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- EMDB-14812: Cryo-EM structure of RCMV-E E27 bound to human DDB1 (deltaBPB) an... -

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Basic information

Entry
Database: EMDB / ID: EMD-14812
TitleCryo-EM structure of RCMV-E E27 bound to human DDB1 (deltaBPB) and full-length rat STAT2
Map dataDDB1 deltaBPB/E27/STAT2 FL main map
Sample
  • Complex: Ternary complex of RCMV-E E27 with human DDB1 (deltaBPB) and rat STAT2
    • Complex: DNA damage-binding protein 1
      • Protein or peptide: DNA damage-binding protein 1
    • Complex: E27
      • Protein or peptide: B27a
    • Complex: Signal transducer and activator of transcription
      • Protein or peptide: Signal transducer and activator of transcription
  • Ligand: ZINC ION
KeywordsInterferon / ubiquitin-proteasome system / Cullin-RING ubiquitin ligases (CRL) / DDB1 / DCAFs / viral DCAF (vDCAF) / cytomegalovirus / STAT2 / IRF9 / VIRUS
Function / homology
Function and homology information


ISGF3 complex / positive regulation by virus of viral protein levels in host cell / epigenetic programming in the zygotic pronuclei / spindle assembly involved in female meiosis / Cul4-RING E3 ubiquitin ligase complex / UV-damage excision repair / biological process involved in interaction with symbiont / regulation of mitotic cell cycle phase transition / WD40-repeat domain binding / negative regulation of type I interferon-mediated signaling pathway ...ISGF3 complex / positive regulation by virus of viral protein levels in host cell / epigenetic programming in the zygotic pronuclei / spindle assembly involved in female meiosis / Cul4-RING E3 ubiquitin ligase complex / UV-damage excision repair / biological process involved in interaction with symbiont / regulation of mitotic cell cycle phase transition / WD40-repeat domain binding / negative regulation of type I interferon-mediated signaling pathway / Cul4A-RING E3 ubiquitin ligase complex / type I interferon-mediated signaling pathway / Cul4B-RING E3 ubiquitin ligase complex / ubiquitin ligase complex scaffold activity / regulation of mitochondrial fission / negative regulation of reproductive process / negative regulation of developmental process / ubiquitin-like protein ligase binding / cullin family protein binding / viral release from host cell / cell surface receptor signaling pathway via JAK-STAT / ectopic germ cell programmed cell death / positive regulation of viral genome replication / proteasomal protein catabolic process / positive regulation of gluconeogenesis / nucleotide-excision repair / Recognition of DNA damage by PCNA-containing replication complex / defense response / regulation of circadian rhythm / DNA Damage Recognition in GG-NER / Dual Incision in GG-NER / Transcription-Coupled Nucleotide Excision Repair (TC-NER) / response to peptide hormone / Formation of TC-NER Pre-Incision Complex / Wnt signaling pathway / Formation of Incision Complex in GG-NER / Dual incision in TC-NER / positive regulation of protein catabolic process / Gap-filling DNA repair synthesis and ligation in TC-NER / cellular response to UV / rhythmic process / regulation of cell population proliferation / site of double-strand break / Neddylation / ubiquitin-dependent protein catabolic process / protein-macromolecule adaptor activity / defense response to virus / proteasome-mediated ubiquitin-dependent protein catabolic process / damaged DNA binding / DNA-binding transcription factor activity, RNA polymerase II-specific / chromosome, telomeric region / protein ubiquitination / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / DNA repair / apoptotic process / DNA damage response / regulation of transcription by RNA polymerase II / protein-containing complex binding / negative regulation of apoptotic process / nucleolus / positive regulation of transcription by RNA polymerase II / protein-containing complex / DNA binding / extracellular space / extracellular exosome / nucleoplasm / identical protein binding / nucleus / cytoplasm
