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- PDB-8qjt: BRM (SMARCA2) Bromodomain in complex with ligand 10 -

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Basic information

Entry
Database: PDB / ID: 8qjt
TitleBRM (SMARCA2) Bromodomain in complex with ligand 10
ComponentsProbable global transcription activator SNF2L2
KeywordsGENE REGULATION / BRM / SMARCA2 / SWI/SNF / CHROMATIN REMODELLING / BROMODOMAIN
Function / homology
Function and homology information


bBAF complex / npBAF complex / brahma complex / nBAF complex / GBAF complex / regulation of G0 to G1 transition / regulation of nucleotide-excision repair / regulation of mitotic metaphase/anaphase transition / ATP-dependent chromatin remodeler activity / SWI/SNF complex ...bBAF complex / npBAF complex / brahma complex / nBAF complex / GBAF complex / regulation of G0 to G1 transition / regulation of nucleotide-excision repair / regulation of mitotic metaphase/anaphase transition / ATP-dependent chromatin remodeler activity / SWI/SNF complex / positive regulation of double-strand break repair / positive regulation of T cell differentiation / intermediate filament cytoskeleton / positive regulation of stem cell population maintenance / RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known / regulation of G1/S transition of mitotic cell cycle / negative regulation of cell differentiation / spermatid development / positive regulation of myoblast differentiation / ATP-dependent activity, acting on DNA / helicase activity / positive regulation of cell differentiation / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / negative regulation of cell growth / RMTs methylate histone arginines / nervous system development / histone binding / transcription coactivator activity / hydrolase activity / transcription cis-regulatory region binding / chromatin remodeling / negative regulation of cell population proliferation / intracellular membrane-bounded organelle / negative regulation of DNA-templated transcription / chromatin binding / positive regulation of cell population proliferation / regulation of DNA-templated transcription / chromatin / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / DNA binding / nucleoplasm / ATP binding / nucleus
Similarity search - Function
BRK domain / BRK domain / BRK domain superfamily / domain in transcription and CHROMO domain helicases / domain in helicases and associated with SANT domains / Glutamine-Leucine-Glutamine, QLQ / QLQ / QLQ domain profile. / QLQ / Snf2, ATP coupling domain ...BRK domain / BRK domain / BRK domain superfamily / domain in transcription and CHROMO domain helicases / 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 / Helicase/SANT-associated domain / HSA domain profile. / : / SNF2-like, N-terminal domain superfamily / SNF2, N-terminal / SNF2-related domain / Helicase conserved C-terminal domain / Bromodomain, conserved site / Bromodomain signature. / Bromodomain / 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 / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Chem-VLC / Probable global transcription activator SNF2L2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.568 Å
AuthorsKerry, P.S. / Hole, A.J. / Perez-Dorado, J.I.
Funding support1items
OrganizationGrant numberCountry
Other private
CitationJournal: J.Med.Chem. / Year: 2024
Title: PROTACs Targeting BRM (SMARCA2) Afford Selective In Vivo Degradation over BRG1 (SMARCA4) and Are Active in BRG1 Mutant Xenograft Tumor Models.
Authors: Berlin, M. / Cantley, J. / Bookbinder, M. / Bortolon, E. / Broccatelli, F. / Cadelina, G. / Chan, E.W. / Chen, H. / Chen, X. / Cheng, Y. / Cheung, T.K. / Davenport, K. / DiNicola, D. / ...Authors: Berlin, M. / Cantley, J. / Bookbinder, M. / Bortolon, E. / Broccatelli, F. / Cadelina, G. / Chan, E.W. / Chen, H. / Chen, X. / Cheng, Y. / Cheung, T.K. / Davenport, K. / DiNicola, D. / Gordon, D. / Hamman, B.D. / Harbin, A. / Haskell, R. / He, M. / Hole, A.J. / Januario, T. / Kerry, P.S. / Koenig, S.G. / Li, L. / Merchant, M. / Perez-Dorado, I. / Pizzano, J. / Quinn, C. / Rose, C.M. / Rousseau, E. / Soto, L. / Staben, L.R. / Sun, H. / Tian, Q. / Wang, J. / Wang, W. / Ye, C.S. / Ye, X. / Zhang, P. / Zhou, Y. / Yauch, R. / Dragovich, P.S.
History
DepositionSep 13, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 17, 2024Provider: repository / Type: Initial release
Revision 1.1Feb 7, 2024Group: Database references / Refinement description
Category: citation / citation_author / pdbx_initial_refinement_model
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID / _pdbx_initial_refinement_model.entity_id_list

