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- EMDB-55233: Local refinement of EloB/EloC/VHL/CV2a/14-3-3zeta/ERa from pose 1 -

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Basic information

Entry
Database: EMDB / ID: EMD-55233
TitleLocal refinement of EloB/EloC/VHL/CV2a/14-3-3zeta/ERa from pose 1
Map data
Sample
  • Complex: Quaternary complex of the VCB (VHL-EloC-EloB) E3 ligase von Hippel-Lindau substrate receptor in complex with small molecule CV2a, 14-3-3zeta and the estrogen receptor alpha
    • Protein or peptide: Elongin-C
    • Protein or peptide: Elongin-B
    • Protein or peptide: Estrogen receptor
    • Protein or peptide: 14-3-3 protein zeta/delta
    • Protein or peptide: von Hippel-Lindau disease tumor suppressor
  • Ligand: ~{N}'-[(2~{S})-3,3-dimethyl-1-[(2~{S},4~{R})-2-[[4-(4-methyl-1,3-thiazol-5-yl)phenyl]methylcarbamoyl]-4-oxidanyl-pyrrolidin-1-yl]-1-oxidanylidene-butan-2-yl]-~{N}-[(2~{S})-2-[(1~{E},3~{R},4~{S},8~{R},9~{R},10~{R},11~{S},14~{S})-14-(methoxymethyl)-3,10-dimethyl-8-[(2~{S},3~{R},4~{S},5~{S},6~{R})-6-(2-methylbut-3-en-2-yloxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]oxy-4,9-bis(oxidanyl)-6-tricyclo[9.3.0.0^{3,7}]tetradeca-1,6-dienyl]propyl]tridecanediamide
KeywordsE3 ligase / von Hippel-Lindau / VHL / 14-3-3 / estrogen receptor alpha / PROTAC / proteolysis targeting chimera / degrader / LIGASE
Function / homology
Function and homology information


