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- PDB-9ifx: Beta-hairpin macrocyclic peptide in complex with STAT1 -

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Basic information

Entry
Database: PDB / ID: 9ifx
TitleBeta-hairpin macrocyclic peptide in complex with STAT1
Components
  • OPG024 protein
  • Signal transducer and activator of transcription 1-alpha/beta
KeywordsTRANSCRIPTION / STAT1 / 018 / poxvirus
Function / homology
Function and homology information


metanephric mesenchymal cell differentiation / negative regulation of metanephric nephron tubule epithelial cell differentiation / negative regulation by virus of viral protein levels in host cell / renal tubule development / ISGF3 complex / response to interferon-beta / metanephric mesenchymal cell proliferation involved in metanephros development / interleukin-27-mediated signaling pathway / negative regulation of mesenchymal to epithelial transition involved in metanephros morphogenesis / CCR5 chemokine receptor binding ...metanephric mesenchymal cell differentiation / negative regulation of metanephric nephron tubule epithelial cell differentiation / negative regulation by virus of viral protein levels in host cell / renal tubule development / ISGF3 complex / response to interferon-beta / metanephric mesenchymal cell proliferation involved in metanephros development / interleukin-27-mediated signaling pathway / negative regulation of mesenchymal to epithelial transition involved in metanephros morphogenesis / CCR5 chemokine receptor binding / Interleukin-9 signaling / Interleukin-21 signaling / interleukin-7-mediated signaling pathway / interleukin-9-mediated signaling pathway / Signaling by cytosolic FGFR1 fusion mutants / tumor necrosis factor receptor binding / Interleukin-27 signaling / Interleukin-35 Signalling / cell surface receptor signaling pathway via STAT / positive regulation of mesenchymal cell proliferation / blood circulation / NOTCH3 Intracellular Domain Regulates Transcription / Interleukin-20 family signaling / Interleukin-6 signaling / type I interferon-mediated signaling pathway / histone acetyltransferase binding / negative regulation of endothelial cell proliferation / ubiquitin-like protein ligase binding / Regulation of IFNA/IFNB signaling / positive regulation of interferon-alpha production / cell surface receptor signaling pathway via JAK-STAT / response to cAMP / type II interferon-mediated signaling pathway / Growth hormone receptor signaling / response to type II interferon / response to mechanical stimulus / Regulation of IFNG signaling / RNA polymerase II core promoter sequence-specific DNA binding / Signaling by PDGFRA transmembrane, juxtamembrane and kinase domain mutants / Signaling by PDGFRA extracellular domain mutants / Signaling by CSF3 (G-CSF) / cellular response to interferon-beta / positive regulation of defense response to virus by host / response to cytokine / response to nutrient / positive regulation of smooth muscle cell proliferation / Downstream signal transduction / positive regulation of erythrocyte differentiation / protein phosphatase 2A binding / Signaling by phosphorylated juxtamembrane, extracellular and kinase domain KIT mutants / negative regulation of angiogenesis / Turbulent (oscillatory, disturbed) flow shear stress activates signaling by PIEZO1 and integrins in endothelial cells / negative regulation of canonical NF-kappaB signal transduction / transcription corepressor binding / tumor necrosis factor-mediated signaling pathway / RNA polymerase II transcription regulatory region sequence-specific DNA binding / promoter-specific chromatin binding / response to hydrogen peroxide / Downregulation of SMAD2/3:SMAD4 transcriptional activity / defense response / Signaling by SCF-KIT / PKR-mediated signaling / Inactivation of CSF3 (G-CSF) signaling / response to peptide hormone / cellular response to type II interferon / RNA polymerase II transcription regulator complex / ISG15 antiviral mechanism / transcription coactivator binding / cellular response to insulin stimulus / Interferon gamma signaling / positive regulation of nitric oxide biosynthetic process / Signaling by CSF1 (M-CSF) in myeloid cells / Regulation of RUNX2 expression and activity / Interferon alpha/beta signaling / Signaling by ALK fusions and activated point mutants / regulation of cell population proliferation / double-stranded DNA binding / Interleukin-4 and Interleukin-13 signaling / regulation of apoptotic process / histone binding / defense response to virus / DNA-binding transcription factor activity, RNA polymerase II-specific / cadherin binding / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / response to xenobiotic stimulus / axon / dendrite / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / chromatin / nucleolus / perinuclear region of cytoplasm / SARS-CoV-2 activates/modulates innate and adaptive immune responses / enzyme binding / negative regulation of transcription by RNA polymerase II / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / protein-containing complex / nucleoplasm
Similarity search - Function
Orthopoxvirus C10L / Orthopoxvirus C10L protein / Signal transducer and activation of transcription 1, TAZ2 binding domain, C-terminal / STAT1, SH2 domain / STAT1, C-terminal domain superfamily / STAT1 TAZ2 binding domain / STAT transcription factor, DNA-binding, N-terminal / STAT transcription factor, protein interaction / STAT transcription factor, all-alpha domain / STAT transcription factor, DNA-binding ...Orthopoxvirus C10L / Orthopoxvirus C10L protein / Signal transducer and activation of transcription 1, TAZ2 binding domain, C-terminal / STAT1, SH2 domain / STAT1, C-terminal domain superfamily / STAT1 TAZ2 binding domain / STAT transcription factor, DNA-binding, N-terminal / STAT transcription factor, protein interaction / STAT transcription factor, all-alpha domain / STAT transcription factor, DNA-binding / : / STAT transcription factor, coiled-coil domain / STAT protein, DNA binding domain / STAT protein, protein interaction domain / Signal transducer and activator of transcription, linker domain / STAT protein, protein interaction domain / STAT transcription factor, N-terminal domain superfamily / Transcription factor STAT / STAT transcription factor, coiled coil / p53-like transcription factor, DNA-binding / SH2 domain / Src homology 2 (SH2) domain profile. / SH2 domain / SH2 domain superfamily
Similarity search - Domain/homology
ORTHO-XYLENE / OPG024 protein / Signal transducer and activator of transcription 1-alpha/beta
Similarity search - Component
Biological speciesHomo sapiens (human)
Vaccinia virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.64 Å
AuthorsPantelejevs, T.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
European Union (EU)RRF grant No.01/OSI/PA RRF project No. 5.2.1.1.i.0/2/24/I/CFLA/001European Union
CitationJournal: Acs Chem.Biol. / Year: 2026
Title: Consequences of Peptide Macrocyclization Revealed by Virus-Inspired beta-Hairpin Mimetics.
Authors: Bula, A.L. / Bobrovs, R. / Arsenyan, P. / Pantelejevs, T.
History
DepositionFeb 18, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 18, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Signal transducer and activator of transcription 1-alpha/beta
C: OPG024 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,7023
Polymers65,5952
Non-polymers1061
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1400 Å2
ΔGint-2 kcal/mol
Surface area25710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)161.135, 161.135, 38.478
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number77
Space group name H-MP42
Space group name HallP4c
Symmetry operation#1: x,y,z
#2: -y,x,z+1/2
#3: y,-x,z+1/2
#4: -x,-y,z

