EMDB-39680: A dimeric STAT1-DNA complex

Basic information

Entry

Database: EMDB / ID: EMD-39680

• Title: A dimeric STAT1-DNA complex
• Map data: map reconstructed with half-maps through "servalcat refine_spa"

Sample

• Complex: Dimeric STAT1-DNA complex
  • Complex: STAT1
    • Protein or peptide: Signal transducer and activator of transcription 1-alpha/beta
  • Complex: DNA
    • DNA: DNA (5'-D(P*AP*CP*AP*GP*TP*TP*TP*CP*CP*CP*GP*TP*AP*AP*AP*TP*GP*C)-3')
    • DNA: DNA (5'-D(P*TP*GP*CP*AP*TP*TP*TP*AP*CP*GP*GP*GP*AP*AP*AP*CP*TP*G)-3')

• Keywords: innate immunity / IMMUNE SYSTEM

Function / homology

Function:

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

Domain/homology:

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

Component:

Signal transducer and activator of transcription 1-alpha/beta

• Biological species: Homo sapiens (human)
• Method: single particle reconstruction / cryo EM / Resolution: 3.07 Å
• Authors: Sugiyama A / Minami M / Sugita Y / Ose T

Funding support

Japan, 1 items

Organization	Grant number	Country
Japan Society for the Promotion of Science (JSPS)	21H02408	Japan

• Citation: Journal: 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 / 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, 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

Deposition	Apr 4, 2024	-
Header (metadata) release	Mar 26, 2025	-
Map release	Mar 26, 2025	-
Update	Mar 26, 2025	-
Current status	Mar 26, 2025	Processing site: PDBj / Status: Released

Map

• File: Download / File: emd_39680.map.gz / Format: CCP4 / Size: 6.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
• Annotation: map reconstructed with half-maps through "servalcat refine_spa"
• Voxel size: X=Y=Z: 1.32 Å

Density

Contour Level	By AUTHOR: 1.5
Minimum - Maximum	-6.0625157 - 7.667187
Average (Standard dev.)	-0.00036973233 (±0.43230602)

• Symmetry: Space group: 1

Details

EMDB XML:

Map geometry	Axis order X Y Z Origin 44 4 34 Dimensions 82 162 122 Spacing 162 82 122
Cell	A: 213.84001 Å / B: 108.240005 Å / C: 161.04001 Å α=β=γ: 90.0 °

Supplemental data

Mask #1

• File: emd_39680_msk_1.map

Half map: A half map

• File: emd_39680_half_map_1.map
• Annotation: A half map

Half map: A half map

• File: emd_39680_half_map_2.map
• Annotation: A half map

Sample components

Entire : Dimeric STAT1-DNA complex

• Entire: Name: Dimeric STAT1-DNA complex

Components

• Complex: Dimeric STAT1-DNA complex
  • Complex: STAT1
    • Protein or peptide: Signal transducer and activator of transcription 1-alpha/beta
  • Complex: DNA
    • DNA: DNA (5'-D(P*AP*CP*AP*GP*TP*TP*TP*CP*CP*CP*GP*TP*AP*AP*AP*TP*GP*C)-3')
    • DNA: DNA (5'-D(P*TP*GP*CP*AP*TP*TP*TP*AP*CP*GP*GP*GP*AP*AP*AP*CP*TP*G)-3')

Supramolecule #1: Dimeric STAT1-DNA complex

• Supramolecule: Name: Dimeric STAT1-DNA complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
• Source (natural): Organism: Homo sapiens (human)

Supramolecule #2: STAT1

• Supramolecule: Name: STAT1 / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1

Supramolecule #3: DNA

• Supramolecule: Name: DNA / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2-#3

Macromolecule #1: Signal transducer and activator of transcription 1-alpha/beta

• Macromolecule: Name: Signal transducer and activator of transcription 1-alpha/beta; type: protein_or_peptide / ID: 1 / Details: signal transducer and activator of transcription / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Homo sapiens (human)
• Molecular weight: Theoretical: 90.766148 KDa
• Recombinant expression: Organism: Escherichia coli BL21(DE3) (bacteria)

Sequence

String:

