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- PDB-3rnu: Structural Basis of Cytosolic DNA Sensing by Innate Immune Receptors -

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Basic information

Entry
Database: PDB / ID: 3rnu
TitleStructural Basis of Cytosolic DNA Sensing by Innate Immune Receptors
Components
  • DNA (5'-D(*GP*CP*CP*AP*TP*CP*AP*AP*AP*GP*AP*GP*AP*GP*AP*G)-3')
  • DNA (5'-D(*TP*CP*TP*CP*TP*CP*TP*TP*TP*GP*AP*TP*GP*GP*CP*C)-3')
  • Gamma-interferon-inducible protein 16
Keywordstranscription activator/dna / OB FOLD / DNA BINDING / CYTOSOLIC DNA SENSOR / CYTOSOLIC / IMMUNE RESPONSE-DNA COMPLEX / transcription activator-dna complex
Function / homology
Function and homology information


negative regulation of AIM2 inflammasome complex assembly / negative regulation of cysteine-type endopeptidase activity / STING mediated induction of host immune responses / myeloid cell differentiation / activation of cysteine-type endopeptidase activity / IRF3-mediated induction of type I IFN / negative regulation of gene expression, epigenetic / negative regulation of viral genome replication / negative regulation of DNA binding / monocyte differentiation ...negative regulation of AIM2 inflammasome complex assembly / negative regulation of cysteine-type endopeptidase activity / STING mediated induction of host immune responses / myeloid cell differentiation / activation of cysteine-type endopeptidase activity / IRF3-mediated induction of type I IFN / negative regulation of gene expression, epigenetic / negative regulation of viral genome replication / negative regulation of DNA binding / monocyte differentiation / transcription factor binding / intrinsic apoptotic signaling pathway by p53 class mediator / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / cellular response to interferon-beta / cellular response to glucose starvation / activation of innate immune response / negative regulation of innate immune response / positive regulation of interleukin-1 beta production / regulation of autophagy / positive regulation of cytokine production / cellular response to ionizing radiation / autophagy / double-stranded DNA binding / defense response to virus / nuclear speck / inflammatory response / innate immune response / negative regulation of DNA-templated transcription / nucleolus / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / RNA binding / nucleoplasm / identical protein binding / membrane / nucleus / cytoplasm / cytosol
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
FORMIC ACID / DNA / DNA (> 10) / Gamma-interferon-inducible protein 16
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.502 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 22, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 25, 2012Provider: repository / Type: Initial release
Revision 1.1May 9, 2012Group: Database references
Revision 1.2Jan 28, 2015Group: Other
Revision 1.3Sep 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: Gamma-interferon-inducible protein 16
B: Gamma-interferon-inducible protein 16
C: Gamma-interferon-inducible protein 16
D: Gamma-interferon-inducible protein 16
K: DNA (5'-D(*GP*CP*CP*AP*TP*CP*AP*AP*AP*GP*AP*GP*AP*GP*AP*G)-3')
L: DNA (5'-D(*TP*CP*TP*CP*TP*CP*TP*TP*TP*GP*AP*TP*GP*GP*CP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,73613
Polymers101,3816
Non-polymers3547
Water1,892105
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)126.841, 126.841, 163.868
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Gamma-interferon-inducible protein 16 / Ifi-16 / Interferon-inducible myeloid differentiation transcriptional activator


Mass: 22896.273 Da / Num. of mol.: 4 / Fragment: Human IFI16 HINb (unp residues 571-766)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IFI16, IFNGIP1 / Plasmid: pET30a / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21(DE3) / References: UniProt: Q16666

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DNA chain , 2 types, 2 molecules KL

#2: DNA chain DNA (5'-D(*GP*CP*CP*AP*TP*CP*AP*AP*AP*GP*AP*GP*AP*GP*AP*G)-3')


Mass: 4965.258 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: 16MER DNA OLIGO
#3: DNA chain DNA (5'-D(*TP*CP*TP*CP*TP*CP*TP*TP*TP*GP*AP*TP*GP*GP*CP*C)-3')


Mass: 4831.125 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: 16MER DNA OLIGO

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Non-polymers , 3 types, 112 molecules

