EMDB-16936: cGAS-Nucleosome in complex with SPSB3-ELOBC (composite structure)

Basic information

Entry

Database: EMDB / ID: EMD-16936

• Title: cGAS-Nucleosome in complex with SPSB3-ELOBC (composite structure)

Sample

• Complex: cGAS-Spsb3-EloBC complex
  • Protein or peptide: x 4 types
• Protein or peptide: x 6 types
• DNA: x 2 types
• Ligand: x 1 types

• Keywords: cGAS / degradation / UPS / IMMUNE SYSTEM

Function / homology

Function:

2',3'-cyclic GMP-AMP synthase activity / cyclic GMP-AMP synthase / paracrine signaling / poly-ADP-D-ribose modification-dependent protein binding / STING mediated induction of host immune responses / regulation of immunoglobulin production / target-directed miRNA degradation / elongin complex / regulation of T cell activation / cGAS/STING signaling pathway / VCB complex / Cul5-RING ubiquitin ligase complex / negative regulation of epithelial to mesenchymal transition / pattern recognition receptor signaling pathway / STAT family protein binding / ubiquitin-dependent protein catabolic process via the C-end degron rule pathway / SCF ubiquitin ligase complex / Cul2-RING ubiquitin ligase complex / negative regulation of cGAS/STING signaling pathway / cellular response to exogenous dsRNA / RSV-host interactions / cytoplasmic pattern recognition receptor signaling pathway / Pausing and recovery of Tat-mediated HIV elongation / Tat-mediated HIV elongation arrest and recovery / ubiquitin-like protein ligase binding / HIV elongation arrest and recovery / Pausing and recovery of HIV elongation / negative regulation of double-strand break repair via homologous recombination / Tat-mediated elongation of the HIV-1 transcript / Formation of HIV-1 elongation complex containing HIV-1 Tat / Formation of HIV elongation complex in the absence of HIV Tat / nucleosome binding / ubiquitin-like ligase-substrate adaptor activity / RNA Polymerase II Transcription Elongation / negative regulation of megakaryocyte differentiation / Formation of RNA Pol II elongation complex / protein localization to CENP-A containing chromatin / positive regulation of defense response to virus by host / Chromatin modifying enzymes / positive regulation of type I interferon production / Replacement of protamines by nucleosomes in the male pronucleus / CENP-A containing nucleosome / phosphatidylinositol-4,5-bisphosphate binding / protein K48-linked ubiquitination / RNA Polymerase II Pre-transcription Events / Packaging Of Telomere Ends / activation of innate immune response / Recognition and association of DNA glycosylase with site containing an affected purine / Cleavage of the damaged purine / Deposition of new CENPA-containing nucleosomes at the centromere / telomere organization / Interleukin-7 signaling / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / RNA Polymerase I Promoter Opening / Inhibition of DNA recombination at telomere / Assembly of the ORC complex at the origin of replication / Meiotic synapsis / SUMOylation of chromatin organization proteins / Regulation of endogenous retroelements by the Human Silencing Hub (HUSH) complex / transcription corepressor binding / DNA methylation / Condensation of Prophase Chromosomes / determination of adult lifespan / Chromatin modifications during the maternal to zygotic transition (MZT) / SIRT1 negatively regulates rRNA expression / HCMV Late Events / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / PRC2 methylates histones and DNA / Regulation of endogenous retroelements by KRAB-ZFP proteins / Defective pyroptosis / TP53 Regulates Transcription of DNA Repair Genes / transcription initiation at RNA polymerase II promoter / HDACs deacetylate histones / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / transcription elongation by RNA polymerase II / molecular condensate scaffold activity / RNA Polymerase I Promoter Escape / Nonhomologous End-Joining (NHEJ) / Transcriptional regulation by small RNAs / HDMs demethylate histones / Formation of the beta-catenin:TCF transactivating complex / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / NoRC negatively regulates rRNA expression / Negative Regulation of CDH1 Gene Transcription / G2/M DNA damage checkpoint / Vif-mediated degradation of APOBEC3G / Inactivation of CSF3 (G-CSF) signaling / PKMTs methylate histone lysines / B-WICH complex positively regulates rRNA expression / DNA Damage/Telomere Stress Induced Senescence / Meiotic recombination / Pre-NOTCH Transcription and Translation / Evasion by RSV of host interferon responses / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / Activation of anterior HOX genes in hindbrain development during early embryogenesis / Transcriptional regulation of granulopoiesis / Metalloprotease DUBs / RMTs methylate histone arginines

Domain/homology:

