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- PDB-7s4e: Crystal Structure of ligand ACBi1 in complex with bromodomain of ... -

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Basic information

Entry
Database: PDB / ID: 7s4e
TitleCrystal Structure of ligand ACBi1 in complex with bromodomain of human Smarca2 and pVHL:ElonginC:ElonginB complex
Components
  • Elongin-B
  • Elongin-C
  • Isoform Short of Probable global transcription activator SNF2L2
  • von Hippel-Lindau disease tumor suppressor
KeywordsGENE REGULATION / Complex / PROTAC / Degradation / Assembly
Function / homology
Function and homology information


regulation of cellular response to hypoxia / RHOBTB3 ATPase cycle / negative regulation of receptor signaling pathway via JAK-STAT / transcription elongation factor activity / target-directed miRNA degradation / elongin complex / VCB complex / Replication of the SARS-CoV-1 genome / Cul5-RING ubiquitin ligase complex / Cul2-RING ubiquitin ligase complex ...regulation of cellular response to hypoxia / RHOBTB3 ATPase cycle / negative regulation of receptor signaling pathway via JAK-STAT / transcription elongation factor activity / target-directed miRNA degradation / elongin complex / VCB complex / Replication of the SARS-CoV-1 genome / Cul5-RING ubiquitin ligase complex / Cul2-RING ubiquitin ligase complex / intracellular non-membrane-bounded organelle / SUMOylation of ubiquitinylation proteins / negative regulation of transcription elongation by RNA polymerase II / 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 / 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 / Evasion by RSV of host interferon responses / 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 / Vif-mediated degradation of APOBEC3G / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / cell morphogenesis / Inactivation of CSF3 (G-CSF) signaling / Regulation of expression of SLITs and ROBOs / ubiquitin-protein transferase activity / transcription corepressor activity / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / Antigen processing: Ubiquitination & Proteasome degradation / protein-macromolecule adaptor activity / Neddylation / Replication of the SARS-CoV-2 genome / cellular response to hypoxia / ubiquitin-dependent protein catabolic process / regulation of gene expression / proteasome-mediated ubiquitin-dependent protein catabolic process / protein-containing complex assembly / DNA-binding transcription factor binding / amyloid fibril formation / molecular adaptor activity / protein stabilization / protein ubiquitination / negative regulation of cell population proliferation / negative regulation of gene expression / ubiquitin protein ligase binding / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / negative regulation of apoptotic process / positive regulation of DNA-templated transcription / enzyme binding / negative regulation of transcription by RNA polymerase II / endoplasmic reticulum / mitochondrion / proteolysis / nucleoplasm / nucleus / plasma membrane / cytosol
Similarity search - Function
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 B / Elongin-C ...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 B / Elongin-C / 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 / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily
Similarity search - Domain/homology
Chem-87A / DI(HYDROXYETHYL)ETHER / von Hippel-Lindau disease tumor suppressor / Isoform Short of Probable global transcription activator SNF2L2 / Elongin-C / Elongin-B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsMacPherson, D.J. / Sherman, W.
Funding support United States, 1items
OrganizationGrant numberCountry
Other private United States
CitationJournal: Nat Commun / Year: 2022
Title: Predicting the structural basis of targeted protein degradation by integrating molecular dynamics simulations with structural mass spectrometry.
Authors: Dixon, T. / MacPherson, D. / Mostofian, B. / Dauzhenka, T. / Lotz, S. / McGee, D. / Shechter, S. / Shrestha, U.R. / Wiewiora, R. / McDargh, Z.A. / Pei, F. / Pal, R. / Ribeiro, J.V. / ...Authors: Dixon, T. / MacPherson, D. / Mostofian, B. / Dauzhenka, T. / Lotz, S. / McGee, D. / Shechter, S. / Shrestha, U.R. / Wiewiora, R. / McDargh, Z.A. / Pei, F. / Pal, R. / Ribeiro, J.V. / Wilkerson, T. / Sachdeva, V. / Gao, N. / Jain, S. / Sparks, S. / Li, Y. / Vinitsky, A. / Zhang, X. / Razavi, A.M. / Kolossvary, I. / Imbriglio, J. / Evdokimov, A. / Bergeron, L. / Zhou, W. / Adhikari, J. / Ruprecht, B. / Dickson, A. / Xu, H. / Sherman, W. / Izaguirre, J.A.
History
DepositionSep 8, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 5, 2022Provider: repository / Type: Initial release
Revision 1.1Feb 1, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._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: Isoform Short of Probable global transcription activator SNF2L2
B: von Hippel-Lindau disease tumor suppressor
C: Elongin-C
D: Elongin-B
E: Isoform Short of 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)114,29327
Polymers111,4298
Non-polymers2,86419
Water1,62190
1
A: Isoform Short of 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)57,38918
Polymers55,7154
Non-polymers1,67514
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
E: Isoform Short of 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)56,9049
Polymers55,7154
Non-polymers1,1895
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)80.140, 116.570, 122.320
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21E
12B
22F
13C
23G
14D
24H

NCS domain segments:

Component-ID: 0 / Refine code: 0

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11LEULEULYSLYSAA1376 - 14908 - 122
21LEULEULYSLYSEE1376 - 14908 - 122
12ARGARGHISHISBB60 - 2089 - 157
22ARGARGHISHISFF60 - 2089 - 157
13METMETCYSCYSCC17 - 1121 - 96
23METMETCYSCYSGG17 - 1121 - 96
14METMETLYSLYSDD1 - 1041 - 104
24METMETLYSLYSHH1 - 1041 - 104

