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

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Basic information

Entry
Database: PDB / ID: 3rln
TitleStructural Basis of Cytosolic DNA Recognition by Innate Immune Receptors
ComponentsGamma-interferon-inducible protein 16
KeywordsDNA BINDING PROTEIN / HIN200/OB fold/DNA binding / cytosolic DNA sensor/DNA binding / DNA / cytosol
Function / homology
Function and homology information


negative regulation of AIM2 inflammasome complex assembly / negative regulation of DNA binding / myeloid cell differentiation / STING mediated induction of host immune responses / IRF3-mediated induction of type I IFN / negative regulation of viral genome replication / transcription factor binding / negative regulation of gene expression, epigenetic / intrinsic apoptotic signaling pathway by p53 class mediator / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator ...negative regulation of AIM2 inflammasome complex assembly / negative regulation of DNA binding / myeloid cell differentiation / STING mediated induction of host immune responses / IRF3-mediated induction of type I IFN / negative regulation of viral genome replication / transcription factor binding / negative regulation of gene expression, epigenetic / intrinsic apoptotic signaling pathway by p53 class mediator / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / monocyte differentiation / cellular response to glucose starvation / cellular response to interferon-beta / activation of innate immune response / negative regulation of innate immune response / positive regulation of cytokine production / positive regulation of interleukin-1 beta production / cellular response to ionizing radiation / regulation of autophagy / autophagy / regulation of inflammatory response / 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 / membrane / identical protein binding / nucleus / cytoplasm / cytosol
Similarity search - Function
HIN-200/IF120x / HIN-200/IF120x domain / HIN-200 A and B domains profile. / HIN-200 family / DAPIN domain profile. / DAPIN domain / PAAD/DAPIN/Pyrin domain / PAAD/DAPIN/Pyrin domain / Nucleic acid-binding proteins / Death-like domain superfamily ...HIN-200/IF120x / HIN-200/IF120x domain / HIN-200 A and B domains profile. / HIN-200 family / DAPIN domain profile. / DAPIN domain / PAAD/DAPIN/Pyrin domain / PAAD/DAPIN/Pyrin domain / Nucleic acid-binding proteins / Death-like domain superfamily / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Nucleic acid-binding, OB-fold / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Gamma-interferon-inducible protein 16
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.251 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 19, 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 / 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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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


Theoretical massNumber of molelcules
Total (without water)22,4091
Polymers22,4091
Non-polymers00
Water1,54986
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)128.673, 128.673, 67.772
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-12-

HOH

21A-51-

HOH

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Components

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


Mass: 22408.717 Da / Num. of mol.: 1 / Fragment: unp residues 571-766 / Mutation: K663A, R667A, N710A
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
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 86 / 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: 2.41 Å3/Da / Density % sol: 48.94 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.2 M KCl, 20% PEG3350, 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: 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: 2.25→50 Å / Num. all: 10327 / Num. obs: 10296 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 9.8 % / Rmerge(I) obs: 0.097 / Net I/σ(I): 23.48
Reflection shellResolution: 2.25→2.29 Å / Redundancy: 7.4 % / Rmerge(I) obs: 0.599 / Mean I/σ(I) obs: 2.76 / Num. unique all: 499 / % possible all: 96.7

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine: dev_723)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 3RLO

