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- PDB-6hr2: Crystal structure of PROTAC 2 in complex with the bromodomain of ... -

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Basic information

Entry
Database: PDB / ID: 6hr2
TitleCrystal structure of PROTAC 2 in complex with the bromodomain of human SMARCA4 and pVHL:ElonginC:ElonginB
Components
  • Elongin-B
  • Elongin-C
  • Transcription activator BRG1
  • von Hippel-Lindau disease tumor suppressor
KeywordsTRANSCRIPTION / bromodomain / BRG1 / SMARCA4 / PROTAC / VHL / ternary complex
Function / homology
Function and homology information


positive regulation of glucose mediated signaling pathway / bBAF complex / npBAF complex / nBAF complex / positive regulation of transcription of nucleolar large rRNA by RNA polymerase I / negative regulation of androgen receptor signaling pathway / regulation of cellular response to hypoxia / neural retina development / GBAF complex / regulation of G0 to G1 transition ...positive regulation of glucose mediated signaling pathway / bBAF complex / npBAF complex / nBAF complex / positive regulation of transcription of nucleolar large rRNA by RNA polymerase I / negative regulation of androgen receptor signaling pathway / regulation of cellular response to hypoxia / neural retina development / GBAF complex / regulation of G0 to G1 transition / Tat protein binding / RHOBTB3 ATPase cycle / EGR2 and SOX10-mediated initiation of Schwann cell myelination / negative regulation of receptor signaling pathway via JAK-STAT / nucleosome disassembly / transcription elongation factor activity / regulation of nucleotide-excision repair / RSC-type complex / target-directed miRNA degradation / elongin complex / VCB complex / RNA polymerase I preinitiation complex assembly / positive regulation by host of viral transcription / 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 / Cul2-RING ubiquitin ligase complex / nuclear androgen receptor binding / 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 / 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 / positive regulation of Wnt signaling pathway / 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 / Chromatin modifying enzymes / negative regulation of signal transduction / DNA polymerase binding / RNA Polymerase II Transcription Elongation / Formation of RNA Pol II elongation complex / negative regulation of TORC1 signaling / transcription initiation-coupled chromatin remodeling / RNA Polymerase II Pre-transcription Events / Interleukin-7 signaling / negative regulation of autophagy / transcription corepressor binding / helicase activity / transcription coregulator binding / 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 / Formation of the beta-catenin:TCF transactivating complex / lysine-acetylated histone binding / cell morphogenesis / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / Inactivation of CSF3 (G-CSF) signaling / negative regulation of cell growth / kinetochore / fibrillar center / RMTs methylate histone arginines / Regulation of expression of SLITs and ROBOs / nuclear matrix / positive regulation of miRNA transcription / ubiquitin-protein transferase activity / transcription corepressor activity / positive regulation of DNA-binding transcription factor activity / protein-macromolecule adaptor activity / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / Antigen processing: Ubiquitination & Proteasome degradation / p53 binding / Neddylation / nervous system development / positive regulation of cold-induced thermogenesis / Replication of the SARS-CoV-2 genome / 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
Similarity search - Function
SWI/SNF complex subunit BRG1 / 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 ...SWI/SNF complex subunit BRG1 / 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 / helicase superfamily c-terminal domain / Bromodomain / Bromodomain-like superfamily / 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 / Transcription activator BRG1 / Elongin-C / Elongin-B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.76 Å
AuthorsRoy, M. / Bader, G. / Diers, E. / Trainor, N. / Farnaby, W. / Ciulli, A.
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
DepositionSep 26, 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 1.3May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: Transcription activator BRG1
B: von Hippel-Lindau disease tumor suppressor
C: Elongin-C
D: Elongin-B
E: Transcription activator BRG1
F: von Hippel-Lindau disease tumor suppressor
G: Elongin-C
H: Elongin-B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,47314
Polymers108,3528
Non-polymers2,1216
Water7,278404
1
A: Transcription activator BRG1
B: von Hippel-Lindau disease tumor suppressor
C: Elongin-C
D: Elongin-B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,1746
Polymers54,1764
Non-polymers9982
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
E: Transcription activator BRG1
F: von Hippel-Lindau disease tumor suppressor
G: Elongin-C
H: Elongin-B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,2988
Polymers54,1764
Non-polymers1,1224
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)60.332, 61.678, 81.603
Angle α, β, γ (deg.)69.430, 83.380, 86.420
Int Tables number1
Space group name H-MP1

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Components

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Protein , 4 types, 8 molecules AEBFCGDH

#1: Protein Transcription activator BRG1 / ATP-dependent helicase SMARCA4 / BRG1-associated factor 190A / BAF190A / Mitotic growth and ...ATP-dependent helicase SMARCA4 / BRG1-associated factor 190A / BAF190A / Mitotic growth and transcription activator / Protein BRG-1 / Protein brahma homolog 1 / SNF2-beta / SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A member 4


Mass: 14155.381 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SMARCA4, BAF190A, BRG1, SNF2B, SNF2L4 / Plasmid: pDEST15 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P51532, 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: 17297.688 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, 410 molecules

