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- PDB-9hyn: CRYSTAL STRUCTURE OF THE SMARCA2-VCB-COMPLEX WITH PROTAC P1 -

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Entry
Database: PDB / ID: 9hyn
TitleCRYSTAL STRUCTURE OF THE SMARCA2-VCB-COMPLEX WITH PROTAC P1
Components
  • Elongin-B
  • Elongin-C
  • Isoform Short of Probable global transcription activator SNF2L2
  • von Hippel-Lindau disease tumor suppressor
KeywordsLIGASE / Bromodomain / Complex / PROTAC / E3-Ligase
Function / homology
Function and homology information


bBAF complex / regulation of cellular response to hypoxia / npBAF complex / nBAF complex / brahma complex / nucleosome array spacer activity / RHOBTB3 ATPase cycle / negative regulation of receptor signaling pathway via JAK-STAT / GBAF complex / regulation of G0 to G1 transition ...bBAF complex / regulation of cellular response to hypoxia / npBAF complex / nBAF complex / brahma complex / nucleosome array spacer activity / RHOBTB3 ATPase cycle / negative regulation of receptor signaling pathway via JAK-STAT / GBAF complex / regulation of G0 to G1 transition / transcription elongation factor activity / intermediate filament cytoskeleton / target-directed miRNA degradation / elongin complex / regulation of nucleotide-excision repair / Replication of the SARS-CoV-1 genome / VCB complex / Cul5-RING ubiquitin ligase complex / SWI/SNF complex / regulation of mitotic metaphase/anaphase transition / Cul2-RING ubiquitin ligase complex / positive regulation of T cell differentiation / intracellular membraneless organelle / positive regulation of double-strand break repair / SUMOylation of ubiquitinylation proteins / RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known / positive regulation of stem cell population maintenance / Regulation of MITF-M-dependent genes involved in pigmentation / regulation of G1/S transition of mitotic cell cycle / Pausing and recovery of Tat-mediated HIV elongation / Tat-mediated HIV elongation arrest and recovery / negative regulation of transcription elongation by RNA polymerase II / HIV elongation arrest and recovery / Pausing and recovery of HIV elongation / negative regulation of cell differentiation / spermatid development / ATP-dependent activity, acting on DNA / positive regulation of myoblast differentiation / 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 / negative regulation of TORC1 signaling / RNA Polymerase II Pre-transcription Events / negative regulation of autophagy / protein serine/threonine kinase binding / transcription corepressor binding / positive regulation of cell differentiation / TP53 Regulates Transcription of DNA Repair Genes / transcription initiation at RNA polymerase II promoter / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / transcription elongation by RNA polymerase II / Vif-mediated degradation of APOBEC3G / helicase activity / negative regulation of cell growth / Inactivation of CSF3 (G-CSF) signaling / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / Evasion by RSV of host interferon responses / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / Regulation of expression of SLITs and ROBOs / RMTs methylate histone arginines / cell morphogenesis / ubiquitin-protein transferase activity / transcription corepressor activity / Antigen processing: Ubiquitination & Proteasome degradation / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / nervous system development / Neddylation / microtubule cytoskeleton / regulation of gene expression / protein-containing complex assembly / ubiquitin-dependent protein catabolic process / Replication of the SARS-CoV-2 genome / protein-macromolecule adaptor activity / histone binding / molecular adaptor activity / cellular response to hypoxia / DNA-binding transcription factor binding / amyloid fibril formation / proteasome-mediated ubiquitin-dependent protein catabolic process / transcription coactivator activity / hydrolase activity / transcription cis-regulatory region binding / protein stabilization / protein ubiquitination / cilium / chromatin remodeling / negative regulation of cell population proliferation / negative regulation of gene expression / negative regulation of DNA-templated transcription / intracellular membrane-bounded organelle / positive regulation of cell population proliferation / ubiquitin protein ligase binding / chromatin binding / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / negative regulation of apoptotic process
Similarity search - Function
BRK domain / BRK domain / BRK domain superfamily / domain in transcription and CHROMO domain helicases / Glutamine-Leucine-Glutamine, QLQ / QLQ / QLQ domain profile. / QLQ / Snf2-ATP coupling, chromatin remodelling complex / Snf2, ATP coupling domain ...BRK domain / BRK domain / BRK domain superfamily / domain in transcription and CHROMO domain helicases / Glutamine-Leucine-Glutamine, QLQ / QLQ / QLQ domain profile. / QLQ / Snf2-ATP coupling, chromatin remodelling complex / Snf2, ATP coupling domain / Snf2-ATP coupling, chromatin remodelling complex / domain in helicases and associated with SANT domains / 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 / HSA domain / Helicase/SANT-associated domain / HSA domain profile. / Elongin-C / Elongin B / S-phase kinase-associated protein 1-like / SKP1 component, POZ domain / Skp1 family, tetramerisation domain / Found in Skp1 protein family / : / SNF2-like, N-terminal domain superfamily / SNF2, N-terminal / SNF2-related domain / SKP1/BTB/POZ domain superfamily / Helicase conserved C-terminal domain / Bromodomain, conserved site / Bromodomain signature. / Bromodomain / bromo domain / Bromodomain / Bromodomain (BrD) profile. / Bromodomain-like superfamily / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / helicase superfamily c-terminal domain / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain / Ubiquitin-like domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
: / von Hippel-Lindau disease tumor suppressor / SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A member 2 / Elongin-C / Elongin-B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.37 Å
AuthorsBader, G. / Wolkerstorfer, B.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Nat Commun / Year: 2025
Title: Frustration in the protein-protein interface plays a central role in the cooperativity of PROTAC ternary complexes.
Authors: Ma, N. / Bhattacharya, S. / Muk, S. / Jandova, Z. / Schmalhorst, P.S. / Ghosh, S. / Le, K. / Diers, E. / Trainor, N. / Farnaby, W. / Roy, M.J. / Kofink, C. / Greb, P. / Weinstabl, H. / ...Authors: Ma, N. / Bhattacharya, S. / Muk, S. / Jandova, Z. / Schmalhorst, P.S. / Ghosh, S. / Le, K. / Diers, E. / Trainor, N. / Farnaby, W. / Roy, M.J. / Kofink, C. / Greb, P. / Weinstabl, H. / Ciulli, A. / Bader, G. / Sankar, K. / Bergner, A. / Vaidehi, N.
History
DepositionJan 10, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 22, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Elongin-B
B: Elongin-C
C: von Hippel-Lindau disease tumor suppressor
D: Elongin-B
E: Elongin-C
F: von Hippel-Lindau disease tumor suppressor
G: Isoform Short of Probable global transcription activator SNF2L2
H: Isoform Short of Probable global transcription activator SNF2L2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)117,71710
Polymers115,7578
Non-polymers1,9602
Water2,846158
1
A: Elongin-B
B: Elongin-C
C: von Hippel-Lindau disease tumor suppressor
G: Isoform Short of Probable global transcription activator SNF2L2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,8585
Polymers57,8784
Non-polymers9801
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: Elongin-B
E: Elongin-C
F: von Hippel-Lindau disease tumor suppressor
H: Isoform Short of Probable global transcription activator SNF2L2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,8585
Polymers57,8784
Non-polymers9801
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)79.941, 118.226, 122.702
Angle α, β, γ (deg.)90, 90, 90
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 4 types, 8 molecules ADBECFGH

