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- PDB-6hax: Crystal structure of PROTAC 2 in complex with the bromodomain of ... -

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Basic information

Entry
Database: PDB / ID: 6hax
TitleCrystal structure of PROTAC 2 in complex with the bromodomain of human SMARCA2 and pVHL:ElonginC:ElonginB
Components
  • Elongin-B
  • Elongin-C
  • Probable global transcription activator SNF2L2
  • von Hippel-Lindau disease tumor suppressor
KeywordsGENE REGULATION / bromodomain / E3 Ubiquitin Protein Ligase
Function / homology
Function and homology information


bBAF complex / npBAF complex / brahma complex / nBAF complex / regulation of cellular response to hypoxia / GBAF complex / regulation of G0 to G1 transition / RHOBTB3 ATPase cycle / negative regulation of receptor signaling pathway via JAK-STAT / transcription elongation factor activity ...bBAF complex / npBAF complex / brahma complex / nBAF complex / regulation of cellular response to hypoxia / GBAF complex / regulation of G0 to G1 transition / RHOBTB3 ATPase cycle / negative regulation of receptor signaling pathway via JAK-STAT / transcription elongation factor activity / regulation of nucleotide-excision repair / target-directed miRNA degradation / elongin complex / VCB complex / SWI/SNF complex / ATP-dependent chromatin remodeler activity / regulation of mitotic metaphase/anaphase transition / Replication of the SARS-CoV-1 genome / Cul5-RING ubiquitin ligase complex / positive regulation of double-strand break repair / positive regulation of T cell differentiation / intermediate filament cytoskeleton / Cul2-RING ubiquitin ligase complex / positive regulation of stem cell population maintenance / intracellular non-membrane-bounded organelle / SUMOylation of ubiquitinylation proteins / RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known / negative regulation of transcription elongation by RNA polymerase II / spermatid development / regulation of G1/S transition of mitotic cell cycle / negative regulation of cell differentiation / 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 / ubiquitin-like ligase-substrate adaptor activity / Tat-mediated elongation of the HIV-1 transcript / Formation of HIV-1 elongation complex containing HIV-1 Tat / positive regulation of myoblast differentiation / ATP-dependent activity, acting on DNA / Formation of HIV elongation complex in the absence of HIV Tat / negative regulation of signal transduction / 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 / transcription corepressor binding / helicase activity / transcription elongation by RNA polymerase II / transcription initiation at RNA polymerase II promoter / positive regulation of cell differentiation / TP53 Regulates Transcription of DNA Repair Genes / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / Vif-mediated degradation of APOBEC3G / cell morphogenesis / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / Inactivation of CSF3 (G-CSF) signaling / negative regulation of cell growth / RMTs methylate histone arginines / Regulation of expression of SLITs and ROBOs / ubiquitin-protein transferase activity / transcription corepressor activity / protein-macromolecule adaptor activity / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / Antigen processing: Ubiquitination & Proteasome degradation / Neddylation / nervous system development / Replication of the SARS-CoV-2 genome / histone binding / ubiquitin-dependent protein catabolic process / cellular response to hypoxia / proteasome-mediated ubiquitin-dependent protein catabolic process / regulation of gene expression / protein-containing complex assembly / DNA-binding transcription factor binding / amyloid fibril formation / transcription coactivator activity / molecular adaptor activity / protein stabilization / protein ubiquitination / transcription cis-regulatory region binding / hydrolase activity / chromatin remodeling / negative regulation of cell population proliferation / negative regulation of gene expression / intracellular membrane-bounded organelle / negative regulation of DNA-templated transcription / ubiquitin protein ligase binding / chromatin binding / positive regulation of cell population proliferation / chromatin / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / negative regulation of apoptotic process / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / enzyme binding / endoplasmic reticulum / positive regulation of transcription by RNA polymerase II
Similarity search - Function