Similarity search - Function
U5-like protein, herpesvirus / Herpesvirus U5-like family / Signal transducer and activation of transcription 2, C-terminal / STAT2, SH2 domain / Signal transducer and activator of transcription 2 C terminal / STAT transcription factor, DNA-binding, N-terminal / STAT transcription factor, protein interaction / STAT transcription factor, all-alpha domain / STAT transcription factor, DNA-binding / : ...U5-like protein, herpesvirus / Herpesvirus U5-like family / Signal transducer and activation of transcription 2, C-terminal / STAT2, SH2 domain / Signal transducer and activator of transcription 2 C terminal / 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 / RSE1/DDB1/CPSF1 second beta-propeller / Cleavage/polyadenylation specificity factor, A subunit, C-terminal / Cleavage/polyadenylation specificity factor, A subunit, N-terminal / : / CPSF A subunit region / RSE1/DDB1/CPSF1 first beta-propeller / p53-like transcription factor, DNA-binding / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains / SH2 domain / SH2 domain superfamily / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
B27a / DNA damage-binding protein 1 / Signal transducer and activator of transcription
Similarity search - Component
Biological speciesMurid betaherpesvirus 8 / Homo sapiens (human) / Rattus norvegicus (Norway rat)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.8 Å
AuthorsLauer S / Spahn CMT / Schwefel D
Funding support Germany, 1 items
OrganizationGrant numberCountry
German Research Foundation (DFG)SCHW 1851/1-1 Germany
CitationJournal: EMBO J / Year: 2023
Title: Structural mechanism of CRL4-instructed STAT2 degradation via a novel cytomegaloviral DCAF receptor.
Authors: Vu Thuy Khanh Le-Trilling / Sofia Banchenko / Darius Paydar / Pia Madeleine Leipe / Lukas Binting / Simon Lauer / Andrea Graziadei / Robin Klingen / Christine Gotthold / Jörg Bürger / ...Authors: Vu Thuy Khanh Le-Trilling / Sofia Banchenko / Darius Paydar / Pia Madeleine Leipe / Lukas Binting / Simon Lauer / Andrea Graziadei / Robin Klingen / Christine Gotthold / Jörg Bürger / Thilo Bracht / Barbara Sitek / Robert Jan Lebbink / Anna Malyshkina / Thorsten Mielke / Juri Rappsilber / Christian Mt Spahn / Sebastian Voigt / Mirko Trilling / David Schwefel /
Abstract: Human cytomegalovirus (CMV) is a ubiquitously distributed pathogen whose rodent counterparts such as mouse and rat CMV serve as common infection models. Here, we conducted global proteome profiling ...Human cytomegalovirus (CMV) is a ubiquitously distributed pathogen whose rodent counterparts such as mouse and rat CMV serve as common infection models. Here, we conducted global proteome profiling of rat CMV-infected cells and uncovered a pronounced loss of the transcription factor STAT2, which is crucial for antiviral interferon signalling. Via deletion mutagenesis, we found that the viral protein E27 is required for CMV-induced STAT2 depletion. Cellular and in vitro analyses showed that E27 exploits host-cell Cullin4-RING ubiquitin ligase (CRL4) complexes to induce poly-ubiquitylation and proteasomal degradation of STAT2. Cryo-electron microscopy revealed how E27 mimics molecular surface properties of cellular CRL4 substrate receptors called DCAFs (DDB1- and Cullin4-associated factors), thereby displacing them from the catalytic core of CRL4. Moreover, structural analyses showed that E27 recruits STAT2 through a bipartite binding interface, which partially overlaps with the IRF9 binding site. Structure-based mutations in M27, the murine CMV homologue of E27, impair the interferon-suppressing capacity and virus replication in mouse models, supporting the conserved importance of DCAF mimicry for CMV immune evasion.
History
DepositionApr 21, 2022-
Header (metadata) releaseNov 9, 2022-
Map releaseNov 9, 2022-
UpdateJul 24, 2024-
Current statusJul 24, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_14812.png