SPRY domain-containing SOCS box protein 3, SPRY domain / : / SOCS box domain / SOCS box domain profile. / SOCS_box / Mab-21-like, nucleotidyltransferase domain / Mab-21 protein nucleotidyltransferase domain / Mab-21-like / Mab-21-like, HhH/H2TH-like domain / Mab-21 protein HhH/H2TH-like domain / Mab-21 / Elongin-C / Elongin B / S-phase kinase-associated protein 1-like / SKP1 component, POZ domain / Skp1 family, tetramerisation domain / Found in Skp1 protein family / SPRY domain / B30.2/SPRY domain / B30.2/SPRY domain profile. / B30.2/SPRY domain superfamily / Domain in SPla and the RYanodine Receptor. / SPRY domain / SKP1/BTB/POZ domain superfamily / : / Histone H2A conserved site / Histone H2A signature. / Histone H2B signature. / Histone H2B / Histone H2B / Histone H2A, C-terminal domain / C-terminus of histone H2A / Histone 2A / Histone H2A / TATA box binding protein associated factor / TATA box binding protein associated factor (TAF), histone-like fold domain / Histone H4, conserved site / Histone H4 signature. / Histone H4 / Histone H4 / CENP-T/Histone H4, histone fold / Centromere kinetochore component CENP-T histone fold / Histone H3 signature 1. / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 domain / Histone-fold / Ubiquitin family / Concanavalin A-like lectin/glucanase domain superfamily / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily

Component:

Histone H4 / Elongin-C / Elongin-B / SPRY domain-containing SOCS box protein 3 / Histone H3.2 / Cyclic GMP-AMP synthase / Histone H2B type 1-H / Histone H2A type 1-H / Histone H2B type 1-N / Histone H2A type 1-J

• Biological species: Homo sapiens (human)
• Method: single particle reconstruction / cryo EM / Resolution: 3.5 Å
• Authors: Xu PB / Ablasser A

Funding support

European Union, 1 items

Organization	Grant number	Country
European Molecular Biology Organization (EMBO)	ALTF 184-2021	European Union

• Citation: Journal: Nature / Year: 2024; Title: The CRL5-SPSB3 ubiquitin ligase targets nuclear cGAS for degradation.; Authors: Pengbiao Xu / Ying Liu / Chong Liu / Baptiste Guey / Lingyun Li / Pauline Melenec / Jonathan Ricci / Andrea Ablasser / ; Abstract: Cyclic GMP-AMP synthase (cGAS) senses aberrant DNA during infection, cancer and inflammatory disease, and initiates potent innate immune responses through the synthesis of 2'3'-cyclic GMP-AMP (cGAMP). The indiscriminate activity of cGAS towards DNA demands tight regulatory mechanisms that are necessary to maintain cell and tissue homeostasis under normal conditions. Inside the cell nucleus, anchoring to nucleosomes and competition with chromatin architectural proteins jointly prohibit cGAS activation by genomic DNA. However, the fate of nuclear cGAS and its role in cell physiology remains unclear. Here we show that the ubiquitin proteasomal system (UPS) degrades nuclear cGAS in cycling cells. We identify SPSB3 as the cGAS-targeting substrate receptor that associates with the cullin-RING ubiquitin ligase 5 (CRL5) complex to ligate ubiquitin onto nuclear cGAS. A cryo-electron microscopy structure of nucleosome-bound cGAS in a complex with SPSB3 reveals a highly conserved Asn-Asn (NN) minimal degron motif at the C terminus of cGAS that directs SPSB3 recruitment, ubiquitylation and cGAS protein stability. Interference with SPSB3-regulated nuclear cGAS degradation primes cells for type I interferon signalling, conferring heightened protection against infection by DNA viruses. Our research defines protein degradation as a determinant of cGAS regulation in the nucleus and provides structural insights into an element of cGAS that is amenable to therapeutic exploitation.

History

Deposition	Mar 29, 2023	-
Header (metadata) release	Feb 14, 2024	-
Map release	Feb 14, 2024	-
Update	Jul 9, 2025	-
Current status	Jul 9, 2025	Processing site: PDBe / Status: Released

Map

• File: Download / File: emd_16936.map.gz / Format: CCP4 / Size: 91.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
• Voxel size: X=Y=Z: 1.268 Å

Density

Contour Level	By AUTHOR: 6.0
Minimum - Maximum	-13.290867 - 37.819077
Average (Standard dev.)	-0.016659513 (±0.9286539)

• Symmetry: Space group: 1

Details

EMDB XML:

Map geometry	Axis order X Y Z Origin 0 0 0 Dimensions 288 288 288 Spacing 288 288 288
Cell	A=B=C: 365.184 Å α=β=γ: 90.0 °

