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- PDB-8vl9: Crystal structure of EloBC-VHL-CDO1 complex bound to compound 8 m... -

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Basic information

Entry
Database: PDB / ID: 8vl9
TitleCrystal structure of EloBC-VHL-CDO1 complex bound to compound 8 molecular glue
Components
  • Cysteine dioxygenase type 1
  • Elongin-B
  • Elongin-C
  • von Hippel-Lindau disease tumor suppressor
KeywordsAPOPTOSIS / VHL / CDO1 / VHL-small molecule-CDO1 ternary complex / degradation
Function / homology
Function and homology information


sulfur amino acid biosynthetic process / Degradation of cysteine and homocysteine / taurine biosynthetic process / cysteine dioxygenase / cysteine dioxygenase activity / response to azide / L-cysteine catabolic process / cysteine metabolic process / regulation of cellular response to hypoxia / negative regulation of receptor signaling pathway via JAK-STAT ...sulfur amino acid biosynthetic process / Degradation of cysteine and homocysteine / taurine biosynthetic process / cysteine dioxygenase / cysteine dioxygenase activity / response to azide / L-cysteine catabolic process / cysteine metabolic process / regulation of cellular response to hypoxia / negative regulation of receptor signaling pathway via JAK-STAT / RHOBTB3 ATPase cycle / transcription elongation factor activity / target-directed miRNA degradation / elongin complex / Replication of the SARS-CoV-1 genome / response to glucagon / VCB complex / Cul5-RING ubiquitin ligase complex / intracellular membraneless organelle / Cul2-RING ubiquitin ligase complex / SUMOylation of ubiquitinylation proteins / nickel cation binding / negative regulation of transcription elongation by RNA polymerase II / Pausing and recovery of Tat-mediated HIV elongation / Tat-mediated HIV elongation arrest and recovery / HIV elongation arrest and recovery / Pausing and recovery of HIV elongation / response to cAMP / response to amino acid / negative regulation of signal transduction / Tat-mediated elongation of the HIV-1 transcript / Formation of HIV-1 elongation complex containing HIV-1 Tat / ubiquitin-like ligase-substrate adaptor activity / Formation of HIV elongation complex in the absence of HIV Tat / RNA Polymerase II Transcription Elongation / Formation of RNA Pol II elongation complex / lactation / negative regulation of TORC1 signaling / RNA Polymerase II Pre-transcription Events / protein serine/threonine kinase binding / negative regulation of autophagy / response to glucocorticoid / transcription corepressor binding / TP53 Regulates Transcription of DNA Repair Genes / positive regulation of cell differentiation / transcription initiation at RNA polymerase II promoter / transcription elongation by RNA polymerase II / ferrous iron binding / Vif-mediated degradation of APOBEC3G / Inactivation of CSF3 (G-CSF) signaling / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / Evasion by RSV of host interferon responses / Regulation of expression of SLITs and ROBOs / cell morphogenesis / ubiquitin-protein transferase activity / transcription corepressor activity / Antigen processing: Ubiquitination & Proteasome degradation / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / Neddylation / microtubule cytoskeleton / regulation of gene expression / protein-containing complex assembly / Replication of the SARS-CoV-2 genome / response to ethanol / ubiquitin-dependent protein catabolic process / protein-macromolecule adaptor activity / cellular response to hypoxia / DNA-binding transcription factor binding / amyloid fibril formation / molecular adaptor activity / proteasome-mediated ubiquitin-dependent protein catabolic process / protein stabilization / cilium / protein ubiquitination / inflammatory response / negative regulation of cell population proliferation / negative regulation of gene expression / ubiquitin protein ligase binding / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / negative regulation of apoptotic process / positive regulation of DNA-templated transcription / enzyme binding / endoplasmic reticulum / negative regulation of transcription by RNA polymerase II / mitochondrion / proteolysis / zinc ion binding / nucleoplasm / nucleus / plasma membrane / cytosol
Similarity search - Function
Cysteine dioxygenase type I / Cysteine dioxygenase type I / 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 ...Cysteine dioxygenase type I / Cysteine dioxygenase type I / 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 / S-phase kinase-associated protein 1-like / SKP1 component, POZ domain / Skp1 family, tetramerisation domain / Found in Skp1 protein family / RmlC-like cupin domain superfamily / SKP1/BTB/POZ domain superfamily / RmlC-like jelly roll fold / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily
Similarity search - Domain/homology
: / CITRIC ACID / : / von Hippel-Lindau disease tumor suppressor / Elongin-C / Elongin-B / Cysteine dioxygenase type 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsShu, W. / Ma, X. / Tutter, A. / Buckley, D. / Golosov, A. / Michaud, G.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Nat.Chem.Biol. / Year: 2025
Title: A small-molecule VHL molecular glue degrader for cysteine dioxygenase 1.
Authors: Tutter, A. / Buckley, D. / Golosov, A.A. / Ma, X. / Shu, W. / McKay, D.J.J. / Darsigny, V. / Dovala, D. / Beckwith, R. / Solomon, J. / Rao, P. / Xu, L. / Fazal, A. / Lingel, A. / Wartchow, C. ...Authors: Tutter, A. / Buckley, D. / Golosov, A.A. / Ma, X. / Shu, W. / McKay, D.J.J. / Darsigny, V. / Dovala, D. / Beckwith, R. / Solomon, J. / Rao, P. / Xu, L. / Fazal, A. / Lingel, A. / Wartchow, C. / Cobb, J.S. / Hachey, A. / Tullai, J. / Michaud, G.A.
History
DepositionJan 11, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 13, 2024Provider: repository / Type: Initial release
Revision 1.1Jul 9, 2025Group: Database references / Structure summary / Category: citation / citation_author / pdbx_entry_details
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _pdbx_entry_details.has_protein_modification
Revision 1.2Nov 5, 2025Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: von Hippel-Lindau disease tumor suppressor
B: Elongin-B
C: Elongin-C
D: Cysteine dioxygenase type 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,5047
Polymers65,7644
Non-polymers7403
Water2,162120
1
A: von Hippel-Lindau disease tumor suppressor
D: Cysteine dioxygenase type 1
hetero molecules

