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- PDB-5yzp: Crystal structure of p204 HINa domain -

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Basic information

Entry
Database: PDB / ID: 5yzp
TitleCrystal structure of p204 HINa domain
ComponentsIfi204
KeywordsIMMUNE SYSTEM / DNA sensor / pattern recognition receptors / type I-IFN / PYHIN family / AIM-2 like receptors
Function / homology
Function and homology information


cellular response to interferon-alpha / nuclear inclusion body / inner ear development / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / cellular response to interferon-beta / positive regulation of osteoblast differentiation / activation of innate immune response / Neutrophil degranulation / transcription coregulator activity / response to bacterium ...cellular response to interferon-alpha / nuclear inclusion body / inner ear development / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / cellular response to interferon-beta / positive regulation of osteoblast differentiation / activation of innate immune response / Neutrophil degranulation / transcription coregulator activity / response to bacterium / double-stranded DNA binding / nuclear speck / innate immune response / nucleolus / regulation of transcription by RNA polymerase II / nucleoplasm / nucleus / cytosol
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
ACETATE ION / Ifi204 / Interferon-activable protein 204
Similarity search - Component
Biological speciesMus musculus domesticus (western European house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.581 Å
AuthorsJin, T.
CitationJournal: Nucleic Acids Res. / Year: 2021
Title: Structural mechanism of DNA recognition by the p204 HIN domain.
Authors: Fan, X. / Jiang, J. / Zhao, D. / Chen, F. / Ma, H. / Smith, P. / Unterholzner, L. / Xiao, T.S. / Jin, T.
History
DepositionDec 15, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 19, 2018Provider: repository / Type: Initial release
Revision 1.1Aug 28, 2019Group: Data collection / Category: reflns / reflns_shell
Item: _reflns.pdbx_Rrim_I_all / _reflns_shell.pdbx_Rrim_I_all
Revision 1.2Mar 10, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.3Nov 22, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ifi204
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,6565
Polymers23,4111
Non-polymers2454
Water3,495194
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area160 Å2
ΔGint-1 kcal/mol
Surface area10720 Å2
Unit cell
Length a, b, c (Å)57.930, 104.210, 90.420
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-634-

HOH

21A-699-

HOH

31A-777-

HOH

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Components

#1: Protein Ifi204


Mass: 23410.787 Da / Num. of mol.: 1 / Fragment: UNP residues 237-438
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus domesticus (western European house mouse)
Gene: Ifi204 / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: A0A1Z3MI45, UniProt: P0DOV2*PLUS
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 194 / 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: 2.89 Å3/Da / Density % sol: 57.44 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 23% PEG4000, 0.2M Ammonium Acetate, 100 mM NaAcO pH 5.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 2, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.58→50 Å / Num. obs: 37551 / % possible obs: 99.3 % / Redundancy: 7.66 % / CC1/2: 0.998 / Rrim(I) all: 0.058 / Net I/σ(I): 20.45
Reflection shellResolution: 1.58→1.68 Å / Redundancy: 7 % / Num. unique obs: 5887 / CC1/2: 0.899 / Rrim(I) all: 0.71 / % possible all: 97.7

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Processing

Software
NameVersionClassification
PHENIX(dev_2481: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2OQ0

2oq0


Resolution: 1.581→44.178 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.09 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2105 1807 4.81 %
Rwork0.1836 --
obs0.1849 37536 99.34 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.581→44.178 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1544 0 16 194 1754
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061633
X-RAY DIFFRACTIONf_angle_d0.8432206
X-RAY DIFFRACTIONf_dihedral_angle_d5.6471358
X-RAY DIFFRACTIONf_chiral_restr0.056250
X-RAY DIFFRACTIONf_plane_restr0.005280
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.581-1.62380.35711490.32822588X-RAY DIFFRACTION96
1.6238-1.67150.30921380.27212725X-RAY DIFFRACTION100
1.6715-1.72550.28371480.23762717X-RAY DIFFRACTION100
1.7255-1.78720.22941410.20532736X-RAY DIFFRACTION100
1.7872-1.85870.21471280.18752757X-RAY DIFFRACTION100
1.8587-1.94330.21481470.18662736X-RAY DIFFRACTION100
1.9433-2.04580.20611350.18162735X-RAY DIFFRACTION100
2.0458-2.17390.20741680.17952713X-RAY DIFFRACTION100
2.1739-2.34180.21071310.18692778X-RAY DIFFRACTION100
2.3418-2.57740.23441130.19762802X-RAY DIFFRACTION100
2.5774-2.95030.24211590.19262761X-RAY DIFFRACTION100
2.9503-3.71680.19191530.16692796X-RAY DIFFRACTION100
3.7168-44.1950.1629970.16532885X-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)
10.3687-0.17930.07540.18050.14280.3216-0.04810.001-0.06350.06890.0857-0.00440.0772-0.013400.21020.0113-0.01820.18170.00370.24356.5019-16.8228-0.8669
20.70490.267-0.0420.7261-0.1125-0.12820.0694-0.11990.11260.0549-0.00040.11040.04210.04530.00010.1992-0.03370.00450.2021-0.00070.2043-5.6657-18.3055-1.9689
30.4219-0.07580.2660.15210.0940.25060.1015-0.40690.11610.2798-0.2920.1443-0.15110.0112-0.00010.2605-0.01740.0170.241-0.04410.2425-3.1487-9.88693.8064
41.475-0.79580.43620.7479-0.59210.5456-0.0991-0.0781-0.02560.15750.1168-0.13560.03380.03120.00010.2351-0.001-0.01080.1988-0.00260.20775.8416-14.75781.7784
50.3001-0.13150.34590.1099-0.22110.352-0.00480.07810.20310.112-0.0130.1479-0.134-0.0147-00.3055-0.04650.01740.26380.01850.2192-0.1415-12.3985-19.6993
60.45170.139-0.570.0464-0.16930.76-0.04420.14920.0837-0.15630.17480.00660.1861-0.2521-00.2532-0.0316-0.02350.28510.07760.2561-12.4635-18.7874-19.4022
70.8019-0.07430.16680.230.06680.1040.01220.46170.2146-0.0360.15410.12090.1065-0.52470.00240.2521-0.03130.02950.38470.07730.2471-19.967-18.8536-18.268
82.2671-0.38940.02210.8273-0.99361.2303-0.08550.3189-0.2331-0.20230.15140.15080.335-0.2803-0.02250.3505-0.0795-0.01780.2869-0.00370.2261-11.4991-23.8561-18.6372
90.56850.029-0.28790.32330.0090.4437-0.00620.05720.2349-0.10120.04410.0502-0.2292-0.32760.00380.31720.01540.00090.28180.03670.2796-14.8193-15.1164-10.3295
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 221 through 236 )
2X-RAY DIFFRACTION2chain 'A' and (resid 237 through 268 )
3X-RAY DIFFRACTION3chain 'A' and (resid 269 through 281 )
4X-RAY DIFFRACTION4chain 'A' and (resid 282 through 315 )
5X-RAY DIFFRACTION5chain 'A' and (resid 316 through 333 )
6X-RAY DIFFRACTION6chain 'A' and (resid 334 through 351 )
7X-RAY DIFFRACTION7chain 'A' and (resid 352 through 384 )
8X-RAY DIFFRACTION8chain 'A' and (resid 385 through 403 )
9X-RAY DIFFRACTION9chain 'A' and (resid 404 through 415 )

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