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- PDB-5dkc: Crystal structure of the bromodomain of human BRM (SMARCA2) in co... -

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Basic information

Entry
Database: PDB / ID: 5dkc
TitleCrystal structure of the bromodomain of human BRM (SMARCA2) in complex with PFI-3 chemical probe
ComponentsProbable global transcription activator SNF2L2
KeywordsHYDROLASE / SWI-SNF complex / chromatin remodeling / Brg associated factors (BAF) / transcription
Function / homology
Function and homology information


bBAF complex / npBAF complex / brahma complex / nBAF complex / Formation of the canonical BAF (cBAF) complex / Formation of neuronal progenitor and neuronal BAF (npBAF and nBAF) / Formation of the polybromo-BAF (pBAF) complex / Formation of the non-canonical BAF (ncBAF) complex / GBAF complex / regulation of G0 to G1 transition ...bBAF complex / npBAF complex / brahma complex / nBAF complex / Formation of the canonical BAF (cBAF) complex / Formation of neuronal progenitor and neuronal BAF (npBAF and nBAF) / Formation of the polybromo-BAF (pBAF) complex / Formation of the non-canonical BAF (ncBAF) complex / GBAF complex / regulation of G0 to G1 transition / nucleosome array spacer activity / intermediate filament cytoskeleton / regulation of nucleotide-excision repair / regulation of mitotic metaphase/anaphase transition / SWI/SNF complex / 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 / spermatid development / negative regulation of cell differentiation / positive regulation of myoblast differentiation / ATP-dependent activity, acting on DNA / helicase activity / positive regulation of cell differentiation / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / 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 / heterochromatin formation / histone binding / transcription coactivator activity / transcription cis-regulatory region binding / chromatin remodeling / negative regulation of cell population proliferation / negative regulation of DNA-templated transcription / positive regulation of cell population proliferation / chromatin binding / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / chromatin / negative regulation of transcription by RNA polymerase II / ATP hydrolysis activity / 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 / Bromodomain-like / Histone Acetyltransferase; Chain A / 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 / Up-down Bundle / P-loop containing nucleoside triphosphate hydrolase / Mainly Alpha
Similarity search - Domain/homology
Chem-5BW / 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: 1.6 Å
AuthorsTallant, C. / Owen, D.R. / Gerstenberger, B.S. / Fedorov, O. / Savitsky, P. / Nunez-Alonso, G. / Fonseca, M. / Krojer, T. / Filippakopoulos, P. / von Delft, F. ...Tallant, C. / Owen, D.R. / Gerstenberger, B.S. / Fedorov, O. / Savitsky, P. / Nunez-Alonso, G. / Fonseca, M. / Krojer, T. / Filippakopoulos, P. / von Delft, F. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Muller, S. / Knapp, S.
CitationJournal: To Be Published
Title: Crystal structure of the bromodomain of human BRM (SMARCA2) in complex with PFI-3 chemical probe
Authors: Tallant, C. / Owen, D.R. / Gerstenberger, B.S. / Fedorov, O. / Savitsky, P. / Nunez-Alonso, G. / Fonseca, M. / Krojer, T. / Filippakopoulos, P. / von Delft, F. / Arrowsmith, C.H. / Edwards, ...Authors: Tallant, C. / Owen, D.R. / Gerstenberger, B.S. / Fedorov, O. / Savitsky, P. / Nunez-Alonso, G. / Fonseca, M. / Krojer, T. / Filippakopoulos, P. / von Delft, F. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Muller, S. / Knapp, S.
History
DepositionSep 3, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Oct 14, 2015Provider: repository / Type: Initial release
Revision 1.1Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Probable global transcription activator SNF2L2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,7673
Polymers14,3811
Non-polymers3872
Water2,054114
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area70 Å2
ΔGint-18 kcal/mol
Surface area6950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.424, 74.424, 89.856
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

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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.: 1 / Fragment: UNP residues 1373-1493
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SMARCA2, BAF190B, BRM, SNF2A, SNF2L2 / Plasmid: pNIC28-Bsa4 / 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.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-5BW / (2E)-1-(2-hydroxyphenyl)-3-[(1R,4R)-5-(pyridin-2-yl)-2,5-diazabicyclo[2.2.1]hept-2-yl]prop-2-en-1-one


Mass: 321.373 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H19N3O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 114 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.34 Å3/Da / Density % sol: 63.15 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 19% PEG 6K, 4% ethyleneglycol, 0.01M ZnCl2 / PH range: 7

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 6, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.6→26.19 Å / Num. all: 24515 / Num. obs: 24515 / % possible obs: 99.4 % / Redundancy: 6.8 % / Rmerge(I) obs: 0.054 / Rsym value: 0.025 / Net I/av σ(I): 17.1 / Net I/σ(I): 17.1
Reflection shellResolution: 1.6→1.62 Å / Redundancy: 6 % / Rmerge(I) obs: 0.8 / Mean I/σ(I) obs: 2.1 / % possible all: 93.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4QY4

4qy4


Resolution: 1.6→26.19 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.954 / SU B: 1.594 / SU ML: 0.055 / Cross valid method: THROUGHOUT / ESU R: 0.074 / ESU R Free: 0.073 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21115 1375 5.6 %RANDOM
Rwork0.1937 ---
obs0.19468 23139 99.47 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 31.676 Å2
Baniso -1Baniso -2Baniso -3
1-0.31 Å20.15 Å2-0 Å2
2--0.31 Å2-0 Å2
3----1 Å2
Refinement stepCycle: 1 / Resolution: 1.6→26.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms908 0 25 114 1047
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.02949
X-RAY DIFFRACTIONr_bond_other_d0.0020.02948
X-RAY DIFFRACTIONr_angle_refined_deg1.5212.0121272
X-RAY DIFFRACTIONr_angle_other_deg0.9683.0062186
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4335109
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.09424.31844
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.63315192
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.114157
X-RAY DIFFRACTIONr_chiral_restr0.1040.2140
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021034
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02216
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.9772.771439
X-RAY DIFFRACTIONr_mcbond_other1.9772.763438
X-RAY DIFFRACTIONr_mcangle_it2.884.131547
X-RAY DIFFRACTIONr_mcangle_other2.8774.141548
X-RAY DIFFRACTIONr_scbond_it3.1233.193510
X-RAY DIFFRACTIONr_scbond_other3.1253.195509
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.0254.589726
X-RAY DIFFRACTIONr_long_range_B_refined6.33922.6661184
X-RAY DIFFRACTIONr_long_range_B_other6.33722.6641185
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.597→1.638 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.307 89 -
Rwork0.28 1673 -
obs--95.92 %

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