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- PDB-7to7: BRD3-BD1 in complex with RaPID linear peptide 1xAcK.4XE (monoAcK.4xE) -

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Basic information

Entry
Database: PDB / ID: 7to7
TitleBRD3-BD1 in complex with RaPID linear peptide 1xAcK.4XE (monoAcK.4xE)
Components
  • 1xAcK.4xE (monoAcK.4xE)
  • Bromodomain-containing protein 3
KeywordsTRANSCRIPTION / BET / bromodomain / RaPID / BRD3 / acetylated
Function / homology
Function and homology information


histone H3K27cr reader activity / histone H3K18cr reader activity / histone H3K9cr reader activity / histone H3K9me2/3 reader activity / lncRNA binding / endodermal cell differentiation / protein localization to chromatin / : / molecular condensate scaffold activity / histone binding ...histone H3K27cr reader activity / histone H3K18cr reader activity / histone H3K9cr reader activity / histone H3K9me2/3 reader activity / 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 / bromo domain / Bromodomain / Bromodomain (BrD) profile. / 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: 1.93 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 1.4Oct 30, 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: 1xAcK.4xE (monoAcK.4xE)
D: Bromodomain-containing protein 3
E: Bromodomain-containing protein 3
F: 1xAcK.4xE (monoAcK.4xE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,1768
Polymers63,9926
Non-polymers1842
Water2,810156
1
A: Bromodomain-containing protein 3
B: Bromodomain-containing protein 3
C: 1xAcK.4xE (monoAcK.4xE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,0884
Polymers31,9963
Non-polymers921
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: Bromodomain-containing protein 3
E: Bromodomain-containing protein 3
F: 1xAcK.4xE (monoAcK.4xE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,0884
Polymers31,9963
Non-polymers921
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)41.862, 99.277, 120.608
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab

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Components

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


Mass: 15095.392 Da / Num. of mol.: 4 / Fragment: BD1 (UNP residues 25-147)
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 1xAcK.4xE (monoAcK.4xE)


Mass: 1805.012 Da / Num. of mol.: 2 / 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.: 156 / 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: 1.85 Å3/Da / Density % sol: 33.64 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 0.1 M PCTP, pH 4.0, 25% w/v PEG1500

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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: 1.93→49.64 