Downloads & links

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Map

FileDownload / File: emd_14812.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationDDB1 deltaBPB/E27/STAT2 FL main map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.25 Å/pix.
x 256 pix.
= 320. Å		1.25 Å/pix.
x 256 pix.
= 320. Å		1.25 Å/pix.
x 256 pix.
= 320. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.25 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.2
Minimum - Maximum-0.21429014 - 0.92418355
Average (Standard dev.)0.0000985942 (±0.035682462)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 320.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_14812_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

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Additional map: unsharpened map

Fileemd_14812_additional_1.map
Annotationunsharpened map
Projections & Slices
AxesZYX

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Density Histograms

Histogram

Histogram (log scale)

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Half map: DDB1 deltaBPB/E27/STAT2 FL half map B

Fileemd_14812_half_map_1.map
AnnotationDDB1 deltaBPB/E27/STAT2 FL half map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: DDB1 deltaBPB/E27/STAT2 FL half map A

Fileemd_14812_half_map_2.map
AnnotationDDB1 deltaBPB/E27/STAT2 FL half map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Ternary complex of RCMV-E E27 with human DDB1 (deltaBPB) and rat STAT2

EntireName: Ternary complex of RCMV-E E27 with human DDB1 (deltaBPB) and rat STAT2
Components
  • Complex: Ternary complex of RCMV-E E27 with human DDB1 (deltaBPB) and rat STAT2
    • Complex: DNA damage-binding protein 1
      • Protein or peptide: DNA damage-binding protein 1
    • Complex: E27
      • Protein or peptide: B27a
    • Complex: Signal transducer and activator of transcription
      • Protein or peptide: Signal transducer and activator of transcription
  • Ligand: ZINC ION

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Supramolecule #1: Ternary complex of RCMV-E E27 with human DDB1 (deltaBPB) and rat STAT2

SupramoleculeName: Ternary complex of RCMV-E E27 with human DDB1 (deltaBPB) and rat STAT2
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Murid betaherpesvirus 8
Molecular weightTheoretical: 100 KDa

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Supramolecule #2: DNA damage-binding protein 1

SupramoleculeName: DNA damage-binding protein 1 / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1 / Details: delta396-705 GNGNSG
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #3: E27

SupramoleculeName: E27 / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2
Source (natural)Organism: Murid betaherpesvirus 8

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Supramolecule #4: Signal transducer and activator of transcription

SupramoleculeName: Signal transducer and activator of transcription / type: complex / ID: 4 / Parent: 1 / Macromolecule list: #3
Source (natural)Organism: Rattus norvegicus (Norway rat)

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Macromolecule #1: DNA damage-binding protein 1