3rlo


Resolution: 2.251→37.145 Å / SU ML: 0.67 / σ(F): 0 / Phase error: 24.02 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2291 496 4.83 %random
Rwork0.1773 ---
all0.1798 10327 --
obs0.1798 10296 99.44 %-
Solvent computationShrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 53.301 Å2 / ksol: 0.342 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.17 Å20 Å2-0 Å2
2--0.17 Å2-0 Å2
3----0.3399 Å2
Refinement stepCycle: LAST / Resolution: 2.251→37.145 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1490 0 0 86 1576
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071533
X-RAY DIFFRACTIONf_angle_d1.1242069
X-RAY DIFFRACTIONf_dihedral_angle_d13.771574
X-RAY DIFFRACTIONf_chiral_restr0.083240
X-RAY DIFFRACTIONf_plane_restr0.005264
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2505-2.4770.34581230.25692391X-RAY DIFFRACTION99
2.477-2.83530.28911190.21342428X-RAY DIFFRACTION100
2.8353-3.57170.25771230.17452445X-RAY DIFFRACTION100
3.5717-37.14970.1811310.15472506X-RAY DIFFRACTION100
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)
12.9388-2.9292-0.99814.08341.37931.2162-0.2243-0.27320.37810.48160.01930.87560.1602-0.0992-0.0710.27360.1654-0.04490.1632-0.33610.99795.168713.02221.0855
22.8427-1.7553-1.89836.49052.4574.0201-0.31210.05330.4214-0.41650.09380.37270.19750.48350.14350.3489-0.0399-0.00170.34960.02570.259525.38667.030110.9586
36.7365-1.6814-2.1325.85731.13735.6342-0.2578-0.61691.02280.1422-0.15570.13660.1295-0.3999-0.0550.1637-0.0211-0.06210.3013-0.16580.458713.565812.145819.1073
46.2243-1.655-0.8576.92581.07794.1833-0.0495-0.19041.1483-0.3026-0.02280.36820.1359-0.25940.05210.1558-0.0213-0.01860.264-0.04160.389212.76411.269916.3833
53.1522-0.4565-0.58216.0019-0.51862.6470.0213-0.19941.2962-0.3397-0.15930.799-0.2004-0.17210.12890.2239-0.0241-0.08210.262-0.05310.60395.725513.096216.4428
67.15352.7342.74036.33591.15716.59780.0384-1.5022-0.26870.74050.36360.33130.5522-0.00280.060.24510.04220.05530.54570.03390.266114.58083.309824.1759
75.52810.4211-0.24566.85661.62445.52670.09770.0761-0.1066-0.2547-0.14690.45180.4122-0.26610.13450.2106-0.0489-0.00410.2110.04750.24649.58593.052814.119
80.2029-0.14620.4181.2175-1.72082.66960.222-0.61981.9918-0.0455-0.64411.4152-1.6359-1.80280.56160.56640.3723-0.16160.8129-0.11.3476-2.91817.172713.1205
97.0232-5.3594-1.00046.55860.2014.53680.36850.6897-0.435-0.4138-0.39211.149-0.1683-0.61010.45070.60910.229-0.11441.1406-0.71511.8399-1.421421.893822.2654
100.6009-0.81091.24321.2015-1.92553.13510.11490.01611.0293-0.3554-0.72720.8655-0.1707-0.18810.61940.38660.0718-0.06720.7116-0.43231.129111.045822.96628.8595
115.22580.3552-1.05414.3675-0.77.0068-0.2269-1.780.21641.14480.27280.33850.2399-0.2827-0.31420.42560.01070.03440.7954-0.01780.329926.327615.614837.3835
124.2398-0.46030.86292.4088-0.72247.8667-0.1969-1.2064-0.3060.47520.60580.63850.5475-0.9214-0.36720.391-0.0587-0.0420.73130.15650.294722.91058.955631.2144
135.6888-1.4231-1.78175.002-2.0912.65660.3557-1.41131.25320.14730.158-0.2471-0.58370.6431-0.2960.2656-0.04120.0310.4972-0.19850.406834.310222.020228.5566
142.2738-1.4371-1.74523.6110.2033.21420.1602-0.60230.24910.01880.0845-0.8590.52071.0112-0.09390.24310.1207-0.00430.4721-0.05450.321444.042811.325523.0687
155.0954-1.9552-2.78015.05920.55342.2971-0.0048-0.85560.40360.2347-0.0679-0.07410.61770.3769-0.05620.24110.0295-0.07790.4849-0.01990.320939.577612.771625.9665
164.7999-2.5629-3.43945.0582.98963.1205-0.073-1.1160.85090.24270.4201-0.35270.17330.0721-0.14280.28930.0664-0.04010.6344-0.1440.304234.519116.619231.5553
178.6349-2.9031-5.3693.63550.4364.04490.19320.6050.1638-0.0535-0.11330.25240.4514-0.3337-0.24440.2602-0.0525-0.01830.4354-0.02730.259635.063111.519615.8279
183.71480.16942.19717.1432-0.02356.5501-0.1113-0.79960.27820.1975-0.0452-0.2006-0.0620.350.07940.15450.00010.02720.3919-0.00750.264932.105115.362326.679
192.89870.33141.95656.93511.01617.65240.0695-0.7172-0.42460.46340.3764-0.02690.59220.2807-0.18220.2190.030.01350.43580.10680.244630.08269.090926.5146
204.91771.8744-0.32362.29162.21837.2346-0.5617-0.13080.9501-0.75590.1314-0.2026-1.58760.82510.34170.5892-0.1598-0.03720.360.0130.513331.908125.904419.0752
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 575:584)
2X-RAY DIFFRACTION2(chain A and resid 585:596)
3X-RAY DIFFRACTION3(chain A and resid 597:608)
4X-RAY DIFFRACTION4(chain A and resid 609:624)
5X-RAY DIFFRACTION5(chain A and resid 625:635)
6X-RAY DIFFRACTION6(chain A and resid 636:642)
7X-RAY DIFFRACTION7(chain A and resid 643:650)
8X-RAY DIFFRACTION8(chain A and resid 651:656)
9X-RAY DIFFRACTION9(chain A and resid 657:661)
10X-RAY DIFFRACTION10(chain A and resid 662:670)
11X-RAY DIFFRACTION11(chain A and resid 671:682)
12X-RAY DIFFRACTION12(chain A and resid 683:688)
13X-RAY DIFFRACTION13(chain A and resid 689:695)
14X-RAY DIFFRACTION14(chain A and resid 696:701)
15X-RAY DIFFRACTION15(chain A and resid 702:706)
16X-RAY DIFFRACTION16(chain A and resid 707:719)
17X-RAY DIFFRACTION17(chain A and resid 720:725)
18X-RAY DIFFRACTION18(chain A and resid 726:745)
19X-RAY DIFFRACTION19(chain A and resid 746:758)
20X-RAY DIFFRACTION20(chain A and resid 759:764)

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