BRK domain / BRK domain / BRK domain superfamily / domain in transcription and CHROMO domain helicases / von Hippel-Lindau disease tumour suppressor, alpha domain / von Hippel-Lindau disease tumour suppressor, beta domain / Elongin C; Chain C, domain 1 / domain in helicases and associated with SANT domains / Glutamine-Leucine-Glutamine, QLQ / QLQ ...BRK domain / BRK domain / BRK domain superfamily / domain in transcription and CHROMO domain helicases / von Hippel-Lindau disease tumour suppressor, alpha domain / von Hippel-Lindau disease tumour suppressor, beta domain / Elongin C; Chain C, domain 1 / domain in helicases and associated with SANT domains / Glutamine-Leucine-Glutamine, QLQ / QLQ / QLQ domain profile. / QLQ / Snf2, ATP coupling domain / Snf2-ATP coupling, chromatin remodelling complex / Snf2-ATP coupling, chromatin remodelling complex / HSA domain / 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 / Helicase/SANT-associated domain / HSA domain profile. / Elongin B / Elongin-C / Potassium Channel Kv1.1; Chain A / Potassium Channel Kv1.1; Chain A / : / SNF2-like, N-terminal domain superfamily / SNF2, N-terminal / SNF2-related domain / S-phase kinase-associated protein 1-like / SKP1 component, POZ domain / Skp1 family, tetramerisation domain / Found in Skp1 protein family / SKP1/BTB/POZ domain superfamily / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Helicase conserved C-terminal domain / Bromodomain-like / Histone Acetyltransferase; Chain A / Ubiquitin-like (UB roll) / Ubiquitin family / Bromodomain, conserved site / Bromodomain signature. / Ubiquitin homologues / Ubiquitin-like domain / Bromodomain / Ubiquitin domain profile. / Bromodomain profile. / bromo domain / Bromodomain / Bromodomain-like superfamily / 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 / Roll / Up-down Bundle / Immunoglobulin-like / Sandwich / P-loop containing nucleoside triphosphate hydrolase / 2-Layer Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-FWZ / von Hippel-Lindau disease tumor suppressor / Probable global transcription activator SNF2L2 / Elongin-C / Elongin-B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.35 Å
AuthorsRoy, M. / Bader, G. / Diers, E. / Trainor, N. / Farnaby, W. / Ciulli, A.
Funding support1items
OrganizationGrant numberCountry
European Research CouncilERC-2012-StG-311460 DrugE3CRLs
CitationJournal: Nat.Chem.Biol. / Year: 2019
Title: BAF complex vulnerabilities in cancer demonstrated via structure-based PROTAC design.
Authors: Farnaby, W. / Koegl, M. / Roy, M.J. / Whitworth, C. / Diers, E. / Trainor, N. / Zollman, D. / Steurer, S. / Karolyi-Oezguer, J. / Riedmueller, C. / Gmaschitz, T. / Wachter, J. / Dank, C. / ...Authors: Farnaby, W. / Koegl, M. / Roy, M.J. / Whitworth, C. / Diers, E. / Trainor, N. / Zollman, D. / Steurer, S. / Karolyi-Oezguer, J. / Riedmueller, C. / Gmaschitz, T. / Wachter, J. / Dank, C. / Galant, M. / Sharps, B. / Rumpel, K. / Traxler, E. / Gerstberger, T. / Schnitzer, R. / Petermann, O. / Greb, P. / Weinstabl, H. / Bader, G. / Zoephel, A. / Weiss-Puxbaum, A. / Ehrenhofer-Wolfer, K. / Wohrle, S. / Boehmelt, G. / Rinnenthal, J. / Arnhof, H. / Wiechens, N. / Wu, M.Y. / Owen-Hughes, T. / Ettmayer, P. / Pearson, M. / McConnell, D.B. / Ciulli, A.
History
DepositionAug 9, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 12, 2019Provider: repository / Type: Initial release
Revision 1.1Jun 19, 2019Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jul 3, 2019Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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: von Hippel-Lindau disease tumor suppressor
C: Elongin-C
D: Elongin-B
E: Probable global transcription activator SNF2L2
F: von Hippel-Lindau disease tumor suppressor
G: Elongin-C
H: Elongin-B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,55925
Polymers111,6128
Non-polymers2,94717
Water3,837213
1
A: Probable global transcription activator SNF2L2
B: von Hippel-Lindau disease tumor suppressor
C: Elongin-C
D: Elongin-B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,46114
Polymers55,8064
Non-polymers1,65510
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
E: Probable global transcription activator SNF2L2
F: von Hippel-Lindau disease tumor suppressor
G: Elongin-C
H: Elongin-B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,09811
Polymers55,8064
Non-polymers1,2937
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)80.508, 116.241, 120.596
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 4 types, 8 molecules AEBFCGDH

