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- PDB-4l5s: p202 HIN1 in complex with 12-mer dsDNA -

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Basic information

Entry
Database: PDB / ID: 4l5s
Titlep202 HIN1 in complex with 12-mer dsDNA
Components
  • 12-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 / activation of innate immune response / negative regulation 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 / activation of innate immune response / negative regulation 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 / Resolution: 2.94 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 1.0Aug 14, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / 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 / 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: Interferon-activable protein 202
B: Interferon-activable protein 202
C: 12-mer DNA
D: 12-mer DNA
E: 12-mer DNA
F: 12-mer DNA
G: 12-mer DNA
H: 12-mer DNA
I: 12-mer DNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,80914
Polymers71,3299
Non-polymers4805
Water1267
1
A: Interferon-activable protein 202
C: 12-mer DNA
D: 12-mer DNA
E: 12-mer DNA
hetero molecules

A: Interferon-activable protein 202
C: 12-mer DNA
D: 12-mer DNA
E: 12-mer DNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,41916
Polymers67,6518
Non-polymers7698
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_554-x,y,-z-1/21
2
B: Interferon-activable protein 202
F: 12-mer DNA
G: 12-mer DNA
hetero molecules

B: Interferon-activable protein 202
F: 12-mer DNA
G: 12-mer DNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,4868
Polymers60,2946
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_554-x,y,-z-1/21
3
H: 12-mer DNA
I: 12-mer DNA


Theoretical massNumber of molelcules
Total (without water)7,3572
Polymers7,3572
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)111.309, 156.118, 117.614
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

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


Mass: 22790.154 Da / Num. of mol.: 2 / Fragment: p202 HIN1, UNP residues 46-243
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
12-mer DNA


Mass: 3678.403 Da / Num. of mol.: 7 / Source method: obtained synthetically / Details: chemically synthesized 12-mer DNA
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 7 / 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: 3.58 Å3/Da / Density % sol: 65.66 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.3
Details: 2.2 M ammonium sulfate, 0.1 M sodium cacodylate pH 5.2-5.4, 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 4 / Detector: CCD / Date: Jul 31, 2011
RadiationMonochromator: Rosenbaum-Rock double crystal sagittal focusing monochrometer and vertical focusing mirror
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
ReflectionResolution: 2.943→46.97 Å / Num. all: 307230 / % possible obs: 100 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3

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Processing

Software
NameVersionClassification
CBASSdata collection
PHASESphasing
PHENIX(phenix.refine: 1.7.1_743)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementStarting model: PDB ENTRY 4L5Q

4l5q


Resolution: 2.94→46.97 Å / SU ML: 0.93 / σ(F): 1.89 / Phase error: 26.63 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.255 1129 5.12 %
Rwork0.204 --
obs0.207 22039 99.7 %
Solvent computationShrinkage radii: 1.06 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 51.82 Å2 / ksol: 0.33 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--6.605 Å20 Å20 Å2
2--4.6177 Å2-0 Å2
3---1.9873 Å2
Refinement stepCycle: LAST / Resolution: 2.94→46.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3186 1487 25 7 4705
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084918
X-RAY DIFFRACTIONf_angle_d1.4916927
X-RAY DIFFRACTIONf_dihedral_angle_d26.681939
X-RAY DIFFRACTIONf_chiral_restr0.092772
X-RAY DIFFRACTIONf_plane_restr0.007622
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9426-3.07650.39341480.33682523X-RAY DIFFRACTION98
3.0765-3.23870.29831490.24022569X-RAY DIFFRACTION100
3.2387-3.44160.28591380.20192597X-RAY DIFFRACTION100
3.4416-3.70720.27971340.20622610X-RAY DIFFRACTION100
3.7072-4.08010.26461380.20622594X-RAY DIFFRACTION100
4.0801-4.670.22251380.15852624X-RAY DIFFRACTION100
4.67-5.88190.23751370.18792654X-RAY DIFFRACTION100
5.8819-46.97560.21751470.20982739X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 4.7265 Å / Origin y: 38.5179 Å / Origin z: -9.8763 Å
111213212223313233
T0.0136 Å20.0004 Å2-0.0678 Å2-0.1535 Å20.0479 Å2--0.0653 Å2
L1.2284 °2-0.801 °2-0.0797 °2-0.8399 °20.0834 °2--0.4668 °2
S0.0275 Å °-0.0126 Å °-0.0779 Å °0.0182 Å °0.0389 Å °-0.0055 Å °0.0123 Å °0.0582 Å °-0.0414 Å °
Refinement TLS groupSelection details: all

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