#5: 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
#6: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE / Dimethyl sulfoxide


Mass: 78.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#7: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 404 / 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: 2.66 Å3/Da / Density % sol: 53.69 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: 20% (w/v) PEG1500, 0.1 M MIB Buffer, pH 6.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Aug 22, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.76→39.8 Å / Num. obs: 68052 / % possible obs: 89.4 % / Redundancy: 2.4 % / Biso Wilson estimate: 36.81 Å2 / Net I/σ(I): 12.1
Reflection shellResolution: 1.76→1.96 Å

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimlessdata scaling
BUSTER2.11.7refinement
PDB_EXTRACT3.24data extraction
PHASERphasing
RefinementResolution: 1.76→39.8 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.935 / SU R Cruickshank DPI: 0.569 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.203 / SU Rfree Blow DPI: 0.162 / SU Rfree Cruickshank DPI: 0.166
RfactorNum. reflection% reflectionSelection details
Rfree0.236 2903 4.27 %RANDOM
Rwork0.216 ---
obs0.216 68052 63.2 %-
Displacement parametersBiso max: 279.02 Å2 / Biso mean: 56.7 Å2 / Biso min: 18.24 Å2
Baniso -1Baniso -2Baniso -3
1--1.5537 Å2-0.2567 Å21.8979 Å2
2--2.0896 Å2-1.225 Å2
3----0.5359 Å2
Refine analyzeLuzzati coordinate error obs: 0.29 Å
Refinement stepCycle: final / Resolution: 1.76→39.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7428 0 148 404 7980
Biso mean--36.9 50.48 -
Num. residues----916
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d3468SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes2480HARMONIC5
X-RAY DIFFRACTIONt_it15558HARMONIC20
X-RAY DIFFRACTIONt_nbd3SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion1002SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies7HARMONIC1
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact16177SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d15558HARMONIC20.008
X-RAY DIFFRACTIONt_angle_deg28230HARMONIC20.94
X-RAY DIFFRACTIONt_omega_torsion3.18
X-RAY DIFFRACTIONt_other_torsion15.1
LS refinement shellResolution: 1.76→1.88 Å / Rfactor Rfree error: 0 / Total num. of bins used: 50
RfactorNum. reflection% reflection
Rfree0.252 72 5.29 %
Rwork0.233 1290 -
all0.234 1362 -
obs--7.07 %
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)
11.96630.85870.59781.82413.13635.39080.10450.11830.0038-0.0721-0.0409-0.07950.24930.0971-0.06360.01830.0902-0.0969-0.1364-0.0287-0.0756-33.1212-17.6876-37.479
22.1114-0.57890.68920.925-0.43431.39390.1128-0.1922-0.3536-0.1217-0.14520.00360.1062-0.11120.0323-0.1074-0.0666-0.031-0.07390.02610.0737-17.8913-5.5606-6.3891
31.4773-0.11741.75092.28760.39122.25670.0909-0.3529-0.11670.2586-0.10880.2680.0611-0.04040.0179-0.1947-0.060.05820.18440.098-0.09130.85333.284911.8011
42.93421.6341-0.26423.8189-0.43590.3810.0167-0.2407-0.0666-0.06830.06960.0698-0.1056-0.0967-0.0863-0.1397-0.00770.02660.0698-0.0279-0.107313.54714.33355.887
51.0240.47211.10792.16492.01983.35620.0451-0.19860.1121-0.0154-0.0179-0.1622-0.21590.2442-0.0272-0.0961-0.10720.05280.0464-0.11-0.0768-24.961636.422911.9118
61.25-0.0514-0.24360.4824-0.24780.83210.1450.16980.1994-0.2737-0.1238-0.2216-0.09310.0235-0.02120.08460.03190.1696-0.0626-0.0029-0.0065-17.519223.2366-22.4906
70.94050.6542-1.58451.66050.28184.36550.11970.28850.081-0.148-0.09240.1885-0.05710.0154-0.0273-0.10090.16330.07060.14260.0514-0.1576-4.446911.8194-43.3321
82.5615-0.6823-1.46062.79370.23611.5170.0183-0.0078-0.08250.0368-0.0231-0.03640.21120.13250.0048-0.06410.12630.02930.1147-0.0002-0.22547.7169-1.2171-40.3328
90.2035-0.4366-0.43021.2110.25570.12440.0904-0.0384-0.0972-0.01590.09360.10030.00680.0101-0.1841-0.0049-0.0209-0.0272-0.0342-0.0750.0344-25.53939.2655-13.4082
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A1452 - 1568
2X-RAY DIFFRACTION2{ B|* }B61 - 209
3X-RAY DIFFRACTION3{ C|* }C16 - 112
4X-RAY DIFFRACTION4{ D|* }D1 - 104
5X-RAY DIFFRACTION5{ E|* }E1449 - 1568
6X-RAY DIFFRACTION6{ F|* }F61 - 209
7X-RAY DIFFRACTION7{ G|* }G16 - 112
8X-RAY DIFFRACTION8{ H|* }H1 - 103
9X-RAY DIFFRACTION9{ I|* }I1 - 2

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