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- PDB-5t35: The PROTAC MZ1 in complex with the second bromodomain of Brd4 and... -

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Basic information

Entry
Database: PDB / ID: 5t35
TitleThe PROTAC MZ1 in complex with the second bromodomain of Brd4 and pVHL:ElonginC:ElonginB
Components
  • (Transcription elongation factor B polypeptide ...) x 2
  • Bromodomain-containing protein 4
  • Von Hippel-Lindau disease tumor suppressor
KeywordsLIGASE / PROTAC complex / targeted degradation / chromatin reader / ubiquitin ligase / bifunctional ligand
Function / homology
Function and homology information


regulation of cellular response to hypoxia / RHOBTB3 ATPase cycle / negative regulation of receptor signaling pathway via JAK-STAT / target-directed miRNA degradation / transcription elongation factor activity / VCB complex / elongin complex / Replication of the SARS-CoV-1 genome / Cul5-RING ubiquitin ligase complex / intracellular membraneless organelle ...regulation of cellular response to hypoxia / RHOBTB3 ATPase cycle / negative regulation of receptor signaling pathway via JAK-STAT / target-directed miRNA degradation / transcription elongation factor activity / VCB complex / elongin complex / Replication of the SARS-CoV-1 genome / Cul5-RING ubiquitin ligase complex / intracellular membraneless organelle / Cul2-RING ubiquitin ligase complex / SUMOylation of ubiquitinylation proteins / negative regulation of transcription elongation by RNA polymerase II / RNA polymerase II C-terminal domain binding / P-TEFb complex binding / Pausing and recovery of Tat-mediated HIV elongation / Tat-mediated HIV elongation arrest and recovery / negative regulation of DNA damage checkpoint / HIV elongation arrest and recovery / Pausing and recovery of HIV elongation / negative regulation by host of viral transcription / Tat-mediated elongation of the HIV-1 transcript / ubiquitin-like ligase-substrate adaptor activity / Formation of HIV-1 elongation complex containing HIV-1 Tat / negative regulation of signal transduction / positive regulation of T-helper 17 cell lineage commitment / 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 / protein serine/threonine kinase binding / positive regulation of G2/M transition of mitotic cell cycle / RNA Polymerase II Pre-transcription Events / RNA polymerase II CTD heptapeptide repeat kinase activity / negative regulation of autophagy / condensed nuclear chromosome / transcription corepressor binding / histone reader activity / : / positive regulation of transcription elongation by RNA polymerase II / positive regulation of cell differentiation / transcription coregulator activity / TP53 Regulates Transcription of DNA Repair Genes / transcription initiation at RNA polymerase II promoter / transcription elongation by RNA polymerase II / Vif-mediated degradation of APOBEC3G / Inactivation of CSF3 (G-CSF) signaling / cell morphogenesis / Evasion by RSV of host interferon responses / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / Regulation of expression of SLITs and ROBOs / ubiquitin-protein transferase activity / transcription corepressor activity / p53 binding / Antigen processing: Ubiquitination & Proteasome degradation / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / Neddylation / chromosome / microtubule cytoskeleton / regulation of gene expression / Replication of the SARS-CoV-2 genome / protein-containing complex assembly / ubiquitin-dependent protein catabolic process / regulation of inflammatory response / protein-macromolecule adaptor activity / DNA-binding transcription factor binding / molecular adaptor activity / cellular response to hypoxia / histone binding / amyloid fibril formation / proteasome-mediated ubiquitin-dependent protein catabolic process / Potential therapeutics for SARS / positive regulation of canonical NF-kappaB signal transduction / transcription coactivator activity / transcription cis-regulatory region binding / protein stabilization / protein ubiquitination / cilium / chromatin remodeling / negative regulation of cell population proliferation / negative regulation of gene expression / protein serine/threonine kinase activity / ubiquitin protein ligase binding / DNA damage response / chromatin binding / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / negative regulation of apoptotic process / chromatin / positive regulation of DNA-templated transcription / enzyme binding / negative regulation of transcription by RNA polymerase II / endoplasmic reticulum / positive regulation of transcription by RNA polymerase II / mitochondrion / proteolysis / nucleoplasm / nucleus / plasma membrane / cytosol
Similarity search - Function
von Hippel-Lindau disease tumour suppressor, alpha domain / von Hippel-Lindau disease tumour suppressor, beta domain / Elongin C; Chain C, domain 1 / 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 ...von Hippel-Lindau disease tumour suppressor, alpha domain / von Hippel-Lindau disease tumour suppressor, beta domain / Elongin C; Chain C, domain 1 / 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 / Potassium Channel Kv1.1; Chain A / Potassium Channel Kv1.1; Chain A / S-phase kinase-associated protein 1-like / SKP1 component, POZ domain / Skp1 family, tetramerisation domain / Found in Skp1 protein family / Bromodomain protein 4, C-terminal / C-terminal domain of bromodomain protein 4 / Brdt, bromodomain, repeat I / Brdt, bromodomain, repeat II / NET domain superfamily / NET domain profile. / : / NET domain / Bromodomain extra-terminal - transcription regulation / SKP1/BTB/POZ domain superfamily / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Bromodomain-like / Histone Acetyltransferase; Chain A / Bromodomain, conserved site / Bromodomain signature. / Ubiquitin-like (UB roll) / Bromodomain / Bromodomain profile. / bromo domain / Bromodomain / Bromodomain-like superfamily / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily / Roll / Up-down Bundle / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-759 / Bromodomain-containing protein 4 / von Hippel-Lindau disease tumor suppressor / Elongin-C / Elongin-B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.7 Å
AuthorsGadd, M.S. / Zengerle, M. / Ciulli, A.
Funding support1items
OrganizationGrant numberCountry
European Research CouncilERC-2012-StG-311460
CitationJournal: Nat. Chem. Biol. / Year: 2017
Title: Structural basis of PROTAC cooperative recognition for selective protein degradation.
Authors: Gadd, M.S. / Testa, A. / Lucas, X. / Chan, K.H. / Chen, W. / Lamont, D.J. / Zengerle, M. / Ciulli, A.
History
DepositionAug 24, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Mar 8, 2017Provider: repository / Type: Initial release
Revision 1.1Mar 22, 2017Group: Database references
Revision 1.2Apr 26, 2017Group: Database references
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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Bromodomain-containing protein 4
B: Transcription elongation factor B polypeptide 2
C: Transcription elongation factor B polypeptide 1
D: Von Hippel-Lindau disease tumor suppressor
E: Bromodomain-containing protein 4
F: Transcription elongation factor B polypeptide 2
G: Transcription elongation factor B polypeptide 1
H: Von Hippel-Lindau disease tumor suppressor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,98110
Polymers112,9718
Non-polymers2,0092
Water1,54986
1
A: Bromodomain-containing protein 4
B: Transcription elongation factor B polypeptide 2
C: Transcription elongation factor B polypeptide 1
D: Von Hippel-Lindau disease tumor suppressor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,4905
Polymers56,4864
Non-polymers1,0051
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
E: Bromodomain-containing protein 4
F: Transcription elongation factor B polypeptide 2
G: Transcription elongation factor B polypeptide 1
H: Von Hippel-Lindau disease tumor suppressor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,4905
Polymers56,4864
Non-polymers1,0051
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)102.306, 102.306, 144.329
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number145
Space group name H-MP32
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21E
12B
22F
13C
23G
14D
24H