MacromoleculeName: DNA damage-binding protein 1 / type: protein_or_peptide / ID: 1
Details: Residues 396-705 from the reference database entry UNP Q16531 have been replaced by a GNGNSG-linker,Residues 396-705 from the reference database entry UNP Q16531 have been replaced by a GNGNSG-linker
Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 93.671461 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: GPGMSYNYVV TAQKPTAVNG CVTGHFTSAE DLNLLIAKNT RLEIYVVTAE GLRPVKEVGM YGKIAVMELF RPKGESKDLL FILTAKYNA CILEYKQSGE SIDIITRAHG NVQDRIGRPS ETGIIGIIDP ECRMIGLRLY DGLFKVIPLD RDNKELKAFN I RLEELHVI ...String:
GPGMSYNYVV TAQKPTAVNG CVTGHFTSAE DLNLLIAKNT RLEIYVVTAE GLRPVKEVGM YGKIAVMELF RPKGESKDLL FILTAKYNA CILEYKQSGE SIDIITRAHG NVQDRIGRPS ETGIIGIIDP ECRMIGLRLY DGLFKVIPLD RDNKELKAFN I RLEELHVI DVKFLYGCQA PTICFVYQDP QGRHVKTYEV SLREKEFNKG PWKQENVEAE ASMVIAVPEP FGGAIIIGQE SI TYHNGDK YLAIAPPIIK QSTIVCHNRV DPNGSRYLLG DMEGRLFMLL LEKEEQMDGT VTLKDLRVEL LGETSIAECL TYL DNGVVF VGSRLGDSQL VKLNVDSNEQ GSYVVAMETF TNLGPIVDMC VVDLERQGQG QLVTCSGAFK EGSLRIIRNG IGIG NGNSG EIQKLHIRTV PLYESPRKIC YQEVSQCFGV LSSRIEVQDT SGGTTALRPS ASTQALSSSV SSSKLFSSST APHET SFGE EVEVHNLLII DQHTFEVLHA HQFLQNEYAL SLVSCKLGKD PNTYFIVGTA MVYPEEAEPK QGRIVVFQYS DGKLQT VAE KEVKGAVYSM VEFNGKLLAS INSTVRLYEW TTEKELRTEC NHYNNIMALY LKTKGDFILV GDLMRSVLLL AYKPMEG NF EEIARDFNPN WMSAVEILDD DNFLGAENAF NLFVCQKDSA ATTDEERQHL QEVGLFHLGE FVNVFCHGSL VMQNLGET S TPTQGSVLFG TVNGMIGLVT SLSESWYNLL LDMQNRLNKV IKSVGKIEHS FWRSFHTERK TEPATGFIDG DLIESFLDI SRPKMQEVVA NLQYDDGSGM KREATADDLI KVVEELTRIH

UniProtKB: DNA damage-binding protein 1, DNA damage-binding protein 1

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Macromolecule #2: B27a

MacromoleculeName: B27a / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Murid betaherpesvirus 8 / Strain: isolate England
Molecular weightTheoretical: 76.341898 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: GPGMDLRDRQ CESDRNEDNG ETERQAIKER PNAMKIVFEL IKDETADPFC RKFILDNLVQ LKDIEQAARF GFAIEPGSED YNRGVRSFI RLKEPYNHVE LKMSYLKNAR FATANGAYGI RGLTPAWDSA IWGLLREVEA VPYSNPFTFP TCERLEGILN R LEYRPEAT ...String:
GPGMDLRDRQ CESDRNEDNG ETERQAIKER PNAMKIVFEL IKDETADPFC RKFILDNLVQ LKDIEQAARF GFAIEPGSED YNRGVRSFI RLKEPYNHVE LKMSYLKNAR FATANGAYGI RGLTPAWDSA IWGLLREVEA VPYSNPFTFP TCERLEGILN R LEYRPEAT DACRTLCRAT VAVQYAISIL YGYDRSASVP RYLRRLIDEY IDLQDRIRRL GIVPVLKISG KDMNIVQNVL PE RVCAQIG IPFTYEACLL DEYYDCIESN IEQMYDLLCM CKECGMRRME RFERVRYNTI GERYPKKKRD RERFFEENYV IIH SHPDLG VLKLPKIRHL NPLQQLMMCR YLSKDLLYDT QFGPSNAFSR AQGVPLPFSA VQETDMNIAY ALYLASNSYF MCFL LRCVR DVLRHEEEAF RKLILRLVNE AVEIIRDDVN SRVWAGADSP VFVCVDPRES GISAEERDLA IARSLEELTF SNELV EGSH FGGFCRDAAR FLDLIDAFHF PKALREHRAR EDLLLHTFKI EKMYDNRPLS AYYGDRLVPY HVLMGGHRRR DGAVVR TGG VNLTDNEIVR GHWRADDMMN ARLRYFDSID SIEMIRNVSI RQETLMFDLD RMYISRSELE SLESDVESDN ESEVLAG GA CALPDRQSSS EVDSMCD

UniProtKB: B27a

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Macromolecule #3: Signal transducer and activator of transcription

