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- EMDB-71877: Insulin receptor bound to S961 -

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Basic information

Entry
Database: EMDB / ID: EMD-71877
TitleInsulin receptor bound to S961
Map data
Sample
  • Complex: Insulin Receptor-A isoform complexed with two S961 molecules.
    • Protein or peptide: Isoform Long of Insulin receptor
    • Protein or peptide: S961 Insulin receptor antagonist
KeywordsAntagonist / receptor tyrosine kinase / MEMBRANE PROTEIN
Function / homology
Function and homology information


regulation of female gonad development / positive regulation of meiotic cell cycle / insulin-like growth factor II binding / positive regulation of developmental growth / insulin receptor complex / insulin-like growth factor I binding / insulin receptor activity / positive regulation of protein-containing complex disassembly / adrenal gland development / dendritic spine maintenance ...regulation of female gonad development / positive regulation of meiotic cell cycle / insulin-like growth factor II binding / positive regulation of developmental growth / insulin receptor complex / insulin-like growth factor I binding / insulin receptor activity / positive regulation of protein-containing complex disassembly / adrenal gland development / dendritic spine maintenance / insulin binding / cargo receptor activity / Signaling by Insulin receptor / PTB domain binding / IRS activation / neuronal cell body membrane / positive regulation of respiratory burst / amyloid-beta clearance / heart morphogenesis / insulin receptor substrate binding / positive regulation of receptor internalization / regulation of embryonic development / positive regulation of glycogen biosynthetic process / Signal attenuation / protein kinase activator activity / phosphatidylinositol 3-kinase binding / transport across blood-brain barrier / Insulin receptor recycling / insulin-like growth factor receptor binding / neuron projection maintenance / positive regulation of mitotic nuclear division / receptor-mediated endocytosis / positive regulation of glycolytic process / Insulin receptor signalling cascade / male gonad development / learning / dendrite membrane / positive regulation of D-glucose import across plasma membrane / receptor protein-tyrosine kinase / memory / caveola / insulin receptor signaling pathway / positive regulation of nitric oxide biosynthetic process / glucose homeostasis / cellular response to insulin stimulus / late endosome / protein autophosphorylation / amyloid-beta binding / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / protein tyrosine kinase activity / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / positive regulation of MAPK cascade / positive regulation of canonical NF-kappaB signal transduction / signaling receptor complex / lysosome / endosome membrane / positive regulation of cell migration / G protein-coupled receptor signaling pathway / external side of plasma membrane / protein domain specific binding / axon / positive regulation of cell population proliferation / symbiont entry into host cell / regulation of DNA-templated transcription / positive regulation of DNA-templated transcription / GTP binding / protein-containing complex binding / extracellular exosome / ATP binding / membrane / identical protein binding / plasma membrane
Similarity search - Function