synaptic target recognition / Golgi reassembly / NOTCH4 Activation and Transmission of Signal to the Nucleus / regulation of cellular response to hypoxia / establishment of Golgi localization / negative regulation of receptor signaling pathway via JAK-STAT / RHOBTB3 ATPase cycle / respiratory system process / tube formation / regulation of synapse maturation ...synaptic target recognition / Golgi reassembly / NOTCH4 Activation and Transmission of Signal to the Nucleus / regulation of cellular response to hypoxia / establishment of Golgi localization / negative regulation of receptor signaling pathway via JAK-STAT / RHOBTB3 ATPase cycle / respiratory system process / tube formation / regulation of synapse maturation / transcription elongation factor activity / Rap1 signalling / target-directed miRNA degradation / elongin complex / negative regulation of protein localization to nucleus / Replication of the SARS-CoV-1 genome / VCB complex / Cul5-RING ubiquitin ligase complex / regulation of epithelial cell apoptotic process / antral ovarian follicle growth / regulation of branching involved in prostate gland morphogenesis / KSRP (KHSRP) binds and destabilizes mRNA / intracellular membraneless organelle / RUNX1 regulates transcription of genes involved in WNT signaling / RUNX1 regulates estrogen receptor mediated transcription / Cul2-RING ubiquitin ligase complex / GP1b-IX-V activation signalling / regulation of toll-like receptor signaling pathway / nuclear estrogen receptor activity / epithelial cell development / steroid hormone receptor signaling pathway / prostate epithelial cord elongation / epithelial cell proliferation involved in mammary gland duct elongation / SUMOylation of ubiquitinylation proteins / prostate epithelial cord arborization involved in prostate glandular acinus morphogenesis / mammary gland branching involved in pregnancy / uterus development / negative regulation of smooth muscle cell apoptotic process / vagina development / TFIIB-class transcription factor binding / androgen metabolic process / negative regulation of transcription elongation by RNA polymerase II / Interleukin-3, Interleukin-5 and GM-CSF signaling / Regulation of localization of FOXO transcription factors / Pausing and recovery of Tat-mediated HIV elongation / Tat-mediated HIV elongation arrest and recovery / mammary gland alveolus development / HIV elongation arrest and recovery / Pausing and recovery of HIV elongation / cellular response to estrogen stimulus / estrogen response element binding / Activation of BAD and translocation to mitochondria / phosphoserine residue binding / Mitochondrial unfolded protein response (UPRmt) / nuclear receptor-mediated steroid hormone signaling pathway / negative regulation of signal transduction / regulation of ERK1 and ERK2 cascade / Tat-mediated elongation of the HIV-1 transcript / protein targeting / : / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / SARS-CoV-2 targets host intracellular signalling and regulatory pathways / Formation of HIV-1 elongation complex containing HIV-1 Tat / : / Nuclear signaling by ERBB4 / ubiquitin-like ligase-substrate adaptor activity / Formation of HIV elongation complex in the absence of HIV Tat / RNA polymerase II preinitiation complex assembly / cellular response to glucose starvation / RHO GTPases activate PKNs / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / positive regulation of nitric-oxide synthase activity / RNA Polymerase II Transcription Elongation / estrogen receptor signaling pathway / Formation of RNA Pol II elongation complex / protein localization to chromatin / steroid binding / 14-3-3 protein binding / negative regulation of TORC1 signaling / ERK1 and ERK2 cascade / TFAP2 (AP-2) family regulates transcription of growth factors and their receptors / negative regulation of canonical NF-kappaB signal transduction / RNA Polymerase II Pre-transcription Events / Transcriptional and post-translational regulation of MITF-M expression and activity / protein serine/threonine kinase binding / negative regulation of autophagy / protein sequestering activity / lung development / negative regulation of innate immune response / ESR-mediated signaling / negative regulation of miRNA transcription / TBP-class protein binding / hippocampal mossy fiber to CA3 synapse / nitric-oxide synthase regulator activity / nuclear estrogen receptor binding / transcription corepressor binding / transcription coregulator binding / TP53 Regulates Metabolic Genes / Translocation of SLC2A4 (GLUT4) to the plasma membrane / stem cell differentiation
Similarity search - Function
von Hippel-Lindau disease tumour suppressor, beta/alpha domain / von Hippel-Lindau disease tumour suppressor, alpha domain / von Hippel-Lindau disease tumour suppressor, beta domain / VHL superfamily / von Hippel-Lindau disease tumour suppressor, alpha domain superfamily / von Hippel-Lindau disease tumour suppressor, beta domain superfamily / VHL beta domain / VHL box domain / Elongin-C / Elongin B ...von Hippel-Lindau disease tumour suppressor, beta/alpha domain / von Hippel-Lindau disease tumour suppressor, alpha domain / von Hippel-Lindau disease tumour suppressor, beta domain / VHL superfamily / von Hippel-Lindau disease tumour suppressor, alpha domain superfamily / von Hippel-Lindau disease tumour suppressor, beta domain superfamily / VHL beta domain / VHL box domain / Elongin-C / Elongin B / Oestrogen-type nuclear receptor final C-terminal domain / Oestrogen-type nuclear receptor final C-terminal / Estrogen receptor / : / Oestrogen receptor / S-phase kinase-associated protein 1-like / SKP1 component, POZ domain / Skp1 family, tetramerisation domain / Found in Skp1 protein family / Estrogen receptor/oestrogen-related receptor / 14-3-3 proteins signature 2. / 14-3-3 protein, conserved site / 14-3-3 proteins signature 1. / 14-3-3 protein / 14-3-3 homologues / 14-3-3 domain / 14-3-3 domain superfamily / 14-3-3 protein / : / SKP1/BTB/POZ domain superfamily / Nuclear hormone receptor / Nuclear hormones receptors DNA-binding region signature. / Zinc finger, nuclear hormone receptor-type / Double treble clef zinc finger, C4 type / Nuclear hormone receptors DNA-binding domain profile. / c4 zinc finger in nuclear hormone receptors / Nuclear hormone receptor, ligand-binding domain / Nuclear hormone receptor-like domain superfamily / Ligand-binding domain of nuclear hormone receptor / Nuclear receptor (NR) ligand-binding (LBD) domain profile. / Ligand binding domain of hormone receptors / Zinc finger, NHR/GATA-type / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily
Similarity search - Domain/homology
Estrogen receptor / von Hippel-Lindau disease tumor suppressor / 14-3-3 protein zeta/delta / Elongin-C / Elongin-B
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.3 Å
AuthorsCrowe C / Nakasone MA / Harzing T / Verhoef CJA / Cossar PJ / Ciulli A
Funding supportEuropean Union, United Kingdom, 3 items
OrganizationGrant numberCountry
European Research Council (ERC)ERC-2012-StG-311460 DrugE3CRLsEuropean Union
European Research Council (ERC)875510European Union
Medical Research Council (MRC, United Kingdom)MR/R015791/1 United Kingdom
CitationJournal: Biorxiv / Year: 2025
Title: Induced ubiquitination of the partially disordered Estrogen Receptor alpha protein via a 14-3-3-directed molecular glue-based PROTAC design
Authors: Verhoef CJA / Crowe C / Nakasone MA / DeLaCuadra-Baste A / Harzing T / Span NAS / Sathe G / Iso K / Ottmann C / Brunsveld L / Ciulli A / Cossar PJ
History
DepositionSep 30, 2025-
Header (metadata) releaseDec 3, 2025-
Map releaseDec 3, 2025-
UpdateDec 3, 2025-
Current statusDec 3, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_55233.png