#4: Chemical
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: CH2O2
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 105 / 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: 2.5 Å3/Da / Density % sol: 50.85 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 20% PEG3350, 0.1 M K Formate, 0.1 M HEPES, pH 7.0, 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 8, 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: 33940 / Num. obs: 33125 / % possible obs: 97.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 5.6 % / Rmerge(I) obs: 0.078 / Net I/σ(I): 21.68
Reflection shellResolution: 2.5→2.54 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.505 / Mean I/σ(I) obs: 2.57 / Num. unique all: 1443 / % possible all: 84.1

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Processing

Software
NameVersionClassification
Blu-Icedata collection
PHASERphasing
PHENIX(phenix.refine: dev_736)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3RLO

3rlo


Resolution: 2.502→41.388 Å / σ(F): 1.97 / Phase error: 27.96 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflectionSelection details
Rfree0.2159 1698 5.13 %random
Rwork0.1762 ---
obs0.1782 33110 97.48 %-
all-33940 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 54.996 Å2 / ksol: 0.298 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--11.6737 Å20 Å20 Å2
2---11.6737 Å20 Å2
3---23.3474 Å2
Refinement stepCycle: LAST / Resolution: 2.502→41.388 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6304 650 23 105 7082
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0067195
X-RAY DIFFRACTIONf_angle_d0.9329769
X-RAY DIFFRACTIONf_dihedral_angle_d16.9992736
X-RAY DIFFRACTIONf_chiral_restr0.0641121
X-RAY DIFFRACTIONf_plane_restr0.0041138
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5024-2.57590.36541360.31822291X-RAY DIFFRACTION80
2.5759-2.6590.36091300.31182414X-RAY DIFFRACTION86
2.659-2.75390.35361700.29022550X-RAY DIFFRACTION90
2.7539-2.8640.2981510.26782655X-RAY DIFFRACTION94
2.864-2.99410.27161430.24992672X-RAY DIFFRACTION95
2.9941-3.15160.2721420.24152690X-RAY DIFFRACTION95
3.1516-3.34860.24491150.21712702X-RAY DIFFRACTION96
3.3486-3.60640.23811450.20092686X-RAY DIFFRACTION95
3.6064-3.96780.18291340.16422708X-RAY DIFFRACTION95
3.9678-4.53870.15791350.12422675X-RAY DIFFRACTION95
4.5387-5.70570.16711370.12852692X-RAY DIFFRACTION95
5.7057-24.08830.19581370.13322673X-RAY DIFFRACTION95
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)
13.75442.9821-3.31488.83792.69567.3205-0.4983-0.1678-0.46070.6890.4838-1.01160.5970.8037-0.06590.3703-0.0019-0.02980.3341-0.16831.1982-6.701710.848815.4763
25.10370.8597-1.81339.1827-1.52283.88190.19530.1918-0.0605-0.1686-0.57780.4028-0.07660.02840.34790.36340.0956-0.08410.201-0.0020.3738-1.478716.2448.791
31.1685-0.1862-1.28286.4728-1.89282.0710.631-0.3393-0.45642.1592-0.99041.1401-0.1495-0.3660.3250.7037-0.17620.09930.5853-0.34770.8942-9.639722.434221.9333
47.83085.57162.10344.27980.31355.03510.3291-0.4963-0.06530.5032-0.75771.1583-1.13530.23030.38350.8568-0.32060.0320.654-0.33231.22723.96842.942416.8777
52.3462-0.2795-0.93261.13540.61171.31040.6589-0.41071.01150.797-0.2064-0.5559-0.415-0.1404-0.23381.0606-0.2740.26360.0225-0.18340.73432.669538.139616.9833