Insulin receptor, trans-membrane domain / Insulin receptor trans-membrane segment / Tyrosine-protein kinase, insulin-like receptor / Tyrosine-protein kinase, receptor class II, conserved site / Receptor tyrosine kinase class II signature. / Receptor L-domain / Furin-like cysteine-rich domain / Receptor L-domain superfamily / Furin-like cysteine rich region / Receptor L domain ...Insulin receptor, trans-membrane domain / Insulin receptor trans-membrane segment / Tyrosine-protein kinase, insulin-like receptor / Tyrosine-protein kinase, receptor class II, conserved site / Receptor tyrosine kinase class II signature. / Receptor L-domain / Furin-like cysteine-rich domain / Receptor L-domain superfamily / Furin-like cysteine rich region / Receptor L domain / Furin-like repeat / Furin-like repeats / Growth factor receptor cysteine-rich domain superfamily / Fibronectin type 3 domain / : / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / Tyrosine-protein kinase, catalytic domain / Tyrosine kinase, catalytic domain / Tyrosine protein kinases specific active-site signature. / Tyrosine-protein kinase, active site / Protein tyrosine and serine/threonine kinase / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Immunoglobulin-like fold / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
Similarity search - Domain/homology
Biological speciesHomo sapiens (human) / Phage #D (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.68 Å
AuthorsVogel A / Blakely A / Hill CP
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)R01DK127268 United States
CitationJournal: Proc Natl Acad Sci U S A / Year: 2026
Title: Structural basis of transcription-coupled RNA damage by incorporation of oxidized ribonucleotides.
Authors: Peini Hou / Chanjoo Lee / Jenny Chong / Juntaek Oh / Dong Wang /
Abstract: Oxidative stress induces damage to DNA, RNA, and nucleotide pools. Unlike well-studied DNA damage, the formation of RNA damage and the impact of an oxidized ribonucleotide pool on transcription ...Oxidative stress induces damage to DNA, RNA, and nucleotide pools. Unlike well-studied DNA damage, the formation of RNA damage and the impact of an oxidized ribonucleotide pool on transcription fidelity are poorly understood. Here, we investigate the structural basis of transcription-coupled RNA damage and the effect of 8-oxo-guanosine triphosphate (8-oxo-rGTP) on RNA polymerase II (Pol II) transcription fidelity control steps. We revealed that the incorporation efficiency of 8-oxo-rGTP opposite a dC template is comparable to that of GTP. In contrast, the incorporation efficiency of 8-oxo-rGTP opposite a dA template is ~150-fold more efficient than that of GTP. For the extension step, Pol II extends substantially faster from a 3'-8-oxo-rG:dC base pair than from a 3'-8-oxo-rG:dA base pair. For the proofreading step, strikingly, Pol II EC with 3'-8-oxo-rG:dA base pair is much more resistant to backtracking and proofreading than Pol II EC with 3'-8-oxo-rG:dC base pair. Using X-ray crystallography, we revealed that 8-oxo-rGTP adopts different prechemistry binding sites depending on whether it is paired with a dC or a dA template. Upon incorporation, the nucleobase of 8-oxo-rG flips to the -conformation to form a Hoogsteen pair with a dA template, whereas it remains in the -conformation to form a Watson-Crick pair with a dC template. Collectively, our work demonstrates that nucleotide-pool oxidation can directly affect Pol II fidelity control steps and elongation dynamics and induce RNA damage in a transcription-coupled manner.
History
DepositionJul 31, 2025-
Header (metadata) releaseJun 10, 2026-
Map releaseJun 10, 2026-
UpdateJun 24, 2026-
Current statusJun 24, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_71877.png