#1: 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: 11748.406 Da / Num. of mol.: 2
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
#2: 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: 11645.476 Da / Num. of mol.: 2
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
#3: Protein von Hippel-Lindau disease tumor suppressor / Protein G7 / pVHL


Mass: 19402.068 Da / Num. of mol.: 2
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
#4: Protein Isoform Short of Probable global transcription activator SNF2L2 / ATP-dependent helicase SMARCA2 / BRG1-associated factor 190B / BAF190B / Protein brahma homolog / ...ATP-dependent helicase SMARCA2 / BRG1-associated factor 190B / BAF190B / Protein brahma homolog / hBRM / SNF2-alpha / SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A member 2


Mass: 15082.383 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SMARCA2, BAF190B, BRM, SNF2A, SNF2L2 / Production host: Escherichia coli (E. coli)
References: UniProt: P51531, Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement

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Non-polymers , 2 types, 160 molecules

#5: Chemical ChemComp-A1IYO / (2~{S},4~{R})-~{N}-[[2-[2-[2-[4-[(6-bromanyl-3-methyl-5-oxidanylidene-4~{H}-imidazo[1,2-a]quinazolin-2-yl)methyl]piperazin-1-yl]ethoxy]ethoxy]-4-(4-methyl-1,3-thiazol-5-yl)phenyl]methyl]-1-[(2~{S})-2-[(1-fluoranylcyclopropyl)carbonylamino]-3,3-dimethyl-butanoyl]-4-oxidanyl-pyrrolidine-2-carboxamide


