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

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Basic information

Entry
Database: PDB / ID: 9iga
TitleBeta-hairpin macrocyclic peptide in complex with STAT1
Components
  • Isoform Alpha of Signal transducer and activator of transcription 1-alpha/beta
  • OPG024 protein
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)
Orthopoxvirus vaccinia
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 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 19, 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: Isoform Alpha of Signal transducer and activator of transcription 1-alpha/beta
C: OPG024 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,5403
Polymers66,4342
Non-polymers1061
Water00
1
A: Isoform Alpha of Signal transducer and activator of transcription 1-alpha/beta
C: OPG024 protein
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)133,0816
Polymers132,8694
Non-polymers2122
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556x,-y,-z+11
Unit cell
Length a, b, c (Å)35.656, 117.272, 130.284
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121
Space group name HallP22ab(z,x,y)
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y+1/2,-z+1/2
#4: -x,-y+1/2,z+1/2

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Components

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


Mass: 64088.586 Da / Num. of mol.: 1 / Mutation: 132-684,delta183-190,H182A,E393A,E394A
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.) Orthopoxvirus vaccinia / 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 modificationN

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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: 2.08 Å3/Da / Density % sol: 40.76 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: Crystallisation conditions: 0.1 M Bis-Tris 5.5 0.2 M Ammonium acetate 25 % w/v PEG 3350 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: 2.8→65.14 Å / Num. obs: 14172 / % possible obs: 100 % / Redundancy: 13.1 % / Biso Wilson estimate: 53.2 Å2 / CC1/2: 1 / Rrim(I) all: 0.451 / Net I/σ(I): 4.1
Reflection shellResolution: 2.8→2.85 Å / Redundancy: 13.3 % / Mean I/σ(I) obs: 0.6 / Num. unique obs: 663 / CC1/2: 0.7 / % possible all: 96.9

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Processing

Software
NameVersionClassification
BUSTERrefinement
PHENIX1.19.2_4158refinement
xia2data reduction
DIALSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→65.14 Å / SU ML: 0.5957 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 35.5
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.3134 681 4.84 %
Rwork0.3076 13400 -
obs0.3078 14081 99.51 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 61 Å2
Refinement stepCycle: LAST / Resolution: 2.8→65.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4194 0 8 0 4202
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01154292
X-RAY DIFFRACTIONf_angle_d1.35015800
X-RAY DIFFRACTIONf_chiral_restr0.0904649
X-RAY DIFFRACTIONf_plane_restr0.0175730
X-RAY DIFFRACTIONf_dihedral_angle_d15.40581619
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-3.020.4591350.42892579X-RAY DIFFRACTION98.44
3.02-3.320.36341450.36492624X-RAY DIFFRACTION99.68
3.32-3.80.30781380.31142642X-RAY DIFFRACTION99.68
3.8-4.790.31131300.26622684X-RAY DIFFRACTION99.86
4.79-65.140.25151330.28512871X-RAY DIFFRACTION99.83

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