Downloads & links

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Map

FileDownload / File: emd_71877.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 320 pix.
= 339.2 Å		1.06 Å/pix.
x 320 pix.
= 339.2 Å		1.06 Å/pix.
x 320 pix.
= 339.2 Å

Surface

Projections

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.06 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0942
Minimum - Maximum-1.2527809 - 1.6309668
Average (Standard dev.)-0.00054153946 (±0.02122834)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 339.19998 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_71877_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

Histogram (log scale)

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Half map: #1

Fileemd_71877_half_map_2.map
Projections & Slices
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Histogram (log scale)

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Sample components

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Entire : Insulin Receptor-A isoform complexed with two S961 molecules.

EntireName: Insulin Receptor-A isoform complexed with two S961 molecules.
Components
  • Complex: Insulin Receptor-A isoform complexed with two S961 molecules.
    • Protein or peptide: Isoform Long of Insulin receptor
    • Protein or peptide: S961 Insulin receptor antagonist

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Supramolecule #1: Insulin Receptor-A isoform complexed with two S961 molecules.

SupramoleculeName: Insulin Receptor-A isoform complexed with two S961 molecules.
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Isoform Long of Insulin receptor

MacromoleculeName: Isoform Long of Insulin receptor / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO / EC number: receptor protein-tyrosine kinase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 156.081453 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: HLYPGEVCPG MDIRNNLTRL HELENCSVIE GHLQILLMFK TRPEDFRDLS FPKLIMITDY LLLFRVYGLE SLKDLFPNLT VIRGSRLFF NYALVIFEMV HLKELGLYNL MNITRGSVRI EKNNELCYLA TIDWSRILDS VEDNYIVLNK DDNEECGDIC P GTAKGKTN ...String:
HLYPGEVCPG MDIRNNLTRL HELENCSVIE GHLQILLMFK TRPEDFRDLS FPKLIMITDY LLLFRVYGLE SLKDLFPNLT VIRGSRLFF NYALVIFEMV HLKELGLYNL MNITRGSVRI EKNNELCYLA TIDWSRILDS VEDNYIVLNK DDNEECGDIC P GTAKGKTN CPATVINGQF VERCWTHSHC QKVCPTICKS HGCTAEGLCC HSECLGNCSQ PDDPTKCVAC RNFYLDGRCV ET CPPPYYH FQDWRCVNFS FCQDLHHKCK NSRRQGCHQY VIHNNKCIPE CPSGYTMNSS NLLCTPCLGP CPKVCHLLEG EKT IDSVTS AQELRGCTVI NGSLIINIRG GNNLAAELEA NLGLIEEISG YLKIRRSYAL VSLSFFRKLR LIRGETLEIG NYSF YALDN QNLRQLWDWS KHNLTITQGK LFFHYNPKLC LSEIHKMEEV SGTKGRQERN DIALKTNGDQ ASCENELLKF SYIRT SFDK ILLRWEPYWP PDFRDLLGFM LFYKEAPYQN VTEFDGQDAC GSNSWTVVDI DPPLRSNDPK SQSHPGWLMR GLKPWT QYA IFVKTLVTFS DERRTYGAKS DIIYVQTDAT NPSVPLDPIS VSNSSSQIIL KWKPPSDPNG NITHYLVFWE RQAEDSE LF ELDYCLKGLK LPSRTWSPPF ESEDSQKHNQ SEYEDSAGEC CSCPKTDSQI LKELEESSFR KTFEDYLHNV VFVPRKTS S GTGAEDPRPS RKRRSLGDVG NVTVAVPTVA AFPNTSSTSV PTSPEEHRPF EKVVNKESLV ISGLRHFTGY RIELQACNQ DTPEERCSVA AYVSARTMPE AKADDIVGPV THEIFENNVV HLMWQEPKEP NGLIVLYEVS YRRYGDEELH LCVSRKHFAL ERGCRLRGL SPGNYSVRIR ATSLAGNGSW TEPTYFYVTD YLDVPSNIAK IIIGPLIFVF LFSVVIGSIY LFLRKRQPDG P LGPLYASS NPEYLSASDV FPCSVYVPDE WEVSREKITL LRELGQGSFG MVYEGNARDI IKGEAETRVA VKTVNESASL RE RIEFLNE ASVMKGFTCH HVVRLLGVVS KGQPTLVVME LMAHGDLKSY LRSLRPEAEN NPGRPPPTLQ EMIQMAAEIA DGM AYLNAK KFVHRDLAAR NCMVAHDFTV KIGDFGMTRD IYETDYYRKG GKGLLPVRWM APESLKDGVF TTSSDMWSFG VVLW EITSL AEQPYQGLSN EQVLKFVMDG GYLDQPDNCP ERVTDLMRMC WQFNPKMRPT FLEIVNLLKD DLHPSFPEVS FFHSE ENKA PESEELEMEF EDMENVPLDR SSHCQREEAG GRDGGSSLGF KRSYEEHIPY THMNGGKKNG RILTLPRSNP SDYKDD DDK DYKDDDDK

UniProtKB: Insulin receptor

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Macromolecule #2: S961 Insulin receptor antagonist

MacromoleculeName: S961 Insulin receptor antagonist / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Phage #D (virus)
Molecular weightTheoretical: 4.806093 KDa
SequenceString:
GSLDESFYDW FERQLGGGSG GSSLEEEWAQ IQCEVWGRGC PSY

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.2 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: NONE
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

7sl1

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.68 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 378182
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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