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- PDB-4l5r: Crystal structure of p202 HIN1 in complex with 20-mer dsDNA -

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Basic information

Entry
Database: PDB / ID: 4l5r
TitleCrystal structure of p202 HIN1 in complex with 20-mer dsDNA
Components
  • 20-mer DNA
  • Interferon-activable protein 202
KeywordsDNA BINDING PROTEIN/DNA / HIN200 / OB fold / dsDNA binding domain / DNA BINDING PROTEIN-DNA complex
Function / homology
Function and homology information


negative regulation of AIM2 inflammasome complex assembly / cellular response to interferon-beta / negative regulation of innate immune response / activation of innate immune response / negative regulation of cysteine-type endopeptidase activity involved in apoptotic process / protein homooligomerization / double-stranded DNA binding / protein homotetramerization / molecular adaptor activity / inflammatory response ...negative regulation of AIM2 inflammasome complex assembly / cellular response to interferon-beta / negative regulation of innate immune response / activation of innate immune response / negative regulation of cysteine-type endopeptidase activity involved in apoptotic process / protein homooligomerization / double-stranded DNA binding / protein homotetramerization / molecular adaptor activity / inflammatory response / innate immune response / nucleolus / nucleoplasm / nucleus / cytosol / cytoplasm
Similarity search - Function
HIN-200/IF120x / HIN-200 family / HIN-200/IF120x domain / HIN-200 A and B domains profile. / 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-activable protein 202
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.873 Å
AuthorsYin, Q. / Tian, Y. / Wu, H.
CitationJournal: Cell Rep / Year: 2013
Title: Molecular Mechanism for p202-Mediated Specific Inhibition of AIM2 Inflammasome Activation.
Authors: Yin, Q. / Sester, D.P. / Tian, Y. / Hsiao, Y.S. / Lu, A. / Cridland, J.A. / Sagulenko, V. / Thygesen, S.J. / Choubey, D. / Hornung, V. / Walz, T. / Stacey, K.J. / Wu, H.
History
DepositionJun 11, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 31, 2013Provider: repository / Type: Initial release
Revision 1.1Aug 21, 2013Group: Database references
Revision 1.2Feb 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

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Assembly

Deposited unit
C: Interferon-activable protein 202
A: 20-mer DNA
B: 20-mer DNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,0264
Polymers35,0033
Non-polymers231
Water3,207178
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3580 Å2
ΔGint-42 kcal/mol
Surface area17030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.347, 86.424, 51.412
Angle α, β, γ (deg.)90.00, 113.34, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Interferon-activable protein 202 / Ifi-202 / Interferon-inducible protein p202 / Lupus susceptibility protein p202


Mass: 22703.076 Da / Num. of mol.: 1 / Fragment: HIN-200 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Strain: Czech II / Gene: Ifi202, Ifi202a, Ifi202b / Plasmid: pSMT3 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3 RIPL / References: UniProt: Q9R002
#2: DNA chain 20-mer DNA


Mass: 6149.978 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: chemically synthesized 20-mer DNA
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 178 / 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: 2.7 Å3/Da / Density % sol: 54.46 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 18% PEG 3350, 0.1 M sodium citrate pH 5.4-6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 31, 2011
RadiationMonochromator: Rosenbaum-Rock double crystal sagittal focusing monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
ReflectionResolution: 1.873→50 Å / Num. all: 30751 / Num. obs: 30351 / % possible obs: 98.7 % / Observed criterion σ(F): 5 / Observed criterion σ(I): 5
Reflection shellResolution: 1.873→1.95 Å / % possible all: 95.9

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASESphasing
PHENIX(phenix.refine: 1.7.1_743)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.873→25.572 Å / SU ML: 0.56 / σ(F): 1.35 / Phase error: 25.57 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2275 1528 5.04 %Random
Rwork0.1914 ---
all0.2 30662 --
obs0.1932 30294 98.8 %-
Solvent computationShrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 46.191 Å2 / ksol: 0.359 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--9.4162 Å2-0 Å22.9158 Å2
2---5.8272 Å2-0 Å2
3---15.2433 Å2
Refinement stepCycle: LAST / Resolution: 1.873→25.572 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1573 816 1 178 2568
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062536
X-RAY DIFFRACTIONf_angle_d1.1643588
X-RAY DIFFRACTIONf_dihedral_angle_d22.8191004
X-RAY DIFFRACTIONf_chiral_restr0.067401
X-RAY DIFFRACTIONf_plane_restr0.004315
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8726-1.9330.35671110.33112449X-RAY DIFFRACTION91
1.933-2.00210.29761520.24862601X-RAY DIFFRACTION99
2.0021-2.08220.24661420.22372594X-RAY DIFFRACTION99
2.0822-2.17690.25821380.20982608X-RAY DIFFRACTION100
2.1769-2.29160.25081520.20262604X-RAY DIFFRACTION100
2.2916-2.43510.23721510.20142646X-RAY DIFFRACTION100
2.4351-2.6230.2851260.20632648X-RAY DIFFRACTION100
2.623-2.88660.28971310.21272663X-RAY DIFFRACTION100
2.8866-3.30350.24221330.19492643X-RAY DIFFRACTION100
3.3035-4.15920.17841420.17052649X-RAY DIFFRACTION100
4.1592-25.57410.20151500.1662661X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: -1.811 Å / Origin y: -16.6707 Å / Origin z: -15.3366 Å
111213212223313233
T0.2114 Å2-0.0335 Å2-0.015 Å2-0.2132 Å20.0416 Å2--0.1846 Å2
L2.1275 °21.2361 °2-0.1548 °2-1.2956 °2-0.0148 °2--0.5922 °2
S0.2506 Å °-0.2446 Å °-0.0307 Å °0.0936 Å °-0.3011 Å °-0.0075 Å °0.0285 Å °0.0426 Å °0.0332 Å °
Refinement TLS groupSelection details: all

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