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- PDB-4qy4: Crystal structure of the bromodomain of human SMARCA2 -

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Basic information

Entry
Database: PDB / ID: 4qy4
TitleCrystal structure of the bromodomain of human SMARCA2
ComponentsSMARCA2 protein
KeywordsUNKNOWN FUNCTION / SMARCA2 BAF190B BRM SNF2A SNF2L2 / Structural Genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


nBAF complex / npBAF complex / RSC-type complex / Formation of the canonical BAF (cBAF) complex / Formation of the polybromo-BAF (pBAF) complex / Formation of neuronal progenitor and neuronal BAF (npBAF and nBAF) / Formation of the non-canonical BAF (ncBAF) complex / nucleosome array spacer activity / regulation of G0 to G1 transition / SWI/SNF complex ...nBAF complex / npBAF complex / RSC-type complex / Formation of the canonical BAF (cBAF) complex / Formation of the polybromo-BAF (pBAF) complex / Formation of neuronal progenitor and neuronal BAF (npBAF and nBAF) / Formation of the non-canonical BAF (ncBAF) complex / nucleosome array spacer activity / regulation of G0 to G1 transition / SWI/SNF complex / regulation of mitotic metaphase/anaphase transition / positive regulation of T cell differentiation / regulation of nucleotide-excision repair / positive regulation of stem cell population maintenance / positive regulation of double-strand break repair / Regulation of MITF-M-dependent genes involved in pigmentation / negative regulation of cell differentiation / RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known / positive regulation of myoblast differentiation / ATP-dependent activity, acting on DNA / regulation of G1/S transition of mitotic cell cycle / 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 transcription by RNA polymerase II / regulation of DNA-templated transcription / positive regulation of DNA-templated transcription / chromatin / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / ATP hydrolysis activity / DNA binding / DNA-templated transcription / nucleoplasm / ATP binding / nucleus
Similarity search - Function
Remodelling complex subunit Rsc/polybromo / BRK domain / BRK domain / BRK domain superfamily / domain in transcription and CHROMO domain helicases / QLQ / Glutamine-Leucine-Glutamine, QLQ / QLQ domain profile. / QLQ / Snf2-ATP coupling, chromatin remodelling complex ...Remodelling complex subunit Rsc/polybromo / BRK domain / BRK domain / BRK domain superfamily / domain in transcription and CHROMO domain helicases / QLQ / Glutamine-Leucine-Glutamine, 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
SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A member 2 / cDNA FLJ36757 fis, clone UTERU2018522, highly similar to Human transcriptional activator hSNF2a
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.97 Å
AuthorsTallant, C. / Savitsky, P. / Nunez-Alonso, G. / Fonseca, M. / Krojer, T. / Filippakopoulos, P. / von Delft, F. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. ...Tallant, C. / Savitsky, P. / Nunez-Alonso, G. / Fonseca, M. / Krojer, T. / Filippakopoulos, P. / von Delft, F. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Knapp, S. / Structural Genomics Consortium (SGC)
CitationJournal: To be Published
Title: Crystal structure of the bromodomain of human SMARCA2
Authors: Tallant, C. / Savitsky, P. / Nunez-Alonso, G. / Fonseca, M. / Krojer, T. / Filippakopoulos, P. / von Delft, F. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Knapp, S.
History
DepositionJul 23, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 27, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2023Group: 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_ref_seq_dif / struct_site
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_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: SMARCA2 protein
B: SMARCA2 protein
C: SMARCA2 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,3386
Polymers43,1423
Non-polymers1963
Water1,76598
1
A: SMARCA2 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,4462
Polymers14,3811
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: SMARCA2 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,4462
Polymers14,3811
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: SMARCA2 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,4462
Polymers14,3811
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)64.346, 64.346, 89.117
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31

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Components

#1: Protein SMARCA2 protein


Mass: 14380.542 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SMARCA2 / Plasmid: pNIC28-Bsa4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-R3 / References: UniProt: Q8N9Q1, UniProt: P51531*PLUS
#2: Chemical ChemComp-ZN / ZINC ION