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Components

#1: Protein Signal transducer and activator of transcription 1-alpha/beta / Transcription factor ISGF-3 components p91/p84


Mass: 63249.660 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: STAT1 / Production host: Escherichia coli (E. coli) / References: UniProt: P42224
#2: Protein/peptide OPG024 protein


Mass: 2345.679 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Vaccinia virus / References: UniProt: P17356
#3: Chemical ChemComp-OXE / ORTHO-XYLENE


Mass: 106.165 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H10 / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
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: 3.81 Å3/Da / Density % sol: 67.7 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: Crystallisation condition: 4% v/v TacsimateTM pH 5.0 12% w/v Polyethylene glycol 3,350 Protein:peptide complex: 5 mg /ml 20 mM Tris pH 8.0, 300 mM NaCl

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9537 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Feb 9, 2025
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 3.64→113.94 Å / Num. obs: 10899 / % possible obs: 93.97 % / Redundancy: 10.6 % / Biso Wilson estimate: 116.8 Å2 / CC1/2: 1 / Net I/σ(I): 5.7
Reflection shellResolution: 3.64→3.71 Å / Num. unique obs: 1090 / CC1/2: 0.2

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
autoPROCdata reduction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.64→72.06 Å / SU ML: 0.446 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.7874
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2712 528 4.85 %
Rwork0.2293 10366 -
obs0.2313 10894 94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 117.13 Å2
Refinement stepCycle: LAST / Resolution: 3.64→72.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4457 0 8 0 4465
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01174561
X-RAY DIFFRACTIONf_angle_d1.37476164
X-RAY DIFFRACTIONf_chiral_restr0.1002685
X-RAY DIFFRACTIONf_plane_restr0.0175782
X-RAY DIFFRACTIONf_dihedral_angle_d14.60361725
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.64-4.010.36541470.30062563X-RAY DIFFRACTION95.59
4.01-4.590.30471350.232594X-RAY DIFFRACTION95.62
4.59-5.780.27291120.24152630X-RAY DIFFRACTION94.98
5.78-72.060.22381340.20092579X-RAY DIFFRACTION90.07

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