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- PDB-4qgu: protein domain complex with ssDNA -

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Basic information

Entry
Database: PDB / ID: 4qgu
Titleprotein domain complex with ssDNA
Components
  • DNA (5'-D(P*AP*GP*GP*CP*CP*GP*GP*CP*GP*TP*GP*A)-3')
  • Gamma-interferon-inducible protein 16
KeywordsTRANSCRIPTION/DNA / OB FOLD / DNA BINDING / CYTOSOLIC DNA SENSOR / CYTOSOLIC / IMMUNE RESPONSE-DNA COMPLEX / TRANSCRIPTION ACTIVATOR-DNA COMPLEX / TRANSCRIPTION-DNA complex
Function / homology
Function and homology information


negative regulation of AIM2 inflammasome complex assembly / negative regulation of DNA binding / myeloid cell differentiation / STING mediated induction of host immune responses / IRF3-mediated induction of type I IFN / negative regulation of viral genome replication / transcription factor binding / negative regulation of gene expression, epigenetic / intrinsic apoptotic signaling pathway by p53 class mediator / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator ...negative regulation of AIM2 inflammasome complex assembly / negative regulation of DNA binding / myeloid cell differentiation / STING mediated induction of host immune responses / IRF3-mediated induction of type I IFN / negative regulation of viral genome replication / transcription factor binding / negative regulation of gene expression, epigenetic / intrinsic apoptotic signaling pathway by p53 class mediator / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / monocyte differentiation / cellular response to glucose starvation / cellular response to interferon-beta / activation of innate immune response / negative regulation of innate immune response / positive regulation of cytokine production / positive regulation of interleukin-1 beta production / regulation of autophagy / cellular response to ionizing radiation / autophagy / regulation of inflammatory response / 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 / membrane / identical protein binding / nucleus / cytoplasm / cytosol
Similarity search - Function
HIN-200/IF120x / HIN-200/IF120x domain / HIN-200 A and B domains profile. / HIN-200 family / DAPIN domain profile. / DAPIN domain / PAAD/DAPIN/Pyrin domain / PAAD/DAPIN/Pyrin domain / Nucleic acid-binding proteins / Death-like domain superfamily ...HIN-200/IF120x / HIN-200/IF120x domain / HIN-200 A and B domains profile. / HIN-200 family / DAPIN domain profile. / DAPIN domain / PAAD/DAPIN/Pyrin domain / PAAD/DAPIN/Pyrin domain / Nucleic acid-binding proteins / Death-like domain superfamily / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Nucleic acid-binding, OB-fold / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
DNA / DNA (> 10) / Gamma-interferon-inducible protein 16
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.545 Å
AuthorsNi, X. / Ru, H. / Zhao, L. / Shaw, N. / Ding, W. / Songying, O. / Liu, Z.-J.
CitationJournal: J Mol Cell Biol / Year: 2016
Title: New insights into the structural basis of DNA recognition by HINa and HINb domains of IFI16.
Authors: Ni, X. / Ru, H. / Ma, F. / Zhao, L. / Shaw, N. / Feng, Y. / Ding, W. / Gong, W. / Wang, Q. / Ouyang, S. / Cheng, G. / Liu, Z.J.
History
DepositionMay 25, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 17, 2015Provider: repository / Type: Initial release
Revision 1.1Jul 20, 2016Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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: Gamma-interferon-inducible protein 16
B: Gamma-interferon-inducible protein 16
C: DNA (5'-D(P*AP*GP*GP*CP*CP*GP*GP*CP*GP*TP*GP*A)-3')
D: DNA (5'-D(P*AP*GP*GP*CP*CP*GP*GP*CP*GP*TP*GP*A)-3')


Theoretical massNumber of molelcules
Total (without water)55,1104
Polymers55,1104
Non-polymers00
Water1,06359
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)85.715, 91.865, 69.978
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11C-101-

HOH

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Components

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


Mass: 23826.699 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IFI16, IFNGIP1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q16666
#2: DNA chain DNA (5'-D(P*AP*GP*GP*CP*CP*GP*GP*CP*GP*TP*GP*A)-3')


Mass: 3728.429 Da / Num. of mol.: 2 / Source method: obtained synthetically
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 59 / 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: 2.5 Å3/Da / Density % sol: 50.79 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 20% (w/v) PEG 3350 and 0.2 M potassium fluoride; 20% (w/v) PEG 3350 and 0.2 M sodium formate; or 20% (w/v) PEG 3350 and 0.2 M lithium acetate dehydrate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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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: Mar 4, 2013
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.545→38.399 Å / Num. all: 18078 / Num. obs: 18078 / % possible obs: 96.47 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASESphasing
PHENIX(phenix.refine: 1.8.4_1496)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.545→38.399 Å / SU ML: 0.4 / σ(F): 1.34 / Phase error: 29.09 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2577 897 4.96 %RANDOM
Rwork0.2377 ---
obs0.2387 18078 96.47 %-
all-18078 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.545→38.399 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3094 455 0 59 3608
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0163657
X-RAY DIFFRACTIONf_angle_d1.5285007
X-RAY DIFFRACTIONf_dihedral_angle_d22.9441432
X-RAY DIFFRACTIONf_chiral_restr0.1570
X-RAY DIFFRACTIONf_plane_restr0.008554
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.545-2.70450.45271380.38172468X-RAY DIFFRACTION84
2.7045-2.91320.35121470.31512842X-RAY DIFFRACTION98
2.9132-3.20620.31871620.29862909X-RAY DIFFRACTION100
3.2062-3.66990.26451480.2532913X-RAY DIFFRACTION98
3.6699-4.62240.24251320.21662971X-RAY DIFFRACTION99
4.6224-38.40370.2081700.19573078X-RAY DIFFRACTION99

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