MacromoleculeName: Signal transducer and activator of transcription / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Rattus norvegicus (Norway rat)
Molecular weightTheoretical: 97.172953 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: GPGMAQWEML QNLDSPFLDQ LHELYSQSLL PMDVRQHLAA WIEDQNWREA VLGSDHSKAN MLYFNILDQL NQWDHYSLDS DYLLLQHNL RKFNRDIQMF PNGPTQLAEM IFNLLLEEKR ILNQAQRAQE MQPRPAPEAA GESQQQLEIE TRILDLQTAV E ALVRSIRQ ...String:
GPGMAQWEML QNLDSPFLDQ LHELYSQSLL PMDVRQHLAA WIEDQNWREA VLGSDHSKAN MLYFNILDQL NQWDHYSLDS DYLLLQHNL RKFNRDIQMF PNGPTQLAEM IFNLLLEEKR ILNQAQRAQE MQPRPAPEAA GESQQQLEIE TRILDLQTAV E ALVRSIRQ LKDVQDVFSF RYTVLNHKKT SSLDPHQSQQ RQLVQTTANE LDRMRKEVLD ISKALVGRLT TLVDLLLPKL DE WKAQQQK SCIGAPAPEL QLDQLEQWLT AGAKVLFHLR QLLKQLKDMS LMLRYEGDMF GQGVDLQNAQ VTELLQRLLQ RSF VVETQP CMPQTLHRPL ILKTGSKFTV RTRLLVRLQE GNESLKAEVS IDRNSELPGF RKFNILTSNQ KSLTPEEGQR QGLI WDFGF LTLVEQRSVG AGKGSNKGPL PVTEELHIIS AMVEYVYQGL KMKLQTDTLP VVIISNMNQL SIAWASILWF NMLSS TPKD QQFFCKVPKA PWSLLGPALS WQFSSYIGRG LDPEQLGMLR NKLFGKNCKT EDALLSWADF SKRESPPGKI PFWTWL DKI LELVHDHLKD LWNDGRIMGF VSRSEERRLL KKMVSGTFLL RFSETSEGGI TCSWVEHQDD DKVLIYSVQP YTKEVLQ SL PLTEIIRHYQ VLAEENAPEN PLRFLYPRVP RDEAFGCYYQ EKVNLEERRK YLKHRLIVIS NRQADELQQP LELKQDPE S LELDAELMSV MELARDLELQ SMLQVGLDLG VEPKPDPTLS PAPQILLEPD PARALNQLLP EPDLPQDLQQ LNTGEMEIF RNNINIDDVM PYGDPVLAGQ SIIEEAYRSC PSHFDVDGPL IPSED

UniProtKB: Signal transducer and activator of transcription

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Macromolecule #4: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 4 / Number of copies: 1 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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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

Concentration0.13 mg/mL
BufferpH: 7.8
Component:
ConcentrationFormulaName
10.0 mMTris-HClTris Hydrochloride
150.0 mMNaClSodium Chloride
4.0 mMMgCl2Magnesium Chloride
0.5 mMTCEPTCEP
VitrificationCryogen name: ETHANE / Chamber humidity: 99 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV / Details: 45 seconds adsorption 2 seconds blot.

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Electron microscopy

MicroscopeFEI POLARA 300
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Digitization - Frames/image: 1-50 / Number grids imaged: 4 / Number real images: 8069 / Average exposure time: 10.0 sec. / Average electron dose: 62.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Cs: 2.0 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 31000
Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 974291
Startup modelType of model: NONE
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 4.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 3.1) / Number images used: 31976
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0.7)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0.7)
Final 3D classificationNumber classes: 3 / Avg.num./class: 24000 / Software - Name: cryoSPARC (ver. 3.1) / Details: 3D variabiliy analysis, 3 clusters

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Atomic model buiding 1

Initial modelPDB ID:

6zue


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL / Protocol: RIGID BODY FIT / Overall B value: 112
Target criteria: Fast gradient-driven minimization of combined map and restraints target
Output model

PDB-7znn:
Cryo-EM structure of RCMV-E E27 bound to human DDB1 (deltaBPB) and full-length rat STAT2

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