63.98761.66231.60052.64590.80036.5927-0.099-0.2130.62091.7684-0.34240.1908-1.1-0.01790.37870.7483-0.1075-0.06120.25880.03390.53540.582137.03315.1799
75.08841.32380.1116.09070.24954.5731-0.0811-0.1374-0.384-0.38730.1845-0.56270.08260.0062-0.10020.2432-0.02550.06230.21840.02620.7979-49.086242.456116.7624
83.0224-0.32560.23970.53950.96362.111-0.34340.5758-0.9007-1.29770.5529-0.4252-0.1830.5741-0.06380.8575-0.24660.27760.5225-0.35270.8369-39.335939.50035.0457
96.67696.33391.63728.3103-1.01675.068-0.45590.49630.1125-1.3290.082-0.4971-0.56070.61310.19540.5486-0.30260.26110.2739-0.00030.9406-28.4660.3478.1616
104.78940.05422.41737.8533-3.43259.104-0.92220.73270.4718-0.30620.242-0.501-0.68030.73210.53190.4994-0.20510.15860.4203-0.04940.7793-32.911757.530911.6515
118.615-0.65140.70841.8507-0.14250.7223-0.13661.9181.409-0.5063-0.4629-0.54140.02580.39450.24740.3949-0.07430.19070.39270.27740.9237-31.866355.643711.8101
124.8868-0.92840.08618.19372.37344.0458-0.0625-0.01660.89280.12070.087-0.53670.22680.12440.01670.15960.0482-0.05950.2869-0.02070.2104-47.199631.0587-22.6228
133.411-0.8064-1.38871.6581.50581.5215-0.7801-0.97340.70970.96860.5485-0.60340.16130.19540.18810.51620.107-0.22230.4478-0.08370.5408-42.338527.8438-13.8654
142.97420.02411.11780.5108-0.5483.5991-0.5653-0.9525-0.72750.93740.5996-0.46670.82770.6601-0.10110.8830.3961-0.07130.582-0.02020.4812-33.61212.8364-14.1855
153.67441.3046-1.53093.8551-0.7114.2487-0.801-0.9295-0.4363-0.43670.4009-1.38860.74070.70090.28420.56520.2134-0.00330.3439-0.06870.5868-30.673118.1577-21.279
163.60060.11090.70376.795-1.15076.78340.10950.1632-0.4791-0.15570.04730.49560.3370.1308-0.1310.2455-0.0041-0.01240.1779-0.06550.6614-2.64855.8353-5.1332
171.53681.11190.03683.2588-0.21192.35210.13210.4463-0.3655-1.1742-0.15720.80150.5294-0.34310.15840.629-0.0185-0.19810.2937-0.14980.5864-3.469851.5589-13.0873
183.50180.75990.11413.85312.48577.8374-0.28240.3711-0.8005-1.0005-0.0312-0.00280.50670.41240.07630.7380.11930.01550.2775-0.18950.78634.877435.087-11.6588
195.4751-1.9252.19285.88212.01726.797-0.02120.8296-1.6943-0.9013-0.0432-0.39431.5892-0.34550.10920.86340.02390.07080.3388-0.19910.95431.922836.3255-10.3433
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resseq 570:585)
2X-RAY DIFFRACTION2chain 'A' and (resseq 586:652)
3X-RAY DIFFRACTION3chain 'A' and (resseq 653:688)
4X-RAY DIFFRACTION4chain 'A' and (resseq 689:701)
5X-RAY DIFFRACTION5chain 'A' and (resseq 702:741)
6X-RAY DIFFRACTION6chain 'A' and (resseq 742:770)
7X-RAY DIFFRACTION7chain 'B' and (resseq 570:652)
8X-RAY DIFFRACTION8chain 'B' and (resseq 653:688)
9X-RAY DIFFRACTION9chain 'B' and (resseq 689:711)
10X-RAY DIFFRACTION10chain 'B' and (resseq 712:741)
11X-RAY DIFFRACTION11chain 'B' and (resseq 742:770)
12X-RAY DIFFRACTION12chain 'C' and (resseq 572:633)
13X-RAY DIFFRACTION13chain 'C' and (resseq 634:699)
14X-RAY DIFFRACTION14chain 'C' and (resseq 700:748)
15X-RAY DIFFRACTION15chain 'C' and (resseq 749:770)
16X-RAY DIFFRACTION16chain 'D' and (resseq 572:627)
17X-RAY DIFFRACTION17chain 'D' and (resseq 628:699)
18X-RAY DIFFRACTION18chain 'D' and (resseq 700:741)
19X-RAY DIFFRACTION19chain 'D' and (resseq 742:770)

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