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- PDB-3b6y: Crystal Structure of the Second HIN-200 Domain of Interferon-Indu... -

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Basic information

Entry
Database: PDB / ID: 3b6y
TitleCrystal Structure of the Second HIN-200 Domain of Interferon-Inducible Protein 16
ComponentsGamma-interferon-inducible protein Ifi-16
KeywordsPROTEIN BINDING / Transcription factor / OB-fold / Structural Genomics / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG / DNA-binding / Interferon induction / Nucleus / Phosphorylation / Repressor / Transcription regulation
Function / homology
Function and homology information


negative regulation of AIM2 inflammasome complex assembly / negative regulation of cysteine-type endopeptidase activity / STING mediated induction of host immune responses / myeloid cell differentiation / activation of cysteine-type endopeptidase activity / IRF3-mediated induction of type I IFN / negative regulation of gene expression, epigenetic / negative regulation of viral genome replication / negative regulation of DNA binding / monocyte differentiation ...negative regulation of AIM2 inflammasome complex assembly / negative regulation of cysteine-type endopeptidase activity / STING mediated induction of host immune responses / myeloid cell differentiation / activation of cysteine-type endopeptidase activity / IRF3-mediated induction of type I IFN / negative regulation of gene expression, epigenetic / negative regulation of viral genome replication / negative regulation of DNA binding / monocyte differentiation / transcription factor binding / intrinsic apoptotic signaling pathway by p53 class mediator / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / cellular response to interferon-beta / cellular response to glucose starvation / activation of innate immune response / negative regulation of innate immune response / positive regulation of interleukin-1 beta production / regulation of autophagy / positive regulation of cytokine production / cellular response to ionizing radiation / autophagy / double-stranded DNA binding / defense response to virus / nuclear speck / inflammatory response / innate immune response / negative regulation of DNA-templated transcription / nucleolus / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / RNA binding / nucleoplasm / identical protein binding / membrane / nucleus / cytoplasm / 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
Gamma-interferon-inducible protein 16
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.35 Å
AuthorsLiao, J.C.C. / Lam, R. / Ravichandran, M. / Duan, S. / Tempel, W. / Chirgadze, N.Y. / Arrowsmith, C.H. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Crystal Structure Analysis of the Second HIN Domain of IFI16.
Authors: Liao, J.C.C. / Lam, R. / Ravichandran, M. / Duan, S. / Tempel, W. / Chirgadze, N.Y. / Arrowsmith, C.H.
History
DepositionOct 29, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 13, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Aug 30, 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: Gamma-interferon-inducible protein Ifi-16
B: Gamma-interferon-inducible protein Ifi-16
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,4944
Polymers45,3022
Non-polymers1922
Water30617
1
A: Gamma-interferon-inducible protein Ifi-16
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,7472
Polymers22,6511
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Gamma-interferon-inducible protein Ifi-16
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,7472
Polymers22,6511
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)42.999, 92.887, 100.372
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Gamma-interferon-inducible protein Ifi-16 / Interferon-inducible myeloid differentiation transcriptional activator / IFI 16


Mass: 22651.082 Da / Num. of mol.: 2 / Fragment: Second (C-terminal) HIN-200 domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IFI16, IFNGIP1 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): Condon-Plus / References: UniProt: Q16666
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 17 / 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: 2.21 Å3/Da / Density % sol: 44.4 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 30% PEG 4000, 0.2M Ammonium sulfate, 0.1M Sodium cacodylate, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.978 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jun 24, 2007
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 2.35→50 Å / Num. obs: 17421 / % possible obs: 99.9 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 7.2 % / Rmerge(I) obs: 0.066 / Χ2: 1.004 / Net I/σ(I): 12.4
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.35-2.437.30.37917010.8041100
2.43-2.537.30.28317170.8451100
2.53-2.657.40.22417060.9051100
2.65-2.797.30.1717020.9751100
2.79-2.967.30.11517081.0971100
2.96-3.197.30.08417261.1331100
3.19-3.517.30.06417501.0341100
3.51-4.027.20.05717461.1291100
4.02-5.067.10.04917781.1051100
5.06-506.60.04818871.008199.5

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefmac_5.2.0019refinement
PDB_EXTRACT3data extraction
HKL-2000data collection
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2OQ0

2oq0


Resolution: 2.35→42.14 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.9 / SU B: 21.308 / SU ML: 0.236 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.432 / ESU R Free: 0.296 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.292 877 5 %RANDOM
Rwork0.226 ---
all0.229 ---
obs0.229 17368 99.76 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 55.569 Å2
Baniso -1Baniso -2Baniso -3
1--1.67 Å20 Å20 Å2
2---1.14 Å20 Å2
3---2.81 Å2
Refinement stepCycle: LAST / Resolution: 2.35→42.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2938 0 10 17 2965
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0222996
X-RAY DIFFRACTIONr_angle_refined_deg1.4661.9614035
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8435365
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.09224.737133
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.91415567
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.9881514
X-RAY DIFFRACTIONr_chiral_restr0.1040.2465
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022180
X-RAY DIFFRACTIONr_nbd_refined0.1980.21003
X-RAY DIFFRACTIONr_nbtor_refined0.3020.21948
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.130.269
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3430.239
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1680.211
X-RAY DIFFRACTIONr_mcbond_it0.7781.51907
X-RAY DIFFRACTIONr_mcangle_it1.25622990
X-RAY DIFFRACTIONr_scbond_it1.86931224
X-RAY DIFFRACTIONr_scangle_it2.8994.51045
LS refinement shellResolution: 2.35→2.411 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.358 60 -
Rwork0.27 1179 -
all-1239 -
obs--98.02 %
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)
110.9741-0.4762-0.52610.8577-0.45561.92030.0226-0.28170.84070.17260.0068-0.031-0.0323-0.0681-0.0294-0.04840.02430.0133-0.0785-0.0413-0.1064-1.69849.46335.864
29.3876-8.63-2.01558.41432.00440.48050.0409-0.2673-0.22520.14020.0249-0.04970.1787-0.2599-0.06580.0361-0.03860.0367-0.07710.0477-0.0934-8.87934.03434.868
33.15882.63210.63426.25250.640.79850.0024-0.1961-0.54850.0066-0.0491-0.48570.03170.01840.0467-0.05880.02760.1032-0.11990.02240.004510.59828.98236.369
47.8834-0.2289-1.1762.2195-0.58872.3067-0.0438-0.250.31050.0946-0.013-0.02730.02570.04340.0568-0.07330.0040.03190.0028-0.0051-0.193810.18995.30137.264
513.5477-8.5443-3.97888.71931.89061.2835-0.3925-0.5812-0.99770.19020.28320.32380.1827-0.21520.1093-0.1046-0.05360.1135-0.07720.14260.01182.33980.41235.849
65.5337-0.14321.25793.69280.52961.29550.0037-0.2167-0.84650.11670.0956-0.05730.14260.0224-0.0993-0.03190.03530.1805-0.12260.11120.055622.39674.70236.633
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA6 - 8410 - 88
2X-RAY DIFFRACTION2AA85 - 11489 - 118
3X-RAY DIFFRACTION3AA115 - 191119 - 195
4X-RAY DIFFRACTION4BB7 - 8411 - 88
5X-RAY DIFFRACTION5BB85 - 11489 - 118
6X-RAY DIFFRACTION6BB115 - 191119 - 195

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