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- PDB-5dkd: Crystal structure of the bromodomain of human BRG1 (SMARCA4) in c... -

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Basic information

Entry
Database: PDB / ID: 5dkd
TitleCrystal structure of the bromodomain of human BRG1 (SMARCA4) in complex with PFI-3 chemical probe
ComponentsTranscription activator BRG1
KeywordsHYDROLASE / SWI-SNF complex / chromatin remodeling / Brg associated factors (BAF) / transcription
Function / homology
Function and homology information


positive regulation of glucose mediated signaling pathway / positive regulation of transcription of nucleolar large rRNA by RNA polymerase I / bBAF complex / neural retina development / npBAF complex / nBAF complex / negative regulation of androgen receptor signaling pathway / EGR2 and SOX10-mediated initiation of Schwann cell myelination / nucleosome array spacer activity / GBAF complex ...positive regulation of glucose mediated signaling pathway / positive regulation of transcription of nucleolar large rRNA by RNA polymerase I / bBAF complex / neural retina development / npBAF complex / nBAF complex / negative regulation of androgen receptor signaling pathway / EGR2 and SOX10-mediated initiation of Schwann cell myelination / nucleosome array spacer activity / GBAF complex / regulation of G0 to G1 transition / Tat protein binding / RNA polymerase I preinitiation complex assembly / RSC-type complex / ATP-dependent chromatin remodeler activity / regulation of nucleotide-excision repair / host-mediated activation of viral transcription / nucleosome disassembly / SWI/SNF complex / regulation of mitotic metaphase/anaphase transition / positive regulation of T cell differentiation / nuclear androgen receptor binding / 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 / positive regulation of signal transduction by p53 class mediator / negative regulation of cell differentiation / positive regulation of Wnt signaling pathway / ATP-dependent activity, acting on DNA / positive regulation of myoblast differentiation / Chromatin modifying enzymes / DNA polymerase binding / Interleukin-7 signaling / transcription initiation-coupled chromatin remodeling / transcription coregulator binding / positive regulation of cell differentiation / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / Formation of the beta-catenin:TCF transactivating complex / helicase activity / negative regulation of cell growth / kinetochore / positive regulation of miRNA transcription / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / RMTs methylate histone arginines / nuclear matrix / fibrillar center / p53 binding / transcription corepressor activity / nervous system development / positive regulation of cold-induced thermogenesis / histone binding / transcription coactivator activity / hydrolase activity / chromatin remodeling / negative regulation of DNA-templated transcription / positive regulation of cell population proliferation / chromatin binding / regulation of transcription by RNA polymerase II / chromatin / positive regulation of DNA-templated transcription / nucleolus / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / protein-containing complex / extracellular space / DNA binding / RNA binding / nucleoplasm / ATP binding / nucleus / membrane
Similarity search - Function
SWI/SNF complex subunit BRG1 / 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 ...SWI/SNF complex subunit BRG1 / 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 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsTallant, C. / Owen, D.R. / Gerstenberger, B.S. / Fedorov, O. / Savitsky, P. / Nunez-Alonso, G. / Newman, J.A. / Filippakopoulos, P. / Burgess-Brown, N. / von Delft, F. ...Tallant, C. / Owen, D.R. / Gerstenberger, B.S. / Fedorov, O. / Savitsky, P. / Nunez-Alonso, G. / Newman, J.A. / Filippakopoulos, P. / Burgess-Brown, N. / 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 BRG1 (SMARCA4) in complex with PFI-3 chemical probe
Authors: Tallant, C. / Owen, D.R. / Gerstenberger, B.S. / Fedorov, O. / Savitsky, P. / Nunez-Alonso, G. / Newman, J.A. / Filippakopoulos, P. / Burgess-Brown, N. / von Delft, F. / Arrowsmith, C.H. / ...Authors: Tallant, C. / Owen, D.R. / Gerstenberger, B.S. / Fedorov, O. / Savitsky, P. / Nunez-Alonso, G. / Newman, J.A. / Filippakopoulos, P. / Burgess-Brown, N. / 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 / struct_ncs_dom_lim
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.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 / _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_symmetry / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Transcription activator BRG1
B: Transcription activator BRG1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,60712
Polymers28,4612
Non-polymers1,14610
Water1,820101
1
A: Transcription activator BRG1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,8036
Polymers14,2301
Non-polymers5735
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Transcription activator BRG1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,8036
Polymers14,2301
Non-polymers5735
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)45.926, 74.566, 52.626
Angle α, β, γ (deg.)90.00, 109.90, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: ASN / Beg label comp-ID: ASN / End auth comp-ID: LYS / End label comp-ID: LYS / Refine code: _ / Auth seq-ID: 1457 - 1566 / Label seq-ID: 9 - 118

