3.29 / Num. unique all: 4442 / % possible all: 100

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Processing

Software
NameVersionClassification
Blu-Icedata collection
PHASERphasing
PHENIX(phenix.refine: dev_736)refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 3RLO

3rlo


Resolution: 2.5→46.015 Å / σ(F): 0 / σ(I): 0 / Phase error: 31.72 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflectionSelection details
Rfree0.2411 2239 5.05 %Random
Rwork0.2006 ---
obs0.2021 44323 99.64 %-
all-44491 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 54.103 Å2 / ksol: 0.313 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.0707 Å2-0 Å2-1.3488 Å2
2---9.0616 Å20 Å2
3---8.9909 Å2
Refinement stepCycle: LAST / Resolution: 2.5→46.015 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6199 1546 36 163 7944
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0088143
X-RAY DIFFRACTIONf_angle_d0.96511124
X-RAY DIFFRACTIONf_dihedral_angle_d20.3353185
X-RAY DIFFRACTIONf_chiral_restr0.0651283
X-RAY DIFFRACTIONf_plane_restr0.0041134
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5013-2.55570.39631420.33732618X-RAY DIFFRACTION95
2.5557-2.61510.36391410.32162620X-RAY DIFFRACTION95
2.6151-2.68050.32651290.322651X-RAY DIFFRACTION95
2.6805-2.7530.38231340.3062619X-RAY DIFFRACTION95
2.753-2.8340.33681500.31492625X-RAY DIFFRACTION94
2.834-2.92540.29391220.3082603X-RAY DIFFRACTION95
2.9254-3.02990.34511470.28212643X-RAY DIFFRACTION95
3.0299-3.15120.32781430.2682592X-RAY DIFFRACTION95
3.1512-3.29460.261370.24282644X-RAY DIFFRACTION94
3.2946-3.46820.25761450.2122615X-RAY DIFFRACTION95
3.4682-3.68530.23991460.20122632X-RAY DIFFRACTION94
3.6853-3.96960.2521320.19092614X-RAY DIFFRACTION95
3.9696-4.36860.21881330.15592640X-RAY DIFFRACTION95
4.3686-4.99970.16791390.13622655X-RAY DIFFRACTION95
4.9997-6.2950.21551390.15842653X-RAY DIFFRACTION95
6.295-39.50450.19171550.15982599X-RAY DIFFRACTION92
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)
17.2525-0.45692.55665.6539-4.73516.88930.17851.08610.2666-1.1982-0.30941.16990.72070.19220.08320.63780.157-0.16520.34110.02860.6743.492643.7933-8.0397
21.807-0.98741.39923.28420.09673.33030.04570.18350.5441-0.4779-0.24810.018-0.78660.06550.08050.47240.12230.05030.1420.13070.646113.426450.9262-3.9401
34.2445-1.46120.44747.7215-3.68726.41920.19080.4520.4158-0.7245-0.20511.0925-0.3485-0.5467-0.06650.62820.1172-0.10540.25460.01350.73482.657546.4184-4.7275
47.80730.49830.43830.1122-0.01580.30620.02640.0732-0.8433-0.0623-0.04720.29350.3026-0.03490.03070.4590.00190.02370.1340.04890.602218.115431.25561.8484
54.51474.6463-0.43165.5205-2.07773.65990.26980.4834-0.4537-0.46470.1073-1.59960.1630.5117-0.28760.44360.00190.17480.2633-0.02990.747429.307438.8238-0.5656
62.92582.03812.8611.42051.99622.81680.08270.39630.3389-0.4293-0.012-0.6838-0.23690.5116-0.02150.30240.00450.21590.34480.08860.987334.999640.562-1.1171
70.6644-0.0342-0.62883.2303-1.14675.65660.10620.18780.6705-0.254-0.1989-1.1306-0.10780.7846-0.01970.38590.0780.14590.36940.13540.919829.976544.23441.2269
