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- PDB-6haz: Crystal structure of the bromodomain of human SMARCA2 in complex ... -

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Basic information

Entry
Database: PDB / ID: 6haz
TitleCrystal structure of the bromodomain of human SMARCA2 in complex with SMARCA-BD ligand
ComponentsProbable global transcription activator SNF2L2
KeywordsGENE REGULATION / bromodomain
Function / homology
Function and homology information


bBAF complex / npBAF complex / nBAF complex / brahma complex / nucleosome array spacer activity / GBAF complex / 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 / nucleosome array spacer activity / GBAF complex / 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 / RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known / positive regulation of stem cell population maintenance / 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 / positive regulation of cell differentiation / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / 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 DNA-templated transcription / regulation of transcription by RNA polymerase II / 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 / 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-FX5 / 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: 1.31 Å
AuthorsBader, G. / Steurer, S. / Weiss-Puxbaum, A. / Zoephel, A. / Roy, M. / Ciulli, A.
CitationJournal: Nat.Chem.Biol. / Year: 2019
Title: BAF complex vulnerabilities in cancer demonstrated via structure-based PROTAC design.
Authors: Farnaby, W. / Koegl, M. / Roy, M.J. / Whitworth, C. / Diers, E. / Trainor, N. / Zollman, D. / Steurer, S. / Karolyi-Oezguer, J. / Riedmueller, C. / Gmaschitz, T. / Wachter, J. / Dank, C. / ...Authors: Farnaby, W. / Koegl, M. / Roy, M.J. / Whitworth, C. / Diers, E. / Trainor, N. / Zollman, D. / Steurer, S. / Karolyi-Oezguer, J. / Riedmueller, C. / Gmaschitz, T. / Wachter, J. / Dank, C. / Galant, M. / Sharps, B. / Rumpel, K. / Traxler, E. / Gerstberger, T. / Schnitzer, R. / Petermann, O. / Greb, P. / Weinstabl, H. / Bader, G. / Zoephel, A. / Weiss-Puxbaum, A. / Ehrenhofer-Wolfer, K. / Wohrle, S. / Boehmelt, G. / Rinnenthal, J. / Arnhof, H. / Wiechens, N. / Wu, M.Y. / Owen-Hughes, T. / Ettmayer, P. / Pearson, M. / McConnell, D.B. / Ciulli, A.
History
DepositionAug 9, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 12, 2019Provider: repository / Type: Initial release
Revision 1.1Jun 19, 2019Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jul 3, 2019Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Jan 17, 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 / software / 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_asym_id / _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.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _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.value / _software.name / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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_asym_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_label_seq_id / _struct_conn.ptnr2_symmetry

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,4376
Polymers28,7612
Non-polymers6754
Water6,143341
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: surface plasmon resonance, Ligand binds to protein using SPR.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1330 Å2
ΔGint-58 kcal/mol
Surface area12730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.549, 42.549, 164.230
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number76
Space group name H-MP41

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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.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SMARCA2, BAF190B, BRM, SNF2A, SNF2L2 / Plasmid: pDEST15 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P51531, Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement
#2: Chemical ChemComp-FX5 / 2-(6-azanyl-5-piperazin-4-ium-1-yl-pyridazin-3-yl)phenol


Mass: 272.326 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H18N5O / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 341 / Source method: isolated from a natural source / Formula: H2O

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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: 2.81 Å3/Da / Density % sol: 56.16 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.1
Details: 25% (w/v) PEG 6000, 0.1 M HEPES, pH 6.1, 0.01M zinc chloride, 0.01 M cobalt (III) hexamine chloride, 8% (v/v) ethylene glycol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.99993 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 19, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99993 Å / Relative weight: 1
ReflectionResolution: 1.31→42.549 Å / Num. obs: 66651 / % possible obs: 99.5 % / Redundancy: 6.7 % / CC1/2: 0.999 / Rmerge(I) obs: 0.072 / Rpim(I) all: 0.044 / Rrim(I) all: 0.084 / Net I/σ(I): 9.9
Reflection shellResolution: 1.31→1.476 Å / Redundancy: 7.1 % / Rmerge(I) obs: 1.059 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 2249 / CC1/2: 0.6 / Rpim(I) all: 0.497 / Rrim(I) all: 1.177 / % possible all: 69.7

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Processing

Software
NameVersionClassification
BUSTER2.11.7refinement
PDB_EXTRACT3.24data extraction
XDSdata reduction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4QY4

4qy4


Resolution: 1.31→26 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.952 / SU R Cruickshank DPI: 0.076 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.071 / SU Rfree Blow DPI: 0.068 / SU Rfree Cruickshank DPI: 0.065 / Details: Hydrogens included in refinement.
RfactorNum. reflection% reflectionSelection details
Rfree0.193 2242 4.99 %RANDOM
Rwork0.178 ---
obs0.179 44968 64.8 %-
Displacement parametersBiso max: 145.92 Å2 / Biso mean: 27.14 Å2 / Biso min: 8.55 Å2
Baniso -1Baniso -2Baniso -3
1-1.1659 Å20 Å20 Å2
2--1.1659 Å20 Å2
3----2.3319 Å2
Refine analyzeLuzzati coordinate error obs: 0.18 Å
Refinement stepCycle: final / Resolution: 1.31→26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1860 0 42 341 2243
Biso mean--15.37 40.1 -
Num. residues----226
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d892SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes630HARMONIC5
X-RAY DIFFRACTIONt_it3900HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion246SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact4456SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d3900HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg7086HARMONIC20.92
X-RAY DIFFRACTIONt_omega_torsion3.6
X-RAY DIFFRACTIONt_other_torsion15.87
LS refinement shellResolution: 1.31→1.41 Å / Rfactor Rfree error: 0 / Total num. of bins used: 50
RfactorNum. reflection% reflection
Rfree0.3467 42 4.67 %
Rwork0.23 858 -
all0.235 900 -
obs--6.78 %
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)
11.3234-0.0841-0.45760.70970.00512.9734-0.04260.183-0.12410.0230.01930.02210.4329-0.00820.0233-0.0530.00040.0041-0.0381-0.0434-0.0967.756-18.12844.847
21.31670.07410.49060.68520.01322.9925-0.0436-0.17770.1228-0.03050.02470.0242-0.4437-0.00940.0189-0.0543-0.002-0.0027-0.0424-0.0429-0.1017-13.4903-3.1459-3.9052
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A1378 - 1490
2X-RAY DIFFRACTION2{ B|* }B1378 - 1490

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