Supplemental data

Sample components

Entire : cGAS-Spsb3-EloBC complex

• Entire: Name: cGAS-Spsb3-EloBC complex

Components

• Complex: cGAS-Spsb3-EloBC complex
  • Protein or peptide: Histone H3.2
  • Protein or peptide: Histone H4
  • Protein or peptide: Histone H2A type 1-H
  • Protein or peptide: Histone H2B type 1-H
• Protein or peptide: Histone H2A type 1-J
• Protein or peptide: Histone H2B type 1-N
• Protein or peptide: Cyclic GMP-AMP synthase
• Protein or peptide: SPRY domain-containing SOCS box protein 3
• Protein or peptide: Elongin-C
• Protein or peptide: Elongin-B
• DNA: DNA (145-MER)
• DNA: DNA (145-MER)
• Ligand: ZINC ION

Supramolecule #1: cGAS-Spsb3-EloBC complex

• Supramolecule: Name: cGAS-Spsb3-EloBC complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
• Source (natural): Organism: Homo sapiens (human)

Macromolecule #1: Histone H3.2

• Macromolecule: Name: Histone H3.2 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
• Source (natural): Organism: Homo sapiens (human)
• Molecular weight: Theoretical: 11.546513 KDa
• Recombinant expression: Organism: Escherichia coli BL21(DE3) (bacteria)

Sequence

String:

KPHRYRPGTV ALREIRRYQK STELLIRKLP FQRLVREIAQ DFKTDLRFQS SAVMALQEAS EAYLVGLFED TNLCAIHAKR VTIMPKDIQ LARRIRGER

UniProtKB: Histone H3.2

Macromolecule #2: Histone H4

• Macromolecule: Name: Histone H4 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
• Source (natural): Organism: Homo sapiens (human)
• Molecular weight: Theoretical: 9.180745 KDa
• Recombinant expression: Organism: Escherichia coli BL21(DE3) (bacteria)

Sequence

String:

LRDNIQGITK PAIRRLARRG GVKRISGLIY EETRGVLKVF LENVIRDAVT YTEHAKRKTV TAMDVVYALK RQGRTLYGFG G

UniProtKB: Histone H4

Macromolecule #3: Histone H2A type 1-H

• Macromolecule: Name: Histone H2A type 1-H / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Homo sapiens (human)
• Molecular weight: Theoretical: 11.763755 KDa
• Recombinant expression: Organism: Escherichia coli BL21(DE3) (bacteria)

Sequence

String:

ARAKAKTRSS RAGLQFPVGR VHRLLRKGNY AERVGAGAPV YLAAVLEYLT AEILELAGNA ARDNKKTRII PRHLQLAIRN DEELNKLLG KVTIAQGGVL PNIQAVLLP

UniProtKB: Histone H2A type 1-H

Macromolecule #4: Histone H2B type 1-H

• Macromolecule: Name: Histone H2B type 1-H / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Homo sapiens (human)
• Molecular weight: Theoretical: 10.623174 KDa
• Recombinant expression: Organism: Escherichia coli BL21(DE3) (bacteria)

Sequence

String:

KRSRKESYSV YVYKVLKQVH PDTGISSKAM GIMNSFVNDI FERIAGEASR LAHYNKRSTI TSREIQTAVR LLLPGELAKH AVSEGTKAV TKYTSS

UniProtKB: Histone H2B type 1-H

Macromolecule #5: Histone H2A type 1-J

• Macromolecule: Name: Histone H2A type 1-J / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Homo sapiens (human)
• Molecular weight: Theoretical: 11.66664 KDa
• Recombinant expression: Organism: Escherichia coli BL21(DE3) (bacteria)

Sequence

String:

ARAKAKTRSS RAGLQFPVGR VHRLLRKGNY AERVGAGAPV YLAAVLEYLT AEILELAGNA ARDNKKTRII PRHLQLAIRN DEELNKLLG KVTIAQGGVL PNIQAVLL

UniProtKB: Histone H2A type 1-J

Macromolecule #6: Histone H2B type 1-N

• Macromolecule: Name: Histone H2B type 1-N / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Homo sapiens (human)
• Molecular weight: Theoretical: 10.493994 KDa
• Recombinant expression: Organism: Escherichia coli BL21(DE3) (bacteria)

Sequence

String:

RSRKESYSVY VYKVLKQVHP DTGISSKAMG IMNSFVNDIF ERIAGEASRL AHYNKRSTIT SREIQTAVRL LLPGELAKHA VSEGTKAVT KYTSS

UniProtKB: Histone H2B type 1-N

Macromolecule #9: Cyclic GMP-AMP synthase

• Macromolecule: Name: Cyclic GMP-AMP synthase / type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO / EC number: cyclic GMP-AMP synthase
• Source (natural): Organism: Homo sapiens (human)
• Molecular weight: Theoretical: 42.20259 KDa
• Recombinant expression: Organism: Escherichia coli BL21(DE3) (bacteria)

Sequence

String:

GASKLRAVLE KLKLSRDDIS TAAGMVKGVV DHLLLRLKCD SAFRGVGLLN TGSYYEHVKI SAPNEFDVMF KLEVPRIQLE EYSNTRAYY FVKFKRNPKE NPLSQFLEGE ILSASKMLSK FRKIIAEEIN DIKDTDVIMK AKRGGSPAVT LLISEKISVD I TLALESKS SWPASTQEGL RIQNWLSAKV RKQLRLKPFY LVPKHAKEGN GFQEETWRLS FSHIEKEILN NHGKSKTCCE NK EEKCCRK DCLKLMKYLL EQLKERFKDK AHLDKFSSYH VKTAFFHVCT QNPQDSQWDR KDLGLCFDNC VTYFLQCLRT EKL ENYFIP EFNLFSSNLI DKRSKEFLTK QIEYERNNEF PVFDEF

UniProtKB: Cyclic GMP-AMP synthase

Macromolecule #10: SPRY domain-containing SOCS box protein 3

• Macromolecule: Name: SPRY domain-containing SOCS box protein 3 / type: protein_or_peptide / ID: 10 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Homo sapiens (human)
• Molecular weight: Theoretical: 27.41524 KDa
• Recombinant expression: Organism: Escherichia coli BL21(DE3) (bacteria)

Sequence

String:

SSLHSAHRGR DCRCGEEDEY FDWVWDDLNK SSATLLSCDN RKVSFHMEYS CGTAAIRGTK ELGEGQHFWE IKMTSPVYGT DMMVGIGTS DVDLDKYRHT FCSLLGRDED SWGLSYTGLL HHKGDKTSFS SRFGQGSIIG VHLDTWHGTL TFFKNRKCIG V AATKLQNK RFYPMVCSTA ARSSMKVTRS CASATSLQYL CCHRLRQLRP DSGDTLEGLP LPPGLKQVLH NKLGWVLSMS CS RRKA

UniProtKB: SPRY domain-containing SOCS box protein 3

Macromolecule #11: Elongin-C

• Macromolecule: Name: Elongin-C / type: protein_or_peptide / ID: 11 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Homo sapiens (human)
• Molecular weight: Theoretical: 12.485135 KDa
• Recombinant expression: Organism: Escherichia coli BL21(DE3) (bacteria)

Sequence

String:

MDGEEKTYGG CEGPDAMYVK LISSDGHEFI VKREHALTSG TIKAMLSGPG QFAENETNEV NFREIPSHVL SKVCMYFTYK VRYTNSSTE IPEFPIAPEI ALELLMAANF LDC

UniProtKB: Elongin-C

Macromolecule #12: Elongin-B

• Macromolecule: Name: Elongin-B / type: protein_or_peptide / ID: 12 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Homo sapiens (human)
• Molecular weight: Theoretical: 13.147781 KDa
• Recombinant expression: Organism: Escherichia coli BL21(DE3) (bacteria)

Sequence

String:

MDVFLMIRRH KTTIFTDAKE SSTVFELKRI VEGILKRPPD EQRLYKDDQL LDDGKTLGEC GFTSQTARPQ APATVGLAFR ADDTFEALC IEPFSSPPEL PDVMKPQDSG SSANEQAVQ

UniProtKB: Elongin-B

Macromolecule #7: DNA (145-MER)

• Macromolecule: Name: DNA (145-MER) / type: dna / ID: 7 / Number of copies: 1 / Classification: DNA
• Source (natural): Organism: Homo sapiens (human)
• Molecular weight: Theoretical: 44.552379 KDa

Sequence

String:

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

Macromolecule #8: DNA (145-MER)

• Macromolecule: Name: DNA (145-MER) / type: dna / ID: 8 / Number of copies: 1 / Classification: DNA
• Source (natural): Organism: Homo sapiens (human)
• Molecular weight: Theoretical: 44.961633 KDa

Sequence

String:

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

Macromolecule #13: ZINC ION

• Macromolecule: Name: ZINC ION / type: ligand / ID: 13 / Number of copies: 1 / Formula: ZN
• Molecular weight: Theoretical: 65.409 Da

Experimental details

Structure determination

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

Sample preparation

• Buffer: pH: 7.4 / Details: PBS buffer
• Vitrification: Cryogen name: ETHANE

Electron microscopy

• Microscope: FEI TITAN KRIOS
• Image recording: Film or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 40.0 e/Ų
• Electron beam: Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
• Electron optics: Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.6 µm
• Experimental equipment: Model: Titan Krios / Image courtesy: FEI Company

Image processing

• CTF correction: Type: NONE
• Startup model: Type of model: INSILICO MODEL; In silico model: alphafold2 prediction of individual proteins
• Final reconstruction: Resolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 592494
• Initial angle assignment: Type: MAXIMUM LIKELIHOOD
• Final angle assignment: Type: MAXIMUM LIKELIHOOD