B: Elongin-B
C: Elongin-C


Theoretical massNumber of molelcules
Total (without water)66,5047
Polymers65,7644
Non-polymers7403
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555x+1/2,-y+1/2,-z1
Buried area6070 Å2
ΔGint-42 kcal/mol
Surface area26930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)116.657, 177.873, 103.824
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

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Protein , 4 types, 4 molecules ABCD

#1: Protein von Hippel-Lindau disease tumor suppressor / Protein G7 / pVHL


Mass: 18712.328 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: VHL / Production host: Escherichia coli (E. coli) / References: UniProt: P40337
#2: Protein Elongin-B / EloB / Elongin 18 kDa subunit / RNA polymerase II transcription factor SIII subunit B / SIII p18 / ...EloB / Elongin 18 kDa subunit / RNA polymerase II transcription factor SIII subunit B / SIII p18 / Transcription elongation factor B polypeptide 2


Mass: 13147.781 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ELOB, TCEB2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q15370
#3: Protein Elongin-C / EloC / Elongin 15 kDa subunit / RNA polymerase II transcription factor SIII subunit C / SIII p15 / ...EloC / Elongin 15 kDa subunit / RNA polymerase II transcription factor SIII subunit C / SIII p15 / Transcription elongation factor B polypeptide 1


Mass: 10843.420 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ELOC, TCEB1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q15369
#4: Protein Cysteine dioxygenase type 1 / Cysteine dioxygenase type I / CDO / CDO-I


Mass: 23060.955 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CDO1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q16878, cysteine dioxygenase

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Non-polymers , 4 types, 123 molecules

#5: Chemical ChemComp-A1ACI / N-acetyl-3-methyl-L-valyl-(4R)-4-hydroxy-N-{[(4P)-4-(1H-pyrazol-3-yl)naphthalen-1-yl]methyl}-L-prolinamide


Mass: 491.582 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N5O4 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#7: Chemical ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 120 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 4.09 Å3/Da / Density % sol: 69.96 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop
Details: 0.2M SODIUM CITRATE, 0.1M BIS-TRIS-PROPANE PH 6.5, 20% PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1.0001 Å
DetectorType: DECTRIS PILATUS 12M / Detector: PIXEL / Date: Apr 18, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0001 Å / Relative weight: 1
ReflectionResolution: 2.5→48.774 Å / Num. obs: 37748 / % possible obs: 100 % / Redundancy: 19.7 % / CC1/2: 0.997 / Rmerge(I) obs: 0.196 / Rpim(I) all: 0.045 / Χ2: 1.06 / Net I/σ(I): 10.1
Reflection shellResolution: 2.5→2.6 Å / Redundancy: 15 % / Mean I/σ(I) obs: 0.467 / Num. unique obs: 4247 / CC1/2: 0.567 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→48.774 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.29 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.216 1894 5.03 %
Rwork0.184 --
obs0.1855 37685 99.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.5→48.774 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4296 0 50 120 4466
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0034450
X-RAY DIFFRACTIONf_angle_d0.5926036
X-RAY DIFFRACTIONf_dihedral_angle_d9.3922707
X-RAY DIFFRACTIONf_chiral_restr0.042659
X-RAY DIFFRACTIONf_plane_restr0.003808
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5001-2.56260.36241400.32592539X-RAY DIFFRACTION100
2.5626-2.63190.32591470.29132479X-RAY DIFFRACTION100
2.6319-2.70930.29511160.27472573X-RAY DIFFRACTION100
2.7093-2.79680.30391460.25412519X-RAY DIFFRACTION100
2.7968-2.89670.2681320.23292517X-RAY DIFFRACTION100
2.8967-3.01270.23651340.21592532X-RAY DIFFRACTION100
3.0127-3.14980.28151270.20752561X-RAY DIFFRACTION100
3.1498-3.31580.25551460.2012526X-RAY DIFFRACTION100
3.3158-3.52350.21541380.19182531X-RAY DIFFRACTION100
3.5235-3.79540.21661380.17952558X-RAY DIFFRACTION100
3.7954-4.17720.18761170.15982576X-RAY DIFFRACTION100
4.1772-4.78120.15671290.13532587X-RAY DIFFRACTION100
4.7812-6.0220.21021470.16712587X-RAY DIFFRACTION100
6.022-48.7740.18511370.17132706X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.21630.032-0.049-0.0033-0.14320.15850.36310.07610.49870.07820.20780.2109-0.56130.2221-0.00030.6373-0.00210.11560.58080.02270.731669.416555.933416.5612
20.4379-0.04550.29460.484-0.29630.3569-0.108-0.1312-0.17960.05980.4976-0.59630.25420.16680.00580.4624-0.11840.0290.3850.01070.43565.834439.917525.4762
31.1731-0.25950.15250.39680.18630.71520.1075-0.0484-0.0757-0.1847-0.1069-0.3096-0.16340.2371-0.00080.4387-0.0050.08240.40920.01250.458571.494740.26318.1596
40.23580.496-0.23650.5401-0.18010.1833-0.05240.30890.00870.12490.10730.05870.05770.0676-0.00010.41810.03760.06790.37350.01490.456464.395442.024715.842
50.6574-0.46860.55250.2548-0.14670.18550.07540.155-0.0883-0.12050.187-0.2135-0.3133-0.00350.00240.40690.01490.04060.3201-0.00680.337259.537638.699621.4237
60.10640.1384-0.12110.4927-0.28380.0728-0.03730.08580.0555-0.0450.2434-0.4514-0.18290.686300.4870.04220.06470.5651-0.04780.480366.688624.0716-2.5233
70.40520.8063-0.05040.32160.2125-0.0296-0.22320.50270.0111-0.62220.24260.2011-0.47050.7528-0.00080.79870.00260.01610.71960.03920.475463.224537.9771-2.3521
80.18590.1453-0.22860.1276-0.11980.2295-0.2498-0.24-0.0375-0.2365-0.27090.18430.03170.08180.0010.5118-0.07820.00970.4662-0.1070.527341.807513.228812.8017
90.7125-0.2435-0.00150.3325-0.2770.23880.2186-0.1648-0.26690.2467-0.25570.55610.2239-0.5085-0.00020.604-0.0960.12560.5582-0.11190.583834.691612.501213.2113
100.36420.2597-0.10990.7646-0.35280.52480.0272-0.3181-0.21060.7517-0.03380.71760.2199-0.431900.7405-0.12530.13240.6576-0.02040.649534.75124.146916.9093
11-0.0074-0.02410.04720.0675-0.04160.01930.547-0.3326-0.34240.3646-0.46260.1050.02230.3302-0.00180.6037-0.0462-0.02930.44930.00780.508449.092614.60917.3626
120.1541-0.2176-0.14460.55240.09380.1862-0.1997-0.0139-0.42810.2593-0.2170.18350.5756-0.2946-0.0040.6502-0.16580.10330.4936-0.110.70935.97421.17856.3314
130.08520.0970.01940.0622-0.007-0.003-0.395-0.1094-0.7324-0.5230.1518-0.34670.1275-0.3722-0.00350.52750.11870.09510.6378-0.10140.873265.58411.142-4.0176
140.5040.5261-0.13310.7743-0.53510.73320.0760.2425-0.1556-0.112-0.15050.53190.15-0.3223-0.00010.48860.0583-0.02690.4911-0.07490.490339.572521.9707-0.6013
150.09370.1222-0.06920.8117-0.03310.43890.52560.229-0.1737-0.8372-0.49610.5088-0.0886-0.24-0.00010.43690.1019-0.11980.5382-0.09040.659135.493221.6935-7.6102
161.3960.2187-0.29640.3091-0.25530.96450.0526-0.01830.0497-0.0573-0.1397-0.0073-0.0747-0.0157-00.42890.0611-0.02260.3576-0.05860.430352.364922.73334.6449
170.03310.23790.0180.1938-0.20410.33740.3317-0.08830.29310.277-0.16720.0649-0.63790.4840.00410.6128-0.24070.04770.5612-0.02760.499697.761762.249719.0912
181.56070.52350.39450.81060.2650.71340.26240.073-0.105-0.0608-0.1586-0.0811-0.05490.35290.00290.4703-0.08180.04190.59280.02330.535488.318147.970218.2131
190.0250.0410.0132-0.05290.02380.0517-0.0283-0.273-0.34150.48990.1697-0.8670.28760.3706-0.00050.53060.0142-0.11150.96540.19410.914396.161341.355928.3287
200.133-0.06150.09891.0759-0.30110.44820.3745-0.9236-0.3330.6033-0.11450.1435-0.6535-0.17360.0270.5467-0.1499-0.06460.8019-0.04370.515992.949449.818530.327
210.17170.0295-0.20380.0043-0.07890.3691-0.68680.1556-0.3069-0.0150.1014-0.1265-0.4912-0.2913-0.00030.90330.1251-0.1981.48590.09491.1031107.041135.465540.3263
220.14380.1041-0.01540.341-0.02730.1044-0.113-0.70230.69481.26150.1666-0.1095-0.7310.1218-0.01290.8641-0.1196-0.01910.86230.05190.509193.633552.155834.6444
230.65440.8418-0.39060.8514-0.1113-0.05010.1833-0.5858-0.21580.3799-0.0149-0.40010.03340.28250.00010.6059-0.0391-0.08820.91040.09090.609197.03141.36228.9786
240.06-0.01360.13780.4647-0.18770.1986-0.43390.54550.0709-0.98160.3055-0.30090.7485-0.0328-0.00530.7705-0.0980.07640.7339-0.07210.73889.637540.150412.5551
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 61 through 70 )
2X-RAY DIFFRACTION2chain 'A' and (resid 71 through 79 )
3X-RAY DIFFRACTION3chain 'A' and (resid 80 through 112 )
4X-RAY DIFFRACTION4chain 'A' and (resid 113 through 141 )
5X-RAY DIFFRACTION5chain 'A' and (resid 142 through 157 )
6X-RAY DIFFRACTION6chain 'A' and (resid 158 through 177 )
7X-RAY DIFFRACTION7chain 'A' and (resid 178 through 208 )
8X-RAY DIFFRACTION8chain 'B' and (resid 1 through 9 )
9X-RAY DIFFRACTION9chain 'B' and (resid 10 through 35 )
10X-RAY DIFFRACTION10chain 'B' and (resid 36 through 60 )
11X-RAY DIFFRACTION11chain 'B' and (resid 61 through 72 )
12X-RAY DIFFRACTION12chain 'B' and (resid 73 through 94 )
13X-RAY DIFFRACTION13chain 'B' and (resid 95 through 104 )
14X-RAY DIFFRACTION14chain 'C' and (resid 17 through 47 )
15X-RAY DIFFRACTION15chain 'C' and (resid 48 through 66 )
16X-RAY DIFFRACTION16chain 'C' and (resid 67 through 112 )
17X-RAY DIFFRACTION17chain 'D' and (resid 6 through 39 )
18X-RAY DIFFRACTION18chain 'D' and (resid 40 through 77 )
19X-RAY DIFFRACTION19chain 'D' and (resid 78 through 91 )
20X-RAY DIFFRACTION20chain 'D' and (resid 92 through 107 )
21X-RAY DIFFRACTION21chain 'D' and (resid 108 through 118 )
22X-RAY DIFFRACTION22chain 'D' and (resid 119 through 133 )
23X-RAY DIFFRACTION23chain 'D' and (resid 134 through 178 )
24X-RAY DIFFRACTION24chain 'D' and (resid 179 through 190 )

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