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


Mass: 18.015 Da / Num. of mol.: 98 / 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: 2.47 Å3/Da / Density % sol: 50.18 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 15% PEG 6K, 8% ethylene glycol, 0.01M ZnCl2, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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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: 1.97→55.73 Å / Num. all: 28970 / Num. obs: 28970 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.6 % / Biso Wilson estimate: 18.046 Å2 / Rmerge(I) obs: 0.219 / Rsym value: 0.141 / Net I/σ(I): 11.9
Reflection shell

Diffraction-ID: 1 / % possible all: 100

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allRsym value
1.99-2.0463.292.8103551.324
2.04-2.16.42.3973.8130990.934
2.1-2.156.81.7474.9133090.663
2.15-2.226.71.1016127440.421
2.22-2.296.20.7417.1114240.294
2.29-2.376.70.5388.1121340.205
2.37-2.456.50.4169.1111460.162
2.45-2.556.50.3710.399440.144
2.55-2.666.20.33311.399000.133
2.66-2.786.50.29312.998280.115
7.36-12.746.90.13425.338470.05

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
REFMAC5.8.0073refinement
XDSdata reduction
Aimlessdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Ensemble of 2GRC, 2OSS, 3D7C, 2OUO, 2OO1, 3DAI, 3DWY.

2grc

2oss

3d7c

2ouo

2oo1

3dai

3dwy


Resolution: 1.97→55.73 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.883 / SU B: 9.877 / SU ML: 0.146 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.183 / ESU R Free: 0.177 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27889 1415 4.9 %RANDOM
Rwork0.22367 ---
all0.22633 28970 --
obs0.22633 27508 98.75 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 36.384 Å2
Baniso -1Baniso -2Baniso -3
1-0.73 Å20.36 Å20 Å2
2--0.73 Å2-0 Å2
3----2.36 Å2
Refinement stepCycle: LAST / Resolution: 1.97→55.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2650 0 3 98 2751
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0192690
X-RAY DIFFRACTIONr_bond_other_d0.0010.022680
X-RAY DIFFRACTIONr_angle_refined_deg1.61.9763607
X-RAY DIFFRACTIONr_angle_other_deg0.8436171
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8665320
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.00824.385130
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.29715547
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.8891520
X-RAY DIFFRACTIONr_chiral_restr0.0910.2403
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022969
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02607
X-RAY DIFFRACTIONr_mcbond_it1.4731.8271289
X-RAY DIFFRACTIONr_mcbond_other1.4721.8251288
X-RAY DIFFRACTIONr_mcangle_it2.2622.7251606
X-RAY DIFFRACTIONr_mcangle_other2.2622.7271607
X-RAY DIFFRACTIONr_scbond_it1.9412.081401
X-RAY DIFFRACTIONr_scbond_other1.942.0821402
X-RAY DIFFRACTIONr_scangle_other3.1623.0162002
X-RAY DIFFRACTIONr_long_range_B_refined5.05414.5233177
X-RAY DIFFRACTIONr_long_range_B_other5.0114.4123155
LS refinement shellResolution: 1.968→2.019 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.333 111 -
Rwork0.326 1758 -
obs--85.85 %
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)
10.4344-0.1047-0.02560.85720.05531.9281-0.00560.1666-0.03470.0862-0.0463-0.124-0.1494-0.10860.05190.11640.05430.03490.13370.03970.107528.047420.407618.473
20.5123-0.13680.04830.39120.23571.62020.02260.0113-0.02130.0465-0.07590.00970.0061-0.15930.05320.13070.06460.04810.1541-0.01030.08741.80034.433726.213
30.96230.99180.32761.3861.17292.089-0.01560.43230.17590.28020.5225-0.04060.52070.3587-0.5070.16810.1634-0.1360.4316-0.01130.16772.738831.58083.6272
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1381 - 1490
2X-RAY DIFFRACTION2B1383 - 1490
3X-RAY DIFFRACTION3C1383 - 1487

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