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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: Probable global transcription activator SNF2L2
C: Probable global transcription activator SNF2L2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,78411
Polymers43,1423
Non-polymers1,6438
Water2,576143
1
A: Probable global transcription activator SNF2L2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,9604
Polymers14,3811
Non-polymers5793
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Probable global transcription activator SNF2L2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,9304
Polymers14,3811
Non-polymers5493
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Probable global transcription activator SNF2L2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,8943
Polymers14,3811
Non-polymers5142
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)63.75, 63.75, 88.51
Angle α, β, γ (deg.)90, 90, 120
Int Tables number144
Space group name H-MP31

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Components

#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.: 3
Source method: isolated from a genetically manipulated source
Details: BRM bromodomain / Source: (gene. exp.) Homo sapiens (human) / Gene: SMARCA2, BAF190B, BRM, SNF2A, SNF2L2 / Plasmid: pET9a / 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: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-VLC / 2-[6-azanyl-5-[(1R,5S)-8-[2-(2-methoxyethoxy)pyridin-4-yl]-3,8-diazabicyclo[3.2.1]octan-3-yl]pyridazin-3-yl]phenol


Mass: 448.518 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C24H28N6O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 143 / Source method: isolated from a natural source / Formula: H2O
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: 2.06 Å3/Da / Density % sol: 40.22 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / Details: 20% PEG 6K, 6% ethylene glycol, 10 mM ZnCl2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97625 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Dec 13, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 2.57→55.21 Å / Num. obs: 12685 / % possible obs: 98.9 % / Redundancy: 5.4 % / CC1/2: 0.996 / Rmerge(I) obs: 0.144 / Net I/σ(I): 9.5
Reflection shellResolution: 2.57→2.61 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.932 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 646 / CC1/2: 0.829 / % possible all: 100

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Processing

Software
NameVersionClassification
BUSTER2.11.8refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.568→55.21 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.887 / SU R Cruickshank DPI: 1.29 / Cross valid method: THROUGHOUT / SU R Blow DPI: 1.053 / SU Rfree Blow DPI: 0.323 / SU Rfree Cruickshank DPI: 0.332
RfactorNum. reflection% reflectionSelection details
Rfree0.263 603 -RANDOM
Rwork0.2025 ---
obs0.2054 12685 98.8 %-
Displacement parametersBiso mean: 58.14 Å2
Baniso -1Baniso -2Baniso -3
1--7.9832 Å20 Å20 Å2
2---7.9832 Å20 Å2
3---15.9664 Å2
Refine analyzeLuzzati coordinate error obs: 0.33 Å
Refinement stepCycle: LAST / Resolution: 2.568→55.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2796 0 104 143 3043
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0082958HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.943974HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1130SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes484HARMONIC5
X-RAY DIFFRACTIONt_it2958HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion376SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact2653SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion2.76
X-RAY DIFFRACTIONt_other_torsion16.33
LS refinement shellResolution: 2.57→2.6 Å
RfactorNum. reflection% reflection
Rfree0.4118 16 -
Rwork0.2571 --
obs0.2621 423 98.12 %
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)
12.60720.11210.62893.6128-0.77734.9054-0.13950.0897-0.2410.08970.06550.3076-0.2410.30760.074-0.14340.0188-0.04440.0769-0.0277-0.18632.7246-3.9614-10.2046
24.91-0.013-0.59433.53280.35495.7728-0.2668-0.12610.1827-0.12610.09390.18040.18270.18040.1729-0.1863-0.01090.05850.0089-0.0937-0.17474.013-34.8005-17.1637
32.7149-0.43821.1664.98690.49727.3447-0.0028-0.26560.1266-0.26560.053-0.74710.1266-0.7471-0.0502-0.1619-0.1613-0.00280.02980.0874-0.19225.4582-18.2625-33.075
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A1380 - 1492
2X-RAY DIFFRACTION2{ B|* }B1380 - 1491
3X-RAY DIFFRACTION3{ C|* }C1378 - 1491

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