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- PDB-7to9: BRD3-BD1 in complex with RaPID linear peptide 2xAcK.4xE (diAcK.4xE) -

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Basic information

Entry
Database: PDB / ID: 7to9
TitleBRD3-BD1 in complex with RaPID linear peptide 2xAcK.4xE (diAcK.4xE)
Components
  • 2xAcK.4xE (diAcK.4xE)
  • Bromodomain-containing protein 3
KeywordsTRANSCRIPTION / BET / bromodomain / RaPID / BRD3 / acetylated
Function / homology
Function and homology information


lncRNA binding / endodermal cell differentiation / protein localization to chromatin / : / molecular condensate scaffold activity / histone binding / chromatin remodeling / protein serine/threonine kinase activity / chromatin binding / regulation of transcription by RNA polymerase II ...lncRNA binding / endodermal cell differentiation / protein localization to chromatin / : / molecular condensate scaffold activity / histone binding / chromatin remodeling / protein serine/threonine kinase activity / chromatin binding / regulation of transcription by RNA polymerase II / chromatin / positive regulation of transcription by RNA polymerase II / nucleus
Similarity search - Function
Brdt, bromodomain, repeat I / Brdt, bromodomain, repeat II / NET domain superfamily / NET domain profile. / : / NET domain / Bromodomain extra-terminal - transcription regulation / Bromodomain-like / Histone Acetyltransferase; Chain A / Bromodomain, conserved site ...Brdt, bromodomain, repeat I / Brdt, bromodomain, repeat II / NET domain superfamily / NET domain profile. / : / NET domain / Bromodomain extra-terminal - transcription regulation / Bromodomain-like / Histone Acetyltransferase; Chain A / Bromodomain, conserved site / Bromodomain signature. / Bromodomain / Bromodomain profile. / bromo domain / Bromodomain / Bromodomain-like superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Bromodomain-containing protein 3
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsMackay, J.P. / Low, J.K.K. / Patel, K.
Funding support Australia, 1items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia)APP1161623 Australia
CitationJournal: J.Biol.Chem. / Year: 2023
Title: mRNA display reveals a class of high-affinity bromodomain-binding motifs that are not found in the human proteome.
Authors: Low, J.K.K. / Patel, K. / Jones, N. / Solomon, P. / Norman, A. / Maxwell, J.W.C. / Pachl, P. / Matthews, J.M. / Payne, R.J. / Passioura, T. / Suga, H. / Walport, L.J. / Mackay, J.P.
History
DepositionJan 23, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 25, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.3Feb 7, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.4Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Bromodomain-containing protein 3
B: Bromodomain-containing protein 3
C: 2xAcK.4xE (diAcK.4xE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,6425
Polymers32,4583
Non-polymers1842
Water3,153175
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2920 Å2
ΔGint-21 kcal/mol
Surface area13290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.582, 64.366, 52.312
Angle α, β, γ (deg.)90.000, 94.935, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein Bromodomain-containing protein 3 / RING3-like protein


Mass: 15095.392 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BRD3, KIAA0043, RING3L / Production host: Escherichia coli (E. coli) / References: UniProt: Q15059
#2: Protein/peptide 2xAcK.4xE (diAcK.4xE)


Mass: 2267.516 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 175 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.05 Å3/Da / Density % sol: 40.04 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.1 M HEPES, pH 7.5, 0.2 M sodium chloride, 10% v/v 2-propanol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.953732 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 12, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.953732 Å / Relative weight: 1
ReflectionResolution: 1.6→40.5 Å / Num. obs: 35429 / % possible obs: 99.9 % / Redundancy: 4.4 % / Biso Wilson estimate: 22.71 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.048 / Rpim(I) all: 0.039 / Rrim(I) all: 0.062 / Net I/σ(I): 12
Reflection shellResolution: 1.6→1.63 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.673 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 1763 / CC1/2: 0.785 / Rpim(I) all: 0.41 / Rrim(I) all: 0.878 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
PHENIX1.17.1_3660refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3S91

3s91


Resolution: 1.6→40.5 Å / SU ML: 0.2231 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.477
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2268 1851 5.23 %
Rwork0.1985 33535 -
obs0.1999 35386 99.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 29.25 Å2
Refinement stepCycle: LAST / Resolution: 1.6→40.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2051 0 12 175 2238
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00632238
X-RAY DIFFRACTIONf_angle_d0.86643024
X-RAY DIFFRACTIONf_chiral_restr0.0494319
X-RAY DIFFRACTIONf_plane_restr0.0045379
X-RAY DIFFRACTIONf_dihedral_angle_d8.0486303
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.640.35671440.33532563X-RAY DIFFRACTION99.89
1.64-1.690.33451630.32072568X-RAY DIFFRACTION99.78
1.69-1.750.34941470.28322528X-RAY DIFFRACTION99.93
1.75-1.810.26581340.24582597X-RAY DIFFRACTION99.85
1.81-1.880.28921590.22372551X-RAY DIFFRACTION99.89
1.88-1.970.24531240.21222583X-RAY DIFFRACTION99.85
1.97-2.070.23781260.20682584X-RAY DIFFRACTION99.93
2.07-2.20.20781350.19092573X-RAY DIFFRACTION99.82
2.2-2.370.26151460.20482604X-RAY DIFFRACTION99.93
2.37-2.610.20191560.19412546X-RAY DIFFRACTION99.78
2.61-2.990.22841380.19932593X-RAY DIFFRACTION99.96
2.99-3.760.19681500.17872602X-RAY DIFFRACTION99.64
3.76-40.50.20471290.17632643X-RAY DIFFRACTION99.5

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