Downloads & links

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Map

FileDownload / File: emd_55233.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 300 pix.
= 248.7 Å		0.83 Å/pix.
x 300 pix.
= 248.7 Å		0.83 Å/pix.
x 300 pix.
= 248.7 Å

Surface

Projections

Slices (1/3)

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.829 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.15
Minimum - Maximum-1.3582987 - 4.6965094
Average (Standard dev.)0.0008858907 (±0.02060351)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 248.7 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: #1

Fileemd_55233_additional_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_55233_half_map_1.map
Projections & Slices
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Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_55233_half_map_2.map
Projections & Slices
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Histogram (log scale)

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Sample components

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Entire : Quaternary complex of the VCB (VHL-EloC-EloB) E3 ligase von Hippe...

EntireName: Quaternary complex of the VCB (VHL-EloC-EloB) E3 ligase von Hippel-Lindau substrate receptor in complex with small molecule CV2a, 14-3-3zeta and the estrogen receptor alpha
Components
  • Complex: Quaternary complex of the VCB (VHL-EloC-EloB) E3 ligase von Hippel-Lindau substrate receptor in complex with small molecule CV2a, 14-3-3zeta and the estrogen receptor alpha
    • Protein or peptide: Elongin-C
    • Protein or peptide: Elongin-B
    • Protein or peptide: Estrogen receptor
    • Protein or peptide: 14-3-3 protein zeta/delta
    • Protein or peptide: von Hippel-Lindau disease tumor suppressor
  • Ligand: ~{N}'-[(2~{S})-3,3-dimethyl-1-[(2~{S},4~{R})-2-[[4-(4-methyl-1,3-thiazol-5-yl)phenyl]methylcarbamoyl]-4-oxidanyl-pyrrolidin-1-yl]-1-oxidanylidene-butan-2-yl]-~{N}-[(2~{S})-2-[(1~{E},3~{R},4~{S},8~{R},9~{R},10~{R},11~{S},14~{S})-14-(methoxymethyl)-3,10-dimethyl-8-[(2~{S},3~{R},4~{S},5~{S},6~{R})-6-(2-methylbut-3-en-2-yloxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]oxy-4,9-bis(oxidanyl)-6-tricyclo[9.3.0.0^{3,7}]tetradeca-1,6-dienyl]propyl]tridecanediamide

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Supramolecule #1: Quaternary complex of the VCB (VHL-EloC-EloB) E3 ligase von Hippe...

SupramoleculeName: Quaternary complex of the VCB (VHL-EloC-EloB) E3 ligase von Hippel-Lindau substrate receptor in complex with small molecule CV2a, 14-3-3zeta and the estrogen receptor alpha
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#5
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Elongin-C

MacromoleculeName: Elongin-C / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 10.974616 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MMYVKLISSD GHEFIVKREH ALTSGTIKAM LSGPGQFAEN ETNEVNFREI PSHVLSKVCM YFTYKVRYTN SSTEIPEFPI APEIALELL MAANFLDC

UniProtKB: Elongin-C

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Macromolecule #2: Elongin-B

MacromoleculeName: Elongin-B / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 11.748406 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MDVFLMIRRH KTTIFTDAKE SSTVFELKRI VEGILKRPPD EQRLYKDDQL LDDGKTLGEC GFTSQTARPQ APATVGLAFR ADDTFEALC IEPFSSPPEL PDVMK

UniProtKB: Elongin-B

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Macromolecule #3: Estrogen receptor

MacromoleculeName: Estrogen receptor / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 45.511188 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MGHHHHHHGG SDSEVNQEAK PEVKPEVKPE THINLKVSDG SSEIFFKIKK TTPLRRLMEA FAKRQGKEMD SLRFLYDGIR IQADQTPED LDMEDNDIIE AHREQIGGKK NALALSLTAD QMVSALLDAE PPILYSEYDP TRPFSEASMM GLLTNLADRE L VHMINWAK ...String:
MGHHHHHHGG SDSEVNQEAK PEVKPEVKPE THINLKVSDG SSEIFFKIKK TTPLRRLMEA FAKRQGKEMD SLRFLYDGIR IQADQTPED LDMEDNDIIE AHREQIGGKK NALALSLTAD QMVSALLDAE PPILYSEYDP TRPFSEASMM GLLTNLADRE L VHMINWAK RVPGFVDLTL HDQVHLLECA WLEILMIGLV WRSMEHPGKL LFAPNLLLDR NQGKCVEGMV EIFDMLLATS SR FRMMNLQ GEEFVCLKSI ILLNSGVYTF LSSTLKSLEE KDHIHRVLDK ITDTLIHLMA KAGLTLQQQH QRLAQLLLIL SHI RHMSNK GMEHLYSMKC KNVVPLYDLL LEMLDAHRLH APTSRGGASV EETDQSHLAT AGSTSSHSLQ KYYITGEAEG RRA (TPO)V

UniProtKB: Estrogen receptor

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Macromolecule #4: 14-3-3 protein zeta/delta

MacromoleculeName: 14-3-3 protein zeta/delta / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 28.819236 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MDKNELVQKA KLAEQAERYD DMAACMKSVT EQGAELSNEE RNLLSVAYKN VVGARRSSWR VVSSIEQKTE GAEKKQQMAR EYREKIETE LRDICNDVLS LLEKFLIPNA SQAESKVFYL KMKGDYYRYL AEVAAGDDKK GIVDQSQQAY QEAFEISKKE M QPTHPIRL ...String:
MDKNELVQKA KLAEQAERYD DMAACMKSVT EQGAELSNEE RNLLSVAYKN VVGARRSSWR VVSSIEQKTE GAEKKQQMAR EYREKIETE LRDICNDVLS LLEKFLIPNA SQAESKVFYL KMKGDYYRYL AEVAAGDDKK GIVDQSQQAY QEAFEISKKE M QPTHPIRL GLALNFSVFY YEILNSPEKA CSLAKTAFDE AIAELDTLSE ESYKDSTLIM QLLRDNLTLW TSDTQGDEAE AG EGGENWS HPQFEK

UniProtKB: 14-3-3 protein zeta/delta

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Macromolecule #5: von Hippel-Lindau disease tumor suppressor

MacromoleculeName: von Hippel-Lindau disease tumor suppressor / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 18.702291 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
GSMEAGRPRP VLRSVNSREP SQVIFCNRSP RVVLPVWLNF DGEPQPYPTL PPGTGRRIHS YRGHLWLFRD AGTHDGLLVN QTELFVPSL NVDGQPIFAN ITLPVYTLKE RCLQVVRSLV KPENYRRLDI VRSLYEDLED HPNVQKDLER LTQERIAHQR M GD

UniProtKB: von Hippel-Lindau disease tumor suppressor

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Macromolecule #6: ~{N}'-[(2~{S})-3,3-dimethyl-1-[(2~{S},4~{R})-2-[[4-(4-methyl-1,3-...

MacromoleculeName: ~{N}'-[(2~{S})-3,3-dimethyl-1-[(2~{S},4~{R})-2-[[4-(4-methyl-1,3-thiazol-5-yl)phenyl]methylcarbamoyl]-4-oxidanyl-pyrrolidin-1-yl]-1-oxidanylidene-butan-2-yl]-~{N}-[(2~{S})-2- ...Name: ~{N}'-[(2~{S})-3,3-dimethyl-1-[(2~{S},4~{R})-2-[[4-(4-methyl-1,3-thiazol-5-yl)phenyl]methylcarbamoyl]-4-oxidanyl-pyrrolidin-1-yl]-1-oxidanylidene-butan-2-yl]-~{N}-[(2~{S})-2-[(1~{E},3~{R},4~{S},8~{R},9~{R},10~{R},11~{S},14~{S})-14-(methoxymethyl)-3,10-dimethyl-8-[(2~{S},3~{R},4~{S},5~{S},6~{R})-6-(2-methylbut-3-en-2-yloxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]oxy-4,9-bis(oxidanyl)-6-tricyclo[9.3.0.0^{3,7}]tetradeca-1,6-dienyl]propyl]tridecanediamide
type: ligand / ID: 6 / Number of copies: 1 / Formula: A1JQT
Molecular weightTheoretical: 1.234625 KDa

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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
Component:
ConcentrationFormulaName
20.0 mMHEPESHEPES
100.0 mMNaClsodium chloride
0.5 mMTCEPTCEP
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 400 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 33.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.7 µm / Nominal defocus min: 1.2 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: cryoSPARC / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 4.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 140642
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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