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- PDB-9hyp: CRYSTAL STRUCTURE OF THE SMARCA2-VCB-COMPLEX WITH PROTAC P5 -

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Entry
Database: PDB / ID: 9hyp
TitleCRYSTAL STRUCTURE OF THE SMARCA2-VCB-COMPLEX WITH PROTAC P5
Components
  • Elongin-B
  • Elongin-C
  • Probable global transcription activator SNF2L2
  • von Hippel-Lindau disease tumor suppressor
KeywordsLIGASE / Bromodomain / Complex / 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: 2.2 Å
AuthorsRoy, M.J.
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

Downloads & links

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Assembly

Deposited unit
A: Probable global transcription activator SNF2L2
B: Elongin-B
C: Elongin-C
D: von Hippel-Lindau disease tumor suppressor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,8595
Polymers55,8064
Non-polymers1,0531
Water1,08160
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5730 Å2
ΔGint-41 kcal/mol
Surface area22650 Å2
Unit cell
Length a, b, c (Å)46.624, 81.585, 58.117
Angle α, β, γ (deg.)90, 97.75, 90
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 4 types, 4 molecules ABCD

#1: Protein 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: 14380.542 Da / Num. of mol.: 1
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
#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: 11748.406 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: 10974.616 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 von Hippel-Lindau disease tumor suppressor / Protein G7 / pVHL


Mass: 18702.291 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

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Non-polymers , 2 types, 61 molecules

#5: Chemical ChemComp-A1IYM / (2~{S},4~{R})-~{N}-[[2-[4-[4-(4-bromanyl-7-cyclopentyl-5-oxidanylidene-6~{H}-benzimidazolo[1,2-a]quinazolin-9-yl)piperidin-1-yl]butoxy]-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: 1053.111 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C54H65BrFN8O6S / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 60 / 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: 1.96 Å3/Da / Density % sol: 37.33 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 28% PEG 3350 0.2 M potassium thiocyanate 0.1 M Bis-Tris Propane pH 7.5
PH range: 7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.96859 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 1, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96859 Å / Relative weight: 1
ReflectionResolution: 2.2→46.2 Å / Num. obs: 21865 / % possible obs: 99.4 % / Redundancy: 2.9 % / Rrim(I) all: 0.102 / Net I/σ(I): 9.3
Reflection shellResolution: 2.2→2.279 Å / Num. unique obs: 999 / Rrim(I) all: 0.603

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Processing

Software
NameVersionClassification
BUSTER2.10.2refinement
XDSdata reduction
XSCALEdata scaling
BUSTERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→47.05 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.912 / SU R Cruickshank DPI: 0.341 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.313 / SU Rfree Blow DPI: 0.221 / SU Rfree Cruickshank DPI: 0.229
RfactorNum. reflection% reflectionSelection details
Rfree0.254 1094 -RANDOM
Rwork0.212 ---
obs0.215 21863 99.5 %-
Displacement parametersBiso mean: 47.92 Å2
Baniso -1Baniso -2Baniso -3
1-3.5763 Å20 Å2-0.1128 Å2
2--1.7869 Å20 Å2
3----5.3632 Å2
Refine analyzeLuzzati coordinate error obs: 0.33 Å
Refinement stepCycle: LAST / Resolution: 2.2→47.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3537 0 71 60 3668
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.013773HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.055208HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1282SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes86HARMONIC2
X-RAY DIFFRACTIONt_gen_planes591HARMONIC5
X-RAY DIFFRACTIONt_it3773HARMONIC20
X-RAY DIFFRACTIONt_chiral_improper_torsion492SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact4280SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion2.84
X-RAY DIFFRACTIONt_other_torsion18.34
LS refinement shellResolution: 2.2→2.31 Å
RfactorNum. reflection% reflection
Rfree0.33 140 -
Rwork0.296 --
obs0.297 2792 96.41 %
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)
15.741-0.08180.37885.32180.12161.96490.00930.4217-0.20070.4217-0.12830.0364-0.20070.03640.11890.104-0.07660.0276-0.06910.0428-0.3071-39.645813.2673-12.7739
21.3631.3077-0.72151.5148-1.34531.68320.02680.3142-0.12820.3142-0.0535-0.0699-0.1282-0.06990.02670.0339-0.0207-0.07790.03990.0165-0.15946.3809-11.405338.912
32.66370.3257-0.27411.9328-0.33812.27990.0679-0.06590.1927-0.0659-0.07790.16980.19270.16980.01-0.0012-0.0122-0.02770.05120.0056-0.172510.2506-6.176123.2368
42.85670.86540.89841.04280.24871.1753-0.0818-0.15080.0879-0.15080.1036-0.0350.0879-0.035-0.0218-0.0143-0.0616-0.00520.1248-0.0005-0.2293-10.18461.88126.8272
50.091-1.3036-0.33650-0.77780.0652-0.0065-0.0833-0.0355-0.08330.05860.0207-0.03550.0207-0.05210.0315-0.0973-0.06860.11050.0751-0.1173-26.52077.7169-1.4819
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }
3X-RAY DIFFRACTION3{ C|* }
4X-RAY DIFFRACTION4{ D|* }

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