MNHKHHHHHH HHHHSSGENL YFQGHMMSQW YELQQLDSKF LEQVHQLYDD SFPMEIRQYL AQWLEKQDWE HAANDVSFAT IRFHDLLSQ LDDQYSRFSL ENNFLLQHNI RKSKRNLQDN FQEDPIQMSM IIYSCLKEER KILENAQRFN QAQSGNIQST V MLDKQKEL DSKVRNVKDK VMCIEHEIKS LEDLQDEYDF KCKTLQNREH ETNGVAKSDQ KQEQLLLKKM YLMLDNKRKE VV HKIIELL NVTELTQNAL INDELVEWKR RQQSACIGGP PNACLDQLQN WFTIVAESLQ QVRQQLKKLE ELEQKYTYEH DPI TKNKQV LWDRTFSLFQ QLIQSSFVVE RQPCMPTHPQ RPLVLKTGVQ FTVKLRLLVK LQELNYNLKV KVLFDKDVNE RNTV KGFRK FNILGTHTKV MNMEESTNGS LAAEFRHLQL KEQKNAGTRT NEGPLIVTEE LHSLSFETQL CQPGLVIDLE TTSLP VVVI SNVSQLPSGW ASILWYNMLV AEPRNLSFFL TPPCARWAQL SEVLSWQFSS VTKRGLNVDQ LNMLGEKLLG PNASPD GLI PWTRFCKENI NDKNFPFWLW IESILELIKK HLLPLWNDGC IMGFISKERE RALLKDQQPG TFLLRFSESS REGAITF TW VERSQNGGEP DFHAVEPYTK KELSAVTFPD IIRNYKVMAA ENIPENPLKY LYPNIDKDHA FGKYYSRPKE APEPMELD G PKGTG(PTR)IKTE LISVSEVHPS RLQTTDNLLP MSPEEFDEVS RIVGSVEFDS MMNTV

UniProtKB: Signal transducer and activator of transcription 1-alpha/beta

Macromolecule #2: DNA (5'-D(P*AP*CP*AP*GP*TP*TP*TP*CP*CP*CP*GP*TP*AP*AP*AP*TP*GP*C)-3')

• Macromolecule: Name: DNA (5'-D(P*AP*CP*AP*GP*TP*TP*TP*CP*CP*CP*GP*TP*AP*AP*AP*TP*GP*C)-3'); type: dna / ID: 2 / Number of copies: 1 / Classification: DNA
• Source (natural): Organism: Homo sapiens (human)
• Molecular weight: Theoretical: 5.475567 KDa

Sequence

String:

(DA)(DC)(DA)(DG)(DT)(DT)(DT)(DC)(DC)(DC) (DG)(DT)(DA)(DA)(DA)(DT)(DG)(DC)

Macromolecule #3: DNA (5'-D(P*TP*GP*CP*AP*TP*TP*TP*AP*CP*GP*GP*GP*AP*AP*AP*CP*TP*G)-3')

• Macromolecule: Name: DNA (5'-D(P*TP*GP*CP*AP*TP*TP*TP*AP*CP*GP*GP*GP*AP*AP*AP*CP*TP*G)-3'); type: dna / ID: 3 / Number of copies: 1 / Classification: DNA
• Source (natural): Organism: Homo sapiens (human)
• Molecular weight: Theoretical: 5.555615 KDa

Sequence

String:

(DT)(DG)(DC)(DA)(DT)(DT)(DT)(DA)(DC)(DG) (DG)(DG)(DA)(DA)(DA)(DC)(DT)(DG)

Experimental details

Structure determination

• Method: cryo EM
• Processing: single particle reconstruction
• Aggregation state: particle

Sample preparation

• Buffer: pH: 7.4
• Grid: Model: Quantifoil R0.6/1 / Material: GOLD / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Pretreatment - Atmosphere: AIR
• Vitrification: Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 4 K / Instrument: FEI VITROBOT MARK IV

Electron microscopy

• Microscope: FEI TITAN KRIOS
• Specialist optics: Spherical aberration corrector: A Cs corrector (CEOS GmbH, Germany); Energy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
• Image recording: Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 50.0 e/Ų
• Electron beam: Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
• Electron optics: C2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 0.032 mm / Nominal defocus max: 18.0 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 81000
• Sample stage: Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
• Experimental equipment: Model: Titan Krios / Image courtesy: FEI Company

Image processing

• Particle selection: Number selected: 4005846
• Startup model: Type of model: INSILICO MODEL
• Final reconstruction: Applied symmetry - Point group: C₂ (2 fold cyclic) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 3.07 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 115824
• Initial angle assignment: Type: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
• Final angle assignment: Type: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
• Final 3D classification: Software - Name: cryoSPARC

Atomic model buiding 1

Initial model

PDB ID:

1bf5

Chain - Source name: PDB / Chain - Initial model type: experimental model

• Refinement: Space: RECIPROCAL / Protocol: AB INITIO MODEL

Output model

PDB-8yyv:
A dimeric STAT1-DNA complex