82.68270.95390.90085.0183-0.33662.6988-0.2853-0.1810.54320.20280.0941-0.601-0.61530.0332-0.08370.5387-0.049-0.10760.1237-0.08130.609322.290235.333340.5334
92.202-0.70520.00654.360.25562.7137-0.1068-0.28530.02340.47690.06360.1587-0.195-0.20380.0720.37370.03880.05340.0797-0.04690.37588.521727.811939.0925
102.8346-0.339-0.92356.7606-0.50063.33130.0027-0.4164-0.65970.3797-0.19740.67920.19690.01020.0910.3884-0.08110.08960.16980.09780.55649.644-10.624542.4149
111.36170.571-0.58650.3658-0.3470.3330.2019-0.3037-0.25370.2546-0.14180.22810.4735-0.18790.07070.8364-0.16230.07870.35530.2380.81967.0453-10.602149.5292
121.42311.7847-0.54154.2176-0.70653.6642-0.0601-0.04790.39070.285-0.04220.59630.1184-0.40440.11120.28890.0191-0.00920.15850.04760.653312.48653.180938.8277
133.1231-2.09950.36751.59540.78215.81340.1083-0.6959-0.32070.2597-0.025-0.87060.36121.0330.00230.25160.0027-0.18530.43550.09290.859935.0393-2.644737.8795
143.9783-2.5927-1.15725.729-0.62378.71030.0382-0.4808-0.36190.26980.1557-0.96980.3960.8468-0.13490.26270.0732-0.14340.35860.10620.698530.2784-6.307637.5261
152.43140.8194-0.81083.87020.49080.8132-0.30250.138-0.7836-0.5840.1163-0.88770.20710.0880.0490.42060.04330.23710.1945-0.02640.727821.98762.9122-1.9872
162.44380.56450.30663.87410.37383.04-0.12570.3614-0.2969-0.56860.07480.19150.09-0.28840.05390.3286-0.11020.00230.1666-0.07980.38.372310.2132-0.6713
171.98820.43610.16281.9219-0.55461.14420.2302-0.00560.5081-0.0602-0.4016-0.2598-0.47470.11910.15640.90360.10070.05310.1138-0.03360.690414.089245.749218.6116
181.647-0.56380.93492.2229-0.94351.21660.74510.04340.70971.0483-1.2381-0.0309-0.96110.11390.33321.18530.00080.39630.55410.18760.876315.308947.515418.4651
190.48720.2253-0.02792.98170.55880.1168-0.11290.0819-0.24480.0784-0.2401-0.1040.280.0148-0.84380.87260.0219-0.00880.0853-0.01920.870915.2596-15.633220.6434
200.60280.47780.23034.1341-0.79110.33790.32370.2209-0.2521-0.5394-0.5850.42230.408-0.04090.16350.9640.0514-0.09520.185-0.05120.902515.0659-13.934619.4274
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resseq 147:161)
2X-RAY DIFFRACTION2chain 'A' and (resseq 162:199)
3X-RAY DIFFRACTION3chain 'A' and (resseq 200:239)
4X-RAY DIFFRACTION4chain 'A' and (resseq 240:257)
5X-RAY DIFFRACTION5chain 'A' and (resseq 258:275)
6X-RAY DIFFRACTION6chain 'A' and (resseq 276:296)
7X-RAY DIFFRACTION7chain 'A' and (resseq 297:340)
8X-RAY DIFFRACTION8chain 'B' and (resseq 147:210)
9X-RAY DIFFRACTION9chain 'B' and (resseq 211:340)
10X-RAY DIFFRACTION10chain 'C' and (resseq 147:210)
11X-RAY DIFFRACTION11chain 'C' and (resseq 211:229)
12X-RAY DIFFRACTION12chain 'C' and (resseq 230:265)
13X-RAY DIFFRACTION13chain 'C' and (resseq 266:296)
14X-RAY DIFFRACTION14chain 'C' and (resseq 297:340)
15X-RAY DIFFRACTION15chain 'D' and (resseq 147:210)
16X-RAY DIFFRACTION16chain 'D' and (resseq 211:340)
17X-RAY DIFFRACTION17chain 'K'
18X-RAY DIFFRACTION18chain 'L'
19X-RAY DIFFRACTION19chain 'M'
20X-RAY DIFFRACTION20chain 'N'

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