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- PDB-4jbm: Structure of murine DNA binding protein bound with ds DNA -

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Basic information

Entry
Database: PDB / ID: 4jbm
TitleStructure of murine DNA binding protein bound with ds DNA
Components
  • DNA (5'-D(*GP*GP*CP*GP*CP*GP*CP*GP*CP*GP*CP*C)-3')
  • Interferon-inducible protein AIM2
KeywordsDNA BINDING PROTEIN/DNA / OB FOLD / DNA / DNA BINDING PROTEIN-DNA complex
Function / homology
Function and homology information


Cytosolic sensors of pathogen-associated DNA / The AIM2 inflammasome / AIM2 inflammasome complex assembly / pyroptosome complex assembly / AIM2 inflammasome complex / cysteine-type endopeptidase activator activity / regulation of behavior / positive regulation of cysteine-type endopeptidase activity / pattern recognition receptor signaling pathway / pattern recognition receptor activity ...Cytosolic sensors of pathogen-associated DNA / The AIM2 inflammasome / AIM2 inflammasome complex assembly / pyroptosome complex assembly / AIM2 inflammasome complex / cysteine-type endopeptidase activator activity / regulation of behavior / positive regulation of cysteine-type endopeptidase activity / pattern recognition receptor signaling pathway / pattern recognition receptor activity / pyroptotic inflammatory response / T cell homeostasis / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / cellular response to interferon-beta / positive regulation of defense response to virus by host / signaling adaptor activity / activation of innate immune response / tumor necrosis factor-mediated signaling pathway / positive regulation of interleukin-1 beta production / brain development / positive regulation of inflammatory response / neuron cellular homeostasis / cellular response to xenobiotic stimulus / site of double-strand break / double-stranded DNA binding / defense response to virus / innate immune response / DNA damage response / mitochondrion / nucleoplasm / identical protein binding / nucleus / cytosol / cytoplasm
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
DNA / DNA (> 10) / Interferon-inducible protein AIM2
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.218 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
Revision 1.2Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Interferon-inducible protein AIM2
B: Interferon-inducible protein AIM2
T: DNA (5'-D(*GP*GP*CP*GP*CP*GP*CP*GP*CP*GP*CP*C)-3')
R: DNA (5'-D(*GP*GP*CP*GP*CP*GP*CP*GP*CP*GP*CP*C)-3')


Theoretical massNumber of molelcules
Total (without water)51,1264
Polymers51,1264
Non-polymers00
Water2,432135
1
A: Interferon-inducible protein AIM2
T: DNA (5'-D(*GP*GP*CP*GP*CP*GP*CP*GP*CP*GP*CP*C)-3')
R: DNA (5'-D(*GP*GP*CP*GP*CP*GP*CP*GP*CP*GP*CP*C)-3')


Theoretical massNumber of molelcules
Total (without water)29,2283
Polymers29,2283
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2040 Å2
ΔGint-13 kcal/mol
Surface area14920 Å2
MethodPISA
2
B: Interferon-inducible protein AIM2


Theoretical massNumber of molelcules
Total (without water)21,8971
Polymers21,8971
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)111.020, 39.120, 137.877
Angle α, β, γ (deg.)90.00, 110.64, 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-inducible protein AIM2 / Interferon-inducible protein 210 / Ifi-210 / Interferon-inducible protein p210


Mass: 21897.428 Da / Num. of mol.: 2 / Fragment: HIN domain, UNP residues 158-349
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Aim2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q91VJ1
#2: DNA chain DNA (5'-D(*GP*GP*CP*GP*CP*GP*CP*GP*CP*GP*CP*C)-3')


Mass: 3665.368 Da / Num. of mol.: 2 / Source method: obtained synthetically
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 135 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.74 Å3/Da / Density % sol: 55.11 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 0.1M sodium malonate, 12%(w/v) polyethylene glycol 3350, pH 6.0, 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: 2.218→50 Å / Num. all: 28054 / Num. obs: 27608 / % possible obs: 98.4 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Biso Wilson estimate: 46.26 Å2
Reflection shellResolution: 2.23→2.31 Å / % possible all: 99.2

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASESphasing
PHENIX(phenix.refine: 1.8_1069)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3RN2

3rn2


Resolution: 2.218→40.973 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.7251 / SU ML: 0.32 / σ(F): 1.35 / Phase error: 33.16 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2827 1996 7.23 %RANDOM
Rwork0.2335 ---
all0.236 28054 --
obs0.2371 27608 98.41 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 203.91 Å2 / Biso mean: 83.6867 Å2 / Biso min: 20 Å2
Refinement stepCycle: LAST / Resolution: 2.218→40.973 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3004 486 0 135 3625
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073599
X-RAY DIFFRACTIONf_angle_d1.3674948
X-RAY DIFFRACTIONf_chiral_restr0.079572
X-RAY DIFFRACTIONf_plane_restr0.006541
X-RAY DIFFRACTIONf_dihedral_angle_d19.3671392
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 (%)
2.2179-2.27330.38351270.3391652177990
2.2733-2.33480.36861460.31681806195299
2.3348-2.40350.35681310.29621825195699
2.4035-2.4810.37461470.3091818196599
2.481-2.56970.36351380.30421839197799
2.5697-2.67260.3911440.27321831197599
2.6726-2.79420.33241380.28791851198999
2.7942-2.94150.28921480.268418191967100
2.9415-3.12570.2941500.267818371987100
3.1257-3.36690.2671330.23161827196098
3.3669-3.70550.27421510.22921842199399
3.7055-4.24130.25491440.212418702014100
4.2413-5.34170.2471480.188818972045100
5.3417-40.98040.25241510.21898204997
Refinement TLS params.Method: refined / Origin x: 157.4146 Å / Origin y: 10.3382 Å / Origin z: 549.5447 Å
111213212223313233
T0.3069 Å20.0532 Å20.0135 Å2-0.2686 Å20.0199 Å2--0.261 Å2
L0.936 °2-0.1075 °20.2679 °2-0.5187 °2-0.0096 °2--0.48 °2
S0.0013 Å °-0.1366 Å °-0.0273 Å °-0.328 Å °-0.0272 Å °-0.0619 Å °-0.0285 Å °-0.0063 Å °-0.0003 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA1 - 193
2X-RAY DIFFRACTION1allB1 - 187
3X-RAY DIFFRACTION1allT2 - 13
4X-RAY DIFFRACTION1allR2 - 13
5X-RAY DIFFRACTION1allA201 - 241
6X-RAY DIFFRACTION1allB201 - 225
7X-RAY DIFFRACTION1allT101 - 137
8X-RAY DIFFRACTION1allR101 - 132

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