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- PDB-9du0: Crystal structure of the bromodomain of human BRM (SMARCA2) in co... -

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Basic information

Entry
Database: PDB / ID: 9du0
TitleCrystal structure of the bromodomain of human BRM (SMARCA2) in complex with a SMARCA-BD binder
ComponentsIsoform Short of Probable global transcription activator SNF2L2
KeywordsTRANSCRIPTION / SMARCA2 / Bromodomain / Protein-ligand complex
Function / homology
Function and homology information


bBAF complex / npBAF complex / nBAF complex / brahma complex / GBAF complex / nucleosome array spacer activity / regulation of G0 to G1 transition / intermediate filament cytoskeleton / regulation of nucleotide-excision repair / SWI/SNF complex ...bBAF complex / npBAF complex / nBAF complex / brahma complex / GBAF complex / nucleosome array spacer activity / regulation of G0 to G1 transition / intermediate filament cytoskeleton / regulation of nucleotide-excision repair / SWI/SNF complex / regulation of mitotic metaphase/anaphase transition / positive regulation of T cell differentiation / positive regulation of double-strand break repair / positive regulation of stem cell population maintenance / RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known / Regulation of MITF-M-dependent genes involved in pigmentation / regulation of G1/S transition of mitotic cell cycle / negative regulation of cell differentiation / spermatid development / ATP-dependent activity, acting on DNA / positive regulation of myoblast differentiation / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / positive regulation of cell differentiation / helicase activity / negative regulation of cell growth / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / 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 / negative regulation of DNA-templated transcription / intracellular membrane-bounded organelle / positive regulation of cell population proliferation / chromatin binding / regulation of transcription by RNA polymerase II / regulation of DNA-templated transcription / chromatin / 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 / Glutamine-Leucine-Glutamine, QLQ / QLQ / QLQ domain profile. / QLQ / Snf2-ATP coupling, chromatin remodelling complex / Snf2, ATP coupling domain ...BRK domain / BRK domain / BRK domain superfamily / domain in transcription and CHROMO domain helicases / Glutamine-Leucine-Glutamine, QLQ / QLQ / QLQ domain profile. / QLQ / Snf2-ATP coupling, chromatin remodelling complex / Snf2, ATP coupling domain / Snf2-ATP coupling, chromatin remodelling complex / domain in helicases and associated with SANT domains / 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 / bromo domain / Bromodomain / Bromodomain (BrD) profile. / 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
: / SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A member 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsWang, M. / Dou, Y. / Xu, C.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Cancer Res. / Year: 2025
Title: PRT3789 is a First-in-Human SMARCA2-Selective Degrader that Induces Synthetic Lethality in SMARCA4-Mutated Cancers
Authors: Hulse, M. / Wang, M. / Xu, C. / Ito, K.
History
DepositionOct 2, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 1, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Isoform Short of Probable global transcription activator SNF2L2
B: Isoform Short of Probable global transcription activator SNF2L2
C: Isoform Short of Probable global transcription activator SNF2L2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,7368
Polymers41,9733
Non-polymers7635
Water23413
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)64.558, 64.558, 89.083
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number144
Space group name H-MP31

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Components

#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: 13991.118 Da / Num. of mol.: 3 / Fragment: UNP residues 1373-1491
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-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: P51531, Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement
#2: Chemical ChemComp-A1BB5 / (2P)-2-[(6aS,11R)-6,6a,7,8,9,10-hexahydro-5H-pyrazino[1',2':4,5]pyrazino[2,3-c]pyridazin-2-yl]phenol


Mass: 283.328 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H17N5O
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 13 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

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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: 2.55 Å3/Da / Density % sol: 51.83 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 0.025~0.1 M zinc acetate, 16~26% w/v PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.979183 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 24, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979183 Å / Relative weight: 1
ReflectionResolution: 3→47.4 Å / Num. obs: 8198 / % possible obs: 98.4 % / Redundancy: 2.3 % / CC1/2: 0.992 / Rmerge(I) obs: 0.132 / Rpim(I) all: 0.105 / Rrim(I) all: 0.17 / Net I/σ(I): 5.3
Reflection shellResolution: 3→3.18 Å / Rmerge(I) obs: 0.827 / Num. unique obs: 1331 / CC1/2: 0.674 / Rpim(I) all: 0.674 / Rrim(I) all: 1.073

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
PDB_EXTRACT3.28data extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3→47.4 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.823 / SU B: 40.505 / SU ML: 0.669 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.698 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.3381 364 5 %RANDOM
Rwork0.2231 ---
obs0.2285 6909 87.47 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 196.89 Å2 / Biso mean: 83.308 Å2 / Biso min: 21.09 Å2
Baniso -1Baniso -2Baniso -3
1-2.98 Å21.49 Å20 Å2
2--2.98 Å20 Å2
3----9.65 Å2
Refinement stepCycle: final / Resolution: 3→47.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2832 0 45 13 2890
Biso mean--81.23 50.21 -
Num. residues----345
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0132928
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172839
X-RAY DIFFRACTIONr_angle_refined_deg1.4061.6743935
X-RAY DIFFRACTIONr_angle_other_deg1.0841.6016625
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1425342
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.38722.5156
X-RAY DIFFRACTIONr_dihedral_angle_3_deg22.98815588
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.6511521
X-RAY DIFFRACTIONr_chiral_restr0.0460.2375
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023142
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02573
X-RAY DIFFRACTIONr_mcbond_it5.4798.7051377
X-RAY DIFFRACTIONr_mcbond_other5.4788.7031376
X-RAY DIFFRACTIONr_mcangle_it8.86313.0411716
LS refinement shellResolution: 3→3.078 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.416 31 -
Rwork0.368 477 -
all-508 -
obs--82.47 %

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