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein Transcription activator BRG1 / ATP-dependent helicase SMARCA4 / BRG1-associated factor 190A / BAF190A / Mitotic growth and ...ATP-dependent helicase SMARCA4 / BRG1-associated factor 190A / BAF190A / Mitotic growth and transcription activator / Protein BRG-1 / Protein brahma homolog 1 / SNF2-beta / SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A member 4


Mass: 14230.447 Da / Num. of mol.: 2 / Fragment: UNP residues 1418-1536
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SMARCA4, BAF190A, BRG1, SNF2B, SNF2L4 / Plasmid: pNIC28-Bsa4 / Production host: Escherichia coli (E. coli)
References: UniProt: P51532, 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.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#4: 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.: 2 / Source method: obtained synthetically / Formula: C19H19N3O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 101 / 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: 2.98 Å3/Da / Density % sol: 58.78 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 7.2
Details: 0.1 M Bis Tris pH 7.2, 0.1 M ammonium acetate, 0.1 M ZnCl2, 15% PEG smear high (mixture from PEG8k to 20k)
PH range: 7.2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9207 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 12, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9207 Å / Relative weight: 1
ReflectionResolution: 2→29.78 Å / Num. obs: 21859 / % possible obs: 96.8 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.076 / Rsym value: 0.054 / Net I/av σ(I): 9.8 / Net I/σ(I): 9.8
Reflection shellResolution: 2→2.05 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.304 / Mean I/σ(I) obs: 3.3 / % possible all: 95.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3UVD

3uvd


Resolution: 2→29.78 Å / Cor.coef. Fo:Fc: 0.849 / Cor.coef. Fo:Fc free: 0.829 / SU B: 9.907 / SU ML: 0.153 / Cross valid method: THROUGHOUT / ESU R: 0.226 / ESU R Free: 0.195 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.29729 1027 4.8 %RANDOM
Rwork0.26773 ---
obs0.2692 20159 93.85 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 32.2 Å2
Baniso -1Baniso -2Baniso -3
1-2.12 Å2-0 Å20.16 Å2
2---1.2 Å2-0 Å2
3----0.82 Å2
Refinement stepCycle: 1 / Resolution: 2→29.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1827 0 74 101 2002
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.021923
X-RAY DIFFRACTIONr_bond_other_d0.0040.021954
X-RAY DIFFRACTIONr_angle_refined_deg1.7412.0292563
X-RAY DIFFRACTIONr_angle_other_deg1.2463.0064508
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1685218
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.76624.41986
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.66715401
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.1551514
X-RAY DIFFRACTIONr_chiral_restr0.1070.2286
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022052
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02420
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_it1.7732.196878
X-RAY DIFFRACTIONr_mcbond_other1.7712.193877
X-RAY DIFFRACTIONr_mcangle_it2.7083.2751094
X-RAY DIFFRACTIONr_mcangle_other2.7073.2791095
X-RAY DIFFRACTIONr_scbond_it2.6472.6511045
X-RAY DIFFRACTIONr_scbond_other2.6472.6511044
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.263.7881470
X-RAY DIFFRACTIONr_long_range_B_refined5.89718.1042324
X-RAY DIFFRACTIONr_long_range_B_other5.8617.9762297
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 6793 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.14 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.002→2.054 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.268 80 -
Rwork0.233 1479 -
obs--95.64 %
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)DetailsOrigin x (Å)Origin y (Å)Origin z (Å)
10.5040.15990.482.05130.74070.6872-0.0218-0.01560.0552-0.0107-0.0920.04950.0321-0.03560.11370.05390.00040.0470.0274-0.00190.054Chain A14.406212.920329.2681
21.28540.9947-0.42241.8019-0.38130.82990.0788-0.114-0.0676-0.1557-0.03050.0269-0.12210.0616-0.04830.0977-0.02280.01280.01440.00810.0334Chain B1.95284.186752.7679
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1B1457 - 1566
2X-RAY DIFFRACTION2B1457 - 1566

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