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- PDB-4jbk: Molecular basis for abrogation of activation of pro-inflammatory ... -

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Basic information

Entry
Database: PDB / ID: 4jbk
TitleMolecular basis for abrogation of activation of pro-inflammatory cytokines
Components
  • DNA (5'-D(P*GP*GP*AP*AP*TP*TP*AP*TP*AP*AP*TP*TP*CP*C)-3')
  • Interferon-activable protein 202
KeywordsDNA BINDING PROTEIN/DNA / OB fold / DNA / 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: 2.963 Å
AuthorsRu, H. / Ni, X. / Crowley, C. / Zhao, L. / Ding, W. / Hung, L.-W. / Shaw, N. / Cheng, G. / Liu, Z.-J.
CitationJournal: Cell Res. / Year: 2013
Title: Structural basis for termination of AIM2-mediated signaling by p202
Authors: Ru, H. / Ni, X. / Zhao, L. / Crowley, C. / Ding, W. / Hung, L.-W. / Shaw, N. / Cheng, G. / Liu, Z.-J.
History
DepositionFeb 19, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 26, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 8, 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: Interferon-activable protein 202
B: Interferon-activable protein 202
C: Interferon-activable protein 202
D: Interferon-activable protein 202
E: DNA (5'-D(P*GP*GP*AP*AP*TP*TP*AP*TP*AP*AP*TP*TP*CP*C)-3')
F: DNA (5'-D(P*GP*GP*AP*AP*TP*TP*AP*TP*AP*AP*TP*TP*CP*C)-3')
G: DNA (5'-D(P*GP*GP*AP*AP*TP*TP*AP*TP*AP*AP*TP*TP*CP*C)-3')
H: DNA (5'-D(P*GP*GP*AP*AP*TP*TP*AP*TP*AP*AP*TP*TP*CP*C)-3')


Theoretical massNumber of molelcules
Total (without water)107,9368
Polymers107,9368
Non-polymers00
Water0
1
A: Interferon-activable protein 202
D: Interferon-activable protein 202
E: DNA (5'-D(P*GP*GP*AP*AP*TP*TP*AP*TP*AP*AP*TP*TP*CP*C)-3')
F: DNA (5'-D(P*GP*GP*AP*AP*TP*TP*AP*TP*AP*AP*TP*TP*CP*C)-3')


Theoretical massNumber of molelcules
Total (without water)53,9684
Polymers53,9684
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3400 Å2
ΔGint-36 kcal/mol
Surface area24890 Å2
MethodPISA
2
B: Interferon-activable protein 202
G: DNA (5'-D(P*GP*GP*AP*AP*TP*TP*AP*TP*AP*AP*TP*TP*CP*C)-3')

B: Interferon-activable protein 202
G: DNA (5'-D(P*GP*GP*AP*AP*TP*TP*AP*TP*AP*AP*TP*TP*CP*C)-3')


Theoretical massNumber of molelcules
Total (without water)53,9684
Polymers53,9684
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_657-x+1,y,-z+21
Buried area3430 Å2
ΔGint-39 kcal/mol
Surface area24550 Å2
MethodPISA
3
C: Interferon-activable protein 202
H: DNA (5'-D(P*GP*GP*AP*AP*TP*TP*AP*TP*AP*AP*TP*TP*CP*C)-3')

C: Interferon-activable protein 202
H: DNA (5'-D(P*GP*GP*AP*AP*TP*TP*AP*TP*AP*AP*TP*TP*CP*C)-3')


Theoretical massNumber of molelcules
Total (without water)53,9684
Polymers53,9684
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_756-x+2,y,-z+11
Buried area3550 Å2
ΔGint-39 kcal/mol
Surface area24500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.304, 109.940, 106.137
Angle α, β, γ (deg.)90.00, 120.03, 90.00
Int Tables number5
Space group name H-MC121
DetailsAUTHOR STATES THAT THE BIOLOGICAL ASSEMBLY IS UNKNOWN.

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Components

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


Mass: 22705.160 Da / Num. of mol.: 4 / Fragment: HINa domain, UNP residues 46-242
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Ifi202a / Production host: Escherichia coli (E. coli) / References: UniProt: Q9R002
#2: DNA chain
DNA (5'-D(P*GP*GP*AP*AP*TP*TP*AP*TP*AP*AP*TP*TP*CP*C)-3')


Mass: 4278.815 Da / Num. of mol.: 4 / Source method: obtained synthetically
Sequence detailsTHIS SEQUECE WAS CAUSED BY STRAIN AKR.

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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: 2.49 Å3/Da / Density % sol: 50.55 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.2M calcium acetate, 0.1M Tris-HCl, 20%(w/v) polyethylene glycol 3000, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jan 12, 2012
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.963→50 Å / Num. all: 22039 / Num. obs: 21825 / % possible obs: 99 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Biso Wilson estimate: 57.95 Å2
Reflection shellResolution: 3→3.11 Å / % possible all: 99.9

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASESphasing
PHENIX(phenix.refine: 1.8.1_1168)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4JBM

4jbm


Resolution: 2.963→47.173 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.7756 / SU ML: 0.41 / σ(F): 1.36 / Phase error: 29.11 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2532 1990 9.12 %RANDOM
Rwork0.2203 ---
all0.2219 22039 --
obs0.2234 21825 99.03 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 214.43 Å2 / Biso mean: 77.3168 Å2 / Biso min: 37.07 Å2
Refinement stepCycle: LAST / Resolution: 2.963→47.173 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6087 1148 0 0 7235
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0067482
X-RAY DIFFRACTIONf_angle_d1.31510279
X-RAY DIFFRACTIONf_chiral_restr0.0881154
X-RAY DIFFRACTIONf_plane_restr0.0051096
X-RAY DIFFRACTIONf_dihedral_angle_d18.5262909
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.9633-3.03740.38761370.34451319145694
3.0374-3.11950.3551340.299114451579100
3.1195-3.21130.37321340.27531412154699
3.2113-3.31490.3131500.27231374152498
3.3149-3.43330.32971490.25221408155799
3.4333-3.57080.27621270.240114141541100
3.5708-3.73320.28361460.23021410155699
3.7332-3.92990.2951460.222314421588100
3.9299-4.1760.24181390.213714291568100
4.176-4.49820.24761420.178214401582100
4.4982-4.95050.19621430.177214161559100
4.9505-5.66580.21251540.195114301584100
5.6658-7.13430.23621370.21414551592100
7.1343-47.17940.19241520.20851441159399
Refinement TLS params.Method: refined / Origin x: 40.4911 Å / Origin y: 11.4431 Å / Origin z: 70.615 Å
111213212223313233
T0.5107 Å20.0264 Å20.008 Å2-0.6014 Å2-0.0049 Å2--0.4829 Å2
L0.3415 °20.078 °2-0.2681 °2-0.2265 °2-0.0123 °2--0.1946 °2
S-0.0714 Å °-0.0953 Å °0.0444 Å °-0.0263 Å °0.0446 Å °-0.0508 Å °0.091 Å °0.1693 Å °0.043 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1ALLA3 - 199
2X-RAY DIFFRACTION1ALLB3 - 199
3X-RAY DIFFRACTION1ALLC3 - 199
4X-RAY DIFFRACTION1ALLD3 - 199
5X-RAY DIFFRACTION1ALLE1 - 14
6X-RAY DIFFRACTION1ALLF1 - 14
7X-RAY DIFFRACTION1ALLG1 - 14
8X-RAY DIFFRACTION1ALLH1 - 14

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