NCS ensembles :
ID
1
2
3
4

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Components

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Protein , 4 types, 8 molecules AEBFCGDH

#1: 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: 14420.502 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 BL21(DE3) (bacteria)
References: UniProt: P51531-2, 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 / 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: 10843.420 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 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 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q15370

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Non-polymers , 5 types, 109 molecules

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


Mass: 62.068 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Na
#7: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#8: Chemical ChemComp-87A / N-(1-fluorocyclopropane-1-carbonyl)-3-methyl-L-valyl-(4R)-N-{[2-{2-[4-({4-[3-amino-6-(2-hydroxyphenyl)pyridazin-4-yl]piperazin-1-yl}methyl)phenoxy]ethoxy}-4-(4-methyl-1,3-thiazol-5-yl)phenyl]methyl}-4-hydroxy-L-prolinamide / ACBi1


Mass: 936.104 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C49H58FN9O7S / Feature type: SUBJECT OF INVESTIGATION
#9: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 90 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.68 Å3/Da / Density % sol: 54.05 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop / pH: 7.85
Details: 0.1 M HEPES, pH 7.85, 13% PEG 3350, 0.2 M sodium formate
PH range: 7.85

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Data collection

DiffractionMean temperature: 77.15 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-2 / Wavelength: 0.97932 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 5, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97932 Å / Relative weight: 1
ReflectionResolution: 2.25→37.92 Å / Num. obs: 55100 / % possible obs: 99.9 % / Redundancy: 7.4 % / CC1/2: 0.998 / Rmerge(I) obs: 0.149 / Rpim(I) all: 0.058 / Rrim(I) all: 0.16 / Net I/σ(I): 8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.25-2.317.42.6022975240080.3171.0172.7970.899.9
10.06-37.896.20.04742986970.9990.0190.05125.298.1

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Processing

Software
NameVersionClassification
Aimless0.7.4data scaling
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
Cootmodel building
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6HAX

6hax


Resolution: 2.25→37.92 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.937 / SU B: 21.882 / SU ML: 0.244 / Cross valid method: FREE R-VALUE / σ(F): 0 / ESU R: 0.296 / ESU R Free: 0.226 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2587 2828 5.1 %RANDOM
Rwork0.219 ---
obs0.221 52206 99.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 138.83 Å2 / Biso mean: 61.139 Å2 / Biso min: 31.42 Å2
Baniso -1Baniso -2Baniso -3
1--3.16 Å20 Å2-0 Å2
2---0.21 Å20 Å2
3---3.37 Å2
Refinement stepCycle: final / Resolution: 2.25→37.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7356 0 196 90 7642
Biso mean--57.67 53.57 -
Num. residues----908
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0137660
X-RAY DIFFRACTIONr_bond_other_d0.0020.0177374
X-RAY DIFFRACTIONr_angle_refined_deg1.5191.65910367
X-RAY DIFFRACTIONr_angle_other_deg1.1851.57916995
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.6015900
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.40421.262420
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.636151326
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.8261563
X-RAY DIFFRACTIONr_chiral_restr0.0650.2988
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.028457
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021725
Refine LS restraints NCS

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

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A35170.1
12E35170.1
21B46150.08
22F46150.08
31C26120.08
32G26120.08
41D29810.1
42H29810.1
LS refinement shellResolution: 2.25→2.308 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.373 215 -
Rwork0.367 3789 -
all-4004 -
obs--99.93 %
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)
16.3451-0.89470.27832.8020.11371.5222-0.0628-0.323-0.30420.1231-0.0831-0.5420.1670.52090.14590.31870.05810.03340.22140.09380.308356.2707-17.3652-34.0936
22.82520.5062-2.63421.9797-1.01213.5987-0.23810.2174-0.3180.080.1140.23170.289-0.25750.12420.27460.01740.0490.0268-0.02070.250822.2908-17.3509-19.505
35.7767-0.0945-1.43452.8981-0.77114.9475-0.28930.2433-0.2589-0.2193-0.00910.22210.2883-0.46510.29840.29730.01580.08960.0568-0.0430.22510.4421-14.6837-3.1188
42.5174-1.6799-0.93863.92921.7532.4226-0.0761-0.1519-0.1631-0.0089-0.0393-0.1692-0.02540.14430.11530.23870.0449-0.00020.08120.06530.13220.0759-1.52029.0762
56.3762-1.54321.02582.1865-0.14541.4013-0.0148-0.3941-0.10490.0686-0.00490.406-0.1329-0.28520.01980.53770.1302-0.14550.2468-0.06050.4215-8.861415.8374-31.3456
64.07411.30342.56072.31241.14273.6882-0.32810.44380.216-0.35070.0717-0.0979-0.61920.19440.25640.43050.05030.01280.06880.04940.198426.565715.7827-20.2418
76.4925-0.01570.97732.88340.39974.2482-0.1440.2511-0.0397-0.34480.0935-0.3308-0.33910.53620.05050.3346-0.0335-0.02970.08590.05010.261548.642212.7587-4.1984
84.4183-0.90221.06213.79830.243.06340.2286-0.7097-0.77650.08770.05560.02660.2584-0.2108-0.28420.283-0.0123-0.06050.1310.14210.429747.9419-0.39438.0865
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1376 - 1503
2X-RAY DIFFRACTION2B60 - 308
3X-RAY DIFFRACTION3C17 - 112
4X-RAY DIFFRACTION4D1 - 202
5X-RAY DIFFRACTION5E1376 - 1490
6X-RAY DIFFRACTION6F60 - 304
7X-RAY DIFFRACTION7G17 - 202
8X-RAY DIFFRACTION8H1 - 104

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