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- PDB-3rlo: Structural Basis of Cytosolic DNA Recognition by Innate Receptors -

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Basic information

Entry
Database: PDB / ID: 3rlo
TitleStructural Basis of Cytosolic DNA Recognition by Innate Receptors
ComponentsGamma-interferon-inducible protein 16
KeywordsDNA BINDING PROTEIN / HIN200/OB fold/DNA binding / DNA binding/cytosolic DNA sensor / 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 / identical protein binding / membrane / 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
FORMIC ACID / Gamma-interferon-inducible protein 16
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 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 1.2Oct 29, 2014Group: Structure summary
Revision 1.3Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,50111
Polymers22,8961
Non-polymers60510
Water3,099172
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)128.562, 128.562, 67.743
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-54-

HOH

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Components

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


Mass: 22896.273 Da / Num. of mol.: 1 / Fragment: 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
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH2O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 172 / 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: 2.4 Å3/Da / Density % sol: 48.67 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 20% PEG1500, 10 mM MgCl2, 0.1 M MES, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.0333 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 22, 2010
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0333 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. all: 39719 / Num. obs: 38686 / % possible obs: 97.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.7 % / Rmerge(I) obs: 0.083 / Net I/σ(I): 13.54
Reflection shellResolution: 1.8→1.83 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.489 / Mean I/σ(I) obs: 1.73 / % possible all: 79.1

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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 / Resolution: 1.8→30 Å / SU ML: 0.44 / σ(F): 1.36 / Phase error: 19.97 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1921 1030 5.14 %
Rwork0.1679 --
obs0.1691 20049 97.59 %
all-39719 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 61.302 Å2 / ksol: 0.4 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.8853 Å20 Å20 Å2
2---0.8853 Å20 Å2
3---1.7707 Å2
Refinement stepCycle: LAST / Resolution: 1.8→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1552 0 39 172 1763
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071620
X-RAY DIFFRACTIONf_angle_d1.2072165
X-RAY DIFFRACTIONf_dihedral_angle_d12.878614
X-RAY DIFFRACTIONf_chiral_restr0.09248
X-RAY DIFFRACTIONf_plane_restr0.007274
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7829-1.87680.29511360.2872449X-RAY DIFFRACTION89
1.8768-1.99440.2731420.21812731X-RAY DIFFRACTION99
1.9944-2.14830.2151550.18362741X-RAY DIFFRACTION100
2.1483-2.36430.20881580.18082755X-RAY DIFFRACTION100
2.3643-2.7060.21281420.17672791X-RAY DIFFRACTION100
2.706-3.40770.20661550.15652775X-RAY DIFFRACTION100
3.4077-23.90230.15851420.15562777X-RAY DIFFRACTION97
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)
17.07652.44662.20563.1420.93634.3146-0.04170.1138-0.21970.0620.05420.1822-0.0336-0.1078-0.05520.20620.03890.00110.17410.01350.258614.0679-11.6207-15.8532
23.5383-1.48410.32593.25892.3255.87820.00810.2269-0.18990.3063-0.20690.60350.2185-0.53470.04970.17160.0058-0.0290.2414-0.00120.29045.8199-10.2371-18.2536
38.8281.4441-0.89322.28620.17763.4978-0.02620.7363-0.8216-0.5239-0.1220.13620.27370.04910.07570.29830.0271-0.09730.4178-0.16140.43819.7667-20.6949-32.6556
45.00640.54230.85053.28910.6274.1929-0.06320.5945-0.3718-0.12730.0918-0.22130.06160.3108-0.05980.219-0.02120.01250.4542-0.04410.263534.9956-15.4053-27.0356
53.2501-0.86120.59413.6121-0.38643.84670.03950.4523-0.3724-0.279-0.02520.06140.18480.28470.03580.162-0.0242-0.01050.305-0.02290.249431.0574-16.1537-24.2811
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resseq 575:628)
2X-RAY DIFFRACTION2chain 'A' and (resseq 629:662)
3X-RAY DIFFRACTION3chain 'A' and (resseq 663:679)
4X-RAY DIFFRACTION4chain 'A' and (resseq 680:731)
5X-RAY DIFFRACTION5chain 'A' and (resseq 732:770)

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