#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.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SMARCA2, BAF190B, BRM, SNF2A, SNF2L2 / Plasmid: pDEST15 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P51531, Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement
#2: Protein von Hippel-Lindau disease tumor suppressor / Protein G7 / pVHL


Mass: 18702.291 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: VHL / Plasmid: pHAT4 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P40337
#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.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ELOC, TCEB1 / Plasmid: pCDF-1b DUET / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q15369
#4: 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 / Plasmid: pCDF-1b DUET / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q15370

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Non-polymers , 4 types, 230 molecules

#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-FWZ / (2~{S},4~{R})-~{N}-[[2-[2-[4-[[4-[3-azanyl-6-(2-hydroxyphenyl)pyridazin-4-yl]piperazin-1-yl]methyl]phenyl]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: 920.105 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C49H58FN9O6S / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 213 / Source method: isolated from a natural source / Formula: H2O

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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: 2.53 Å3/Da / Density % sol: 51.34 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.75
Details: 13% (w/v) PEG 3350, 0.2 M sodium formate, 0.1 M HEPES, pH 8.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.97998 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 24, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97998 Å / Relative weight: 1
ReflectionResolution: 2.35→34.41 Å / Num. obs: 47960 / % possible obs: 99.6 % / Redundancy: 11.9 % / Biso Wilson estimate: 55.72 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.179 / Rrim(I) all: 0.187 / Net I/σ(I): 11.76
Reflection shellResolution: 2.35→2.49 Å / Redundancy: 11.79 % / Rmerge(I) obs: 0.96 / Mean I/σ(I) obs: 2.08 / Num. unique obs: 7495 / CC1/2: 0.835 / Rrim(I) all: 1.003 / % possible all: 97.9

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.25 Å48.33 Å
Translation2.25 Å48.33 Å

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Processing

Software
NameVersionClassification
XDSJan 26, 2018data reduction
XSCALEJan 26, 2018data scaling
PHASER2.4.0phasing
BUSTER2.10.2refinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5T35, 4QY4

5t35

4qy4


Resolution: 2.35→34.41 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.912 / Rfactor Rfree error: 0 / SU R Cruickshank DPI: 0.371 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.371 / SU Rfree Blow DPI: 0.25 / SU Rfree Cruickshank DPI: 0.253 / Details: TLS, NCS
RfactorNum. reflection% reflectionSelection details
Rfree0.268 2391 5 %RANDOM
Rwork0.232 ---
obs0.234 47827 100 %-
Displacement parametersBiso max: 153.25 Å2 / Biso mean: 51.93 Å2 / Biso min: 24.48 Å2
Baniso -1Baniso -2Baniso -3
1--3.009 Å20 Å20 Å2
2--2.2928 Å20 Å2
3---0.7162 Å2
Refine analyzeLuzzati coordinate error obs: 0.36 Å
Refinement stepCycle: final / Resolution: 2.35→34.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7364 0 203 213 7780
Biso mean--47.03 47.03 -
Num. residues----927
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d2710SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes194HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1089HARMONIC5
X-RAY DIFFRACTIONt_it7724HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion1001SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact8541SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d7724HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg10469HARMONIC21.08
X-RAY DIFFRACTIONt_omega_torsion3.17
X-RAY DIFFRACTIONt_other_torsion18.36
LS refinement shellResolution: 2.35→2.41 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.235 174 4.98 %
Rwork0.208 3319 -
all0.21 3493 -
obs--99.91 %
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)
12.6499-0.6717-0.17922.62850.05331.4299-0.0314-0.1780.19650.1838-0.20230.3136-0.2106-0.11620.2338-0.098-0.0155-0.0115-0.2907-0.04920.1303-56.059916.8235-32.7326
21.60740.54141.22540.7120.52651.1014-0.10490.01710.31810.06150.0665-0.0078-0.04680.02430.0384-0.1269-0.0225-0.0767-0.2630.02740.2112-21.279317.6241-20.7351
33.935-0.72060.96223.61070.77922.4808-0.02370.16750.11780.0761-0.2099-0.17290.01560.11650.2336-0.15090.0063-0.0306-0.2678-0.01190.12790.861314.6811-4.6168
40.5616-0.08910.39631.7542-1.50971.334-0.0506-0.12080.0442-0.00050.03190.10680.0106-0.20330.0187-0.1120.0298-0.0334-0.1877-0.07040.12040.74682.45818.3892
53.0751-0.46630.30910.0446-0.50111.2922-0.0735-0.1422-0.19860.06690.0411-0.06750.10150.04470.0324-0.1154-0.01660.0621-0.2674-0.01230.192810.2385-15.1145-29.8636
62.45860.1951-2.22550.7166-0.12922.716-0.20350.1308-0.0820.07270.1042-0.11930.1911-0.04010.0993-0.10840.01260.0196-0.2726-0.0440.0865-25.8781-15.6333-20.5458
74.0087-0.4615-1.01771.5577-0.29172.8074-0.0220.27120.11760.0877-0.14670.18130.1452-0.35520.1687-0.11110.0071-0.0079-0.2742-0.0560.1051-49.4854-11.8846-4.5696
81.1255-0.2463-0.94022.32451.0591.92030.0715-0.07710.11-0.07950.017-0.0352-0.02570.1554-0.0885-0.11320.02650.0189-0.2263-0.02360.1056-47.17690.45338.9393
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A1376 - 1490
2X-RAY DIFFRACTION2{ B|* }B60 - 208
3X-RAY DIFFRACTION3{ C|* }C16 - 112
4X-RAY DIFFRACTION4{ D|* }D1 - 104
5X-RAY DIFFRACTION5{ E|* }E1372 - 1492
6X-RAY DIFFRACTION6{ F|* }F61 - 209
7X-RAY DIFFRACTION7{ G|* }G16 - 112
8X-RAY DIFFRACTION8{ H|* }H1 - 104

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