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- PDB-7lhy: Caenorhabditis elegans SWSN-4 (SMARCA4-BRG1) ATPase Bromodomain i... -

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Basic information

Entry
Database: PDB / ID: 7lhy
TitleCaenorhabditis elegans SWSN-4 (SMARCA4-BRG1) ATPase Bromodomain in complex with a modified histone H3, N6-epsilon-acetyl-L-lysine 14 (H3K14ac) polypeptide
Components
  • H3(7-20)K14ac
  • SWI/SNF nucleosome remodeling complex component
KeywordsPEPTIDE BINDING PROTEIN / bromodomain / acetyl-lysine / histone reader
Function / homology
Function and homology information


RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known / RMTs methylate histone arginines / chromatin remodeling => GO:0006338 / ATP-dependent chromatin remodeler activity => GO:0140658 / gonad development / transcription factor binding / ATP-dependent activity, acting on DNA / helicase activity / histone binding / positive regulation of transcription by RNA polymerase II ...RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known / RMTs methylate histone arginines / chromatin remodeling => GO:0006338 / ATP-dependent chromatin remodeler activity => GO:0140658 / gonad development / transcription factor binding / ATP-dependent activity, acting on DNA / helicase activity / histone binding / positive regulation of transcription by RNA polymerase II / DNA binding / 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
SWI/SNF nucleosome remodeling complex component
Similarity search - Component
Biological speciesCaenorhabditis elegans (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å
AuthorsEnriquez, P. / Rose, R.B.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)DUE-1643814 United States
CitationJournal: J.Biol.Chem. / Year: 2021
Title: Binding specificity and function of the SWI/SNF subunit SMARCA4 bromodomain interaction with acetylated histone H3K14.
Authors: Enriquez, P. / Krajewski, K. / Strahl, B.D. / Rothbart, S.B. / Dowen, R.H. / Rose, R.B.
History
DepositionJan 26, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 8, 2021Provider: repository / Type: Initial release
Revision 1.1Sep 15, 2021Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Nov 10, 2021Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.3Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.4Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: SWI/SNF nucleosome remodeling complex component
B: H3(7-20)K14ac


Theoretical massNumber of molelcules
Total (without water)15,9572
Polymers15,9572
Non-polymers00
Water2,072115
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: isothermal titration calorimetry, Selectivity for H3K14ac was identified with a peptide microarray
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area860 Å2
ΔGint-3 kcal/mol
Surface area6560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.064, 69.064, 55.320
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/4
#3: y+1/2,-x+1/2,z+3/4
#4: x+1/2,-y+1/2,-z+3/4
#5: -x+1/2,y+1/2,-z+1/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2

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Components

#1: Protein SWI/SNF nucleosome remodeling complex component / SWI2/SNF2-like protein


Mass: 14413.140 Da / Num. of mol.: 1 / Fragment: UNP Residues 1176-1296
Source method: isolated from a genetically manipulated source
Details: The initial GP remains after cleaving off the N-terminal His-tag with Precision Protease
Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Gene: swsn-4, psa-4, CELE_F01G4.1, F01G4.1 / Plasmid: pET24b / Production host: Escherichia coli (E. coli) / Strain (production host): DH5alpha / References: UniProt: G5EF53
#2: Protein/peptide H3(7-20)K14ac


Mass: 1543.813 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: K14 is acetylated / Source: (synth.) Caenorhabditis elegans (invertebrata) / References: DNA helicase
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 115 / 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: 2.07 Å3/Da / Density % sol: 40.49 % / Description: prism
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.3
Details: 35% total PEG concentration, divided equally among PEG 400, PEG 550 MME, PEG 600 and PEG 1,000. There was no buffer in this condition, but the protein was purified in 10 mM HEPES, pH 7.3

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Data collection

DiffractionMean temperature: 170 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 22, 2016
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.29→50 Å / Num. obs: 34008 / % possible obs: 99.65 % / Redundancy: 13.8 % / Biso Wilson estimate: 17.25 Å2 / Rmerge(I) obs: 0.075 / Rpim(I) all: 0.023 / Rrim(I) all: 0.078 / Net I/σ(I): 13.9
Reflection shellResolution: 1.29→1.34 Å / Redundancy: 12 % / Rmerge(I) obs: 0.93 / Num. unique obs: 3306 / Rpim(I) all: 0.3 / Rrim(I) all: 0.97 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
HKL-20002.3.8data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2grc

2grc


Resolution: 1.3→48.84 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.961 / SU ML: 0.03 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.047 / ESU R Free: 0.048 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1978 1998 6 %RANDOM
Rwork0.1813 ---
obs0.1822 31468 99.34 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 64.98 Å2 / Biso mean: 21.9287 Å2 / Biso min: 10.63 Å2
Baniso -1Baniso -2Baniso -3
1--0.53 Å20 Å20 Å2
2---0.53 Å20 Å2
3---1.06 Å2
Refinement stepCycle: final / Resolution: 1.3→48.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms907 0 0 115 1022
Biso mean---30.83 -
Num. residues----115
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0270.02932
X-RAY DIFFRACTIONr_bond_other_d0.0030.02843
X-RAY DIFFRACTIONr_angle_refined_deg2.3411.9861264
X-RAY DIFFRACTIONr_angle_other_deg1.09131963
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.8695117
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.72825.90944
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.96615163
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.23154
X-RAY DIFFRACTIONr_chiral_restr0.1340.2142
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.0211035
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02171
LS refinement shellResolution: 1.3→1.331 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.312 144 -
Rwork0.311 2252 -
obs--97.92 %

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