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- PDB-8yyv: A dimeric STAT1-DNA complex -

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Basic information

Entry
Database: PDB / ID: 8yyv
TitleA dimeric STAT1-DNA complex
Components
  • DNA (5'-D(P*AP*CP*AP*GP*TP*TP*TP*CP*CP*CP*GP*TP*AP*AP*AP*TP*GP*C)-3')
  • DNA (5'-D(P*TP*GP*CP*AP*TP*TP*TP*AP*CP*GP*GP*GP*AP*AP*AP*CP*TP*G)-3')
  • Signal transducer and activator of transcription 1-alpha/beta
KeywordsIMMUNE SYSTEM / innate immunity
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 / negative regulation of mesenchymal to epithelial transition involved in metanephros morphogenesis / interleukin-27-mediated signaling pathway / 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 / negative regulation of mesenchymal to epithelial transition involved in metanephros morphogenesis / interleukin-27-mediated signaling pathway / CCR5 chemokine receptor binding / Interleukin-9 signaling / Interleukin-21 signaling / interleukin-7-mediated signaling pathway / interleukin-9-mediated signaling pathway / Interleukin-27 signaling / Interleukin-35 Signalling / Signaling by cytosolic FGFR1 fusion mutants / tumor necrosis factor receptor binding / cell surface receptor signaling pathway via STAT / blood circulation / positive regulation of mesenchymal cell proliferation / 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 / response to type II interferon / cell surface receptor signaling pathway via JAK-STAT / type II interferon-mediated signaling pathway / Regulation of IFNG signaling / Growth hormone receptor signaling / Signaling by PDGFRA transmembrane, juxtamembrane and kinase domain mutants / Signaling by PDGFRA extracellular domain mutants / cellular response to interferon-beta / RNA polymerase II core promoter sequence-specific DNA binding / Signaling by CSF3 (G-CSF) / response to mechanical stimulus / response to cAMP / tumor necrosis factor-mediated signaling pathway / negative regulation of canonical NF-kappaB signal transduction / positive regulation of defense response to virus by host / response to nutrient / response to cytokine / Downstream signal transduction / Signaling by phosphorylated juxtamembrane, extracellular and kinase domain KIT mutants / negative regulation of angiogenesis / positive regulation of erythrocyte differentiation / protein phosphatase 2A binding / Turbulent (oscillatory, disturbed) flow shear stress activates signaling by PIEZO1 and integrins in endothelial cells / transcription corepressor binding / RNA polymerase II transcription regulatory region sequence-specific DNA binding / positive regulation of smooth muscle cell proliferation / promoter-specific chromatin binding / Downregulation of SMAD2/3:SMAD4 transcriptional activity / transcription coactivator binding / defense response / Signaling by SCF-KIT / Inactivation of CSF3 (G-CSF) signaling / PKR-mediated signaling / response to hydrogen peroxide / cellular response to type II interferon / ISG15 antiviral mechanism / response to peptide hormone / RNA polymerase II transcription regulator complex / cellular response to insulin stimulus / Signaling by CSF1 (M-CSF) in myeloid cells / Interferon gamma signaling / Regulation of RUNX2 expression and activity / Interferon alpha/beta signaling / positive regulation of nitric oxide biosynthetic process / 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 / defense response to virus / histone binding / DNA-binding transcription factor activity, RNA polymerase II-specific / cadherin binding / RNA polymerase II cis-regulatory region sequence-specific DNA binding / response to xenobiotic stimulus / DNA-binding transcription factor activity / axon / dendrite / regulation of transcription by RNA polymerase II / chromatin / positive regulation of DNA-templated transcription / 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
Similarity search - Function
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 ...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
DNA / DNA (> 10) / Signal transducer and activator of transcription 1-alpha/beta
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.07 Å
AuthorsSugiyama, A. / Minami, M. / Sugita, Y. / Ose, T.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)21H02408 Japan
CitationJournal: Sci Signal / Year: 2025
Title: Structural analysis reveals how tetrameric tyrosine-phosphorylated STAT1 is targeted by the rabies virus P-protein.
Authors: Aoi Sugiyama / Miku Minami / Kaito Ugajin / Satomi Inaba-Inoue / Nana Yabuno / Yuichiro Takekawa / Sun Xiaomei / Shiho Takei / Mina Sasaki / Tomo Nomai / Xinxin Jiang / Shunsuke Kita / ...Authors: Aoi Sugiyama / Miku Minami / Kaito Ugajin / Satomi Inaba-Inoue / Nana Yabuno / Yuichiro Takekawa / Sun Xiaomei / Shiho Takei / Mina Sasaki / Tomo Nomai / Xinxin Jiang / Shunsuke Kita / Katsumi Maenaka / Mika Hirose / Min Yao / Paul R Gooley / Gregory W Moseley / Yukihiko Sugita / Toyoyuki Ose /
Abstract: Signal transducer and activator of transcription (STAT) family members mediate signaling in the Janus kinase (JAK)-STAT pathway and are activated by phosphorylation at a conserved tyrosine residue, ...Signal transducer and activator of transcription (STAT) family members mediate signaling in the Janus kinase (JAK)-STAT pathway and are activated by phosphorylation at a conserved tyrosine residue, resulting in dimerization through reciprocal interactions between the phosphotyrosine and a Src homology 2 (SH2) domain. Tyrosine-phosphorylated STAT (pY-STAT) then translocates to the nucleus to induce the expression of genes encoding antiviral proteins. Although the active and functional forms of STATs are conventionally considered to be dimers, STATs can undergo higher-order oligomerization, which is implicated in regulating transcriptional activity. We present the cryo-electron microscopy (cryo-EM) structure of the tetrameric form of intact pY-STAT1 in complex with DNA, which indicates that interactions between the amino-terminal domains (NTDs) of STAT1 induce oligomerization. The tetrameric structure revealed a compact conformation with a previously uncharacterized binding interface: Two DNA-bound dimers are twofold symmetrically aligned to transform into a tandem DNA-binding model without NTD dimer separation. Moreover, biochemical analyses indicated that the rabies virus P-protein selectively targeted tetrameric pY-STAT1. Combined with data showing which regions contribute to the interaction between pY-STAT1 and the P-protein, we constructed a binding model explaining how P recognizes the pY-STAT1 tetramer. These data provide insight into how pathogenic viruses target signaling pathways that mediate the host immune response.
History
DepositionApr 4, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 26, 2025Provider: 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: DNA (5'-D(P*AP*CP*AP*GP*TP*TP*TP*CP*CP*CP*GP*TP*AP*AP*AP*TP*GP*C)-3')
B: DNA (5'-D(P*TP*GP*CP*AP*TP*TP*TP*AP*CP*GP*GP*GP*AP*AP*AP*CP*TP*G)-3')


Theoretical massNumber of molelcules
Total (without water)101,7973
Polymers101,7973
Non-polymers00
Water00
1
A: Signal transducer and activator of transcription 1-alpha/beta
C: DNA (5'-D(P*AP*CP*AP*GP*TP*TP*TP*CP*CP*CP*GP*TP*AP*AP*AP*TP*GP*C)-3')
B: DNA (5'-D(P*TP*GP*CP*AP*TP*TP*TP*AP*CP*GP*GP*GP*AP*AP*AP*CP*TP*G)-3')

A: Signal transducer and activator of transcription 1-alpha/beta
C: DNA (5'-D(P*AP*CP*AP*GP*TP*TP*TP*CP*CP*CP*GP*TP*AP*AP*AP*TP*GP*C)-3')
B: DNA (5'-D(P*TP*GP*CP*AP*TP*TP*TP*AP*CP*GP*GP*GP*AP*AP*AP*CP*TP*G)-3')


Theoretical massNumber of molelcules
Total (without water)203,5956
Polymers203,5956
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation1
2


  • Idetical with deposited unit
  • point asymmetric unit
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit in distinct coordinate
  • point asymmetric unit, std point frame
TypeNameSymmetry operationNumber
transform to point frame1
SymmetryPoint symmetry: (Schoenflies symbol: C2 (2 fold cyclic))
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2generate(-1), (-1), (1)224.4, 224.4

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Components

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


Mass: 90766.148 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: signal transducer and activator of transcription / Source: (gene. exp.) Homo sapiens (human) / Gene: STAT1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P42224
#2: DNA chain DNA (5'-D(P*AP*CP*AP*GP*TP*TP*TP*CP*CP*CP*GP*TP*AP*AP*AP*TP*GP*C)-3')


Mass: 5475.567 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: DNA chain DNA (5'-D(P*TP*GP*CP*AP*TP*TP*TP*AP*CP*GP*GP*GP*AP*AP*AP*CP*TP*G)-3')


Mass: 5555.615 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

Component
IDNameTypeEntity IDParent-IDSource
1Dimeric STAT1-DNA complexCOMPLEXall0MULTIPLE SOURCES
2STAT1COMPLEX#11RECOMBINANT
3DNACOMPLEX#2-#31SYNTHETIC
Molecular weightExperimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Escherichia coli BL21(DE3) (bacteria)
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R0.6/1
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 4 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 81000 X / Nominal defocus max: 18000 nm / Nominal defocus min: 800 nm / Cs: 0.032 mm / C2 aperture diameter: 50 µm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)
EM imaging opticsEnergyfilter name: GIF Bioquantum / Energyfilter slit width: 20 eV
Spherical aberration corrector: A Cs corrector (CEOS GmbH, Germany)

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Processing

EM software
IDNameCategoryDetails
1cryoSPARCparticle selection
2SerialEMimage acquisition
4cryoSPARCCTF correction
7UCSF ChimeraXmodel fitting
8Cootmodel fitting
10cryoSPARCinitial Euler assignment
11cryoSPARCfinal Euler assignment
12cryoSPARCclassification
13cryoSPARC3D reconstruction
14PHENIXmodel refinementreal space refinement
15Servalcatmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 4005846
SymmetryPoint symmetry: C2 (2 fold cyclic)
3D reconstructionResolution: 3.07 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 115824 / Algorithm: BACK PROJECTION / Symmetry type: POINT
Atomic model buildingProtocol: AB INITIO MODEL / Space: RECIPROCAL
Atomic model buildingPDB-ID: 1BF5

1bf5


Accession code: 1BF5 / Source name: PDB / Type: experimental model
RefinementResolution: 3.07→3.07 Å / Cor.coef. Fo:Fc: 0.943 / SU B: 7.494 / SU ML: 0.121 / ESU R: 0.135
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflection
Rwork0.26634 --
obs0.26634 211593 100 %
Solvent computationSolvent model: PARAMETERS FOR MASK CACLULATION
Displacement parametersBiso mean: 113.477 Å2
Refinement stepCycle: 1 / Total: 5249
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
ELECTRON MICROSCOPYr_bond_refined_d0.0160.0125475
ELECTRON MICROSCOPYr_bond_other_d00.0164819
ELECTRON MICROSCOPYr_angle_refined_deg2.6891.847504
ELECTRON MICROSCOPYr_angle_other_deg0.9021.75811161
ELECTRON MICROSCOPYr_dihedral_angle_1_deg9.4475.226737
ELECTRON MICROSCOPYr_dihedral_angle_2_deg10.283526
ELECTRON MICROSCOPYr_dihedral_angle_3_deg20.59210862
ELECTRON MICROSCOPYr_dihedral_angle_4_deg
ELECTRON MICROSCOPYr_chiral_restr0.1580.212870
ELECTRON MICROSCOPYr_gen_planes_refined0.0120.025790
ELECTRON MICROSCOPYr_gen_planes_other0.0020.021172
ELECTRON MICROSCOPYr_nbd_refined
ELECTRON MICROSCOPYr_nbd_other
ELECTRON MICROSCOPYr_nbtor_refined
ELECTRON MICROSCOPYr_nbtor_other
ELECTRON MICROSCOPYr_xyhbond_nbd_refined
ELECTRON MICROSCOPYr_xyhbond_nbd_other
ELECTRON MICROSCOPYr_metal_ion_refined
ELECTRON MICROSCOPYr_metal_ion_other
ELECTRON MICROSCOPYr_symmetry_vdw_refined
ELECTRON MICROSCOPYr_symmetry_vdw_other
ELECTRON MICROSCOPYr_symmetry_hbond_refined
ELECTRON MICROSCOPYr_symmetry_hbond_other
ELECTRON MICROSCOPYr_symmetry_metal_ion_refined
ELECTRON MICROSCOPYr_symmetry_metal_ion_other
ELECTRON MICROSCOPYr_mcbond_it18.57410.132209
ELECTRON MICROSCOPYr_mcbond_other18.57410.132209
ELECTRON MICROSCOPYr_mcangle_it27.66518.0692756
ELECTRON MICROSCOPYr_mcangle_other27.6618.0692757
ELECTRON MICROSCOPYr_scbond_it21.24712.1553266
ELECTRON MICROSCOPYr_scbond_other21.24712.1553266
ELECTRON MICROSCOPYr_scangle_it
ELECTRON MICROSCOPYr_scangle_other32.30121.4214749
ELECTRON MICROSCOPYr_long_range_B_refined51.972151.2810351
ELECTRON MICROSCOPYr_long_range_B_other51.971151.2910352
ELECTRON MICROSCOPYr_rigid_bond_restr
ELECTRON MICROSCOPYr_sphericity_free
ELECTRON MICROSCOPYr_sphericity_bonded
LS refinement shellResolution: 3.05→3.129 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0 0 -
Rwork0.892 15592 -
obs--100 %

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