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11LYSLYSASPASPAA349 - 45919 - 129
21LYSLYSASPASPEE349 - 45919 - 129
12METMETLYSLYSBB1 - 1041 - 104
22METMETLYSLYSFF1 - 1041 - 104
13METMETCYSCYSCC16 - 1121 - 97
23METMETCYSCYSGG16 - 1121 - 97
14PROPROILEILEDD61 - 20610 - 155
24PROPROILEILEHH61 - 20610 - 155

NCS ensembles :
ID
1
2
3
4

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Components

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Protein , 2 types, 4 molecules AEDH

#1: Protein Bromodomain-containing protein 4 / Protein HUNK1


Mass: 15060.332 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BRD4, HUNK1 / Plasmid: pNIC28 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O60885
#4: 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

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Transcription elongation factor B polypeptide ... , 2 types, 4 molecules BFCG

#2: Protein Transcription elongation factor B polypeptide 2 / Elongin 18 kDa subunit / Elongin-B / EloB / RNA polymerase II transcription factor SIII subunit B / SIII p18


Mass: 11748.406 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TCEB2 / Plasmid: pCDFDuet-1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q15370
#3: Protein Transcription elongation factor B polypeptide 1 / Elongin 15 kDa subunit / Elongin-C / EloC / RNA polymerase II transcription factor SIII subunit C / SIII p15


Mass: 10974.616 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TCEB1 / Plasmid: pCDFDuet-1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q15369

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Non-polymers , 2 types, 88 molecules

#5: Chemical ChemComp-759 / (2~{S},4~{R})-1-[(2~{S})-2-[2-[2-[2-[2-[2-[(9~{S})-7-(4-chlorophenyl)-4,5,13-trimethyl-3-thia-1,8,11,12-tetrazatricyclo[8.3.0.0^{2,6}]trideca-2(6),4,7,10,12-pentaen-9-yl]ethanoylamino]ethoxy]ethoxy]ethoxy]ethanoylamino]-3,3-dimethyl-butanoyl]-~{N}-[[4-(4-methyl-2,3-dihydro-1,3-thiazol-5-yl)phenyl]methyl]-4-oxidanyl-pyrrolidine-2-carboxamide


Mass: 1004.655 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C49H62ClN9O8S2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 86 / 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: 3.86 Å3/Da / Density % sol: 68.14 % / Mosaicity: 0.1 °
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.3 / Details: PEG 8000, Sodium citrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9282 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Sep 21, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9282 Å / Relative weight: 1
ReflectionResolution: 2.7→48.21 Å / Num. obs: 46323 / % possible obs: 99.7 % / Redundancy: 4.2 % / Biso Wilson estimate: 47.2 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.079 / Net I/σ(I): 14.7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsCC1/2Diffraction-ID% possible all
2.7-2.793.70.662.10.571199.3
10.46-48.214.10.021197.9