Mass: 979.976 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C46H58BrFN9O7S / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 158 / 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: 2.5 Å3/Da / Density % sol: 50.89 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1 M K2HPO4 16 % PEG 8000 0.2 M sodium chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.99991 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Dec 5, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99991 Å / Relative weight: 1
ReflectionResolution: 2.366→85.14 Å / Num. obs: 40863 / % possible obs: 94.4 % / Redundancy: 10.3 % / CC1/2: 0.998 / Net I/σ(I): 16.6
Reflection shellResolution: 2.366→2.491 Å / Num. unique obs: 1523 / CC1/2: 0.608

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Processing

Software
NameVersionClassification
BUSTER2.11.7refinement
STARANISOdata scaling
XDSdata reduction
BUSTERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.37→45.01 Å / Cor.coef. Fo:Fc: 0.904 / Cor.coef. Fo:Fc free: 0.895 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.526 / SU Rfree Blow DPI: 0.279
RfactorNum. reflection% reflectionSelection details
Rfree0.262 1981 -RANDOM
Rwork0.246 ---
obs0.247 40856 84.8 %-
Displacement parametersBiso mean: 53.61 Å2
Baniso -1Baniso -2Baniso -3
1-4.4834 Å20 Å20 Å2
2---3.117 Å20 Å2
3----1.3664 Å2
Refine analyzeLuzzati coordinate error obs: 0.43 Å
Refinement stepCycle: LAST / Resolution: 2.37→45.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7333 0 130 158 7621
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.00815141HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.9727488HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d3365SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes2304HARMONIC5
X-RAY DIFFRACTIONt_it15141HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_chiral_improper_torsion982SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact15288SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion2.62
X-RAY DIFFRACTIONt_other_torsion17.29
LS refinement shellResolution: 2.37→2.46 Å
RfactorNum. reflection% reflection
Rfree0.3115 38 -
Rwork0.2533 --
obs0.256 818 15.56 %
Refinement TLS params.

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)
100.5457-0.51891.46530.15722.0652-0.02260.0013-0.0220.0013-0.0029-0.0172-0.022-0.01720.0255-0.0869-0.07550.1061-0.0441-0.020.04847.6064-0.1481-8.5403
22.0166-0.0971-1.14820.1449-0.28481.1178-0.0120.0360.04030.036-0.05530.07910.04030.07910.06730.0037-0.00850.128-0.0544-0.0058-0.00578.2813-12.45734.3316
31.8617-0.7731-2.15252.29980.61711.6916-0.04530.02510.14310.0251-0.06950.04180.14310.04180.11480.1106-0.11090.0535-0.09150.0117-0.1329-14.4727-15.7520.8251
400.98341.61551.5490.9242.0482-0.03280.05350.00890.0535-0.0538-0.01170.0089-0.01170.0866-0.0617-0.05480.03680.07160.0212-0.1006-39.82431.4895-9.1845
51.49980.03470.59610.3331-0.69321.0402-0.02770.0417-0.01380.0417-0.0482-0.106-0.0138-0.1060.0758-0.00130.0921-0.1341-0.0031-0.1148-0.0414-39.990714.23083.1639
60.9045-0.09051.87540.6395-0.42711.6608-0.0439-0.1053-0.0981-0.1053-0.049-0.0062-0.0981-0.00620.09280.05330.0013-0.1483-0.1112-0.0758-0.0122-17.539217.494719.6583
71.33270.5802-0.06150.2682-0.48940.10990.00320.0464-0.00640.04640.007-0.0243-0.0064-0.0243-0.01020.0748-0.14540.1332-0.049-0.0849-0.0444-48.5434-16.18231.4666
82.23571.0558-0.39620.03760.20960.6279-0.00480.0002-0.01680.0002-0.0665-0.0052-0.0168-0.00520.0713-0.0392-0.0693-0.0479-0.04240.05740.031715.587717.869533.1359
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }
3X-RAY DIFFRACTION3{ C|* }
4X-RAY DIFFRACTION4{ D|* }
5X-RAY DIFFRACTION5{ E|* }
6X-RAY DIFFRACTION6{ F|* }
7X-RAY DIFFRACTION7{ G|* }
8X-RAY DIFFRACTION8{ H|* }

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