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation7.58 Å48.21 Å
Translation7.58 Å48.21 Å

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimless0.3.11data scaling
PHASER2.5.6phasing
REFMAC5.8.0073refinement
PDB_EXTRACT3.2data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1VCB and 2OUO

1vcb

2ouo


Resolution: 2.7→48.21 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.914 / SU B: 23.438 / SU ML: 0.239 / SU R Cruickshank DPI: 0.4036 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.404 / ESU R Free: 0.26
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2307 2135 4.6 %RANDOM
Rwork0.2055 ---
obs0.2067 44157 99.67 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 182.62 Å2 / Biso mean: 62.348 Å2 / Biso min: 22.92 Å2
Baniso -1Baniso -2Baniso -3
1--0.05 Å2-0.02 Å2-0 Å2
2---0.05 Å2-0 Å2
3---0.15 Å2
Refinement stepCycle: final / Resolution: 2.7→48.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7185 0 138 86 7409
Biso mean--42.5 39.72 -
Num. residues----901
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0197511
X-RAY DIFFRACTIONr_bond_other_d0.0030.027116
X-RAY DIFFRACTIONr_angle_refined_deg1.1441.99410196
X-RAY DIFFRACTIONr_angle_other_deg0.843.00516394
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2515893
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.01923.559340
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.315151258
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.2511555
X-RAY DIFFRACTIONr_chiral_restr0.0570.21119
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0218335
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021682
X-RAY DIFFRACTIONr_mcbond_it4.3755.1293602
X-RAY DIFFRACTIONr_mcbond_other4.3595.1273595
X-RAY DIFFRACTIONr_mcangle_it6.6198.6214482
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A61950.05
12E61950.05
21B58640.05
22F58640.05
31C49020.03
32G49020.03
41D86590.04
42H86590.04
LS refinement shellResolution: 2.7→2.77 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.374 143 -
Rwork0.323 3322 -
all-3465 -
obs--99.26 %
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)
12.2378-1.892-0.24634.4085-0.04350.5188-0.074-0.1486-0.1640.1334-0.10330.43050.2372-0.00820.17720.29560.08580.07130.1019-0.0520.12124.6187-46.8493-11.7242
21.16030.4591-2.09810.8675-0.65073.92930.1370.12670.1073-0.03340.01690.0324-0.1594-0.2922-0.15390.17240.03010.0350.1774-0.0440.0342-12.88064.897916.4673
31.9232-0.1653-0.69181.06291.05843.0380.3104-0.21340.2532-0.05650.0053-0.1015-0.40710.0893-0.31580.20460.00810.08740.0568-0.02230.05621.77649.95747.4619
41.9998-0.0426-0.12481.8244-0.1742.01120.07580.2135-0.0878-0.2164-0.0458-0.11230.10190.2079-0.03010.1280.05760.01270.0998-0.00830.012419.0132-15.7009-6.8523
53.1996-1.48872.88132.9906-0.56194.88730.12970.10150.2836-0.5116-0.0808-0.2427-0.23080.1396-0.04890.23960.07340.13120.04270.04170.10665.87898.4117-11.5911
63.8514-1.599-0.10281.99440.2340.9712-0.1361-0.0089-0.0813-0.1460.00930.1268-0.0565-0.1490.12680.320.07980.00180.069-0.04040.0531-17.290832.8274-28.86
72.0961-0.02761.14212.91791.99233.62170.03510.2814-0.1985-0.09640.289-0.54540.60551.0012-0.32410.27990.31630.05490.6152-0.12710.184936.6471-2.1694-56.6466
82.85580.4569-1.2833.41470.36843.3875-0.1784-0.0630.50210.02370.5093-1.08720.08641.1991-0.3310.06440.0623-0.08910.7423-0.24230.542441.092312.3801-46.7974
91.7077-0.7233-0.17992.15791.15743.5060.0225-0.22450.28720.29830.2545-0.171-0.24510.4528-0.2770.2197-0.0055-0.00870.1184-0.08130.080214.652827.5178-32.6108
100.1830.56550.24563.53022.7152.497-0.021-0.264-0.11280.38680.3916-0.63450.39250.9434-0.37060.36650.3723-0.3551.3395-0.22020.59738.977614.8548-27.3493
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A349 - 459
2X-RAY DIFFRACTION2B1 - 104
3X-RAY DIFFRACTION3C16 - 112
4X-RAY DIFFRACTION4D63 - 152
5X-RAY DIFFRACTION4D193 - 204
6X-RAY DIFFRACTION5D155 - 190
7X-RAY DIFFRACTION6E349 - 459
8X-RAY DIFFRACTION7F1 - 104
9X-RAY DIFFRACTION8G16 - 112
10X-RAY DIFFRACTION9H63 - 152
11X-RAY DIFFRACTION9H193 - 204
12X-RAY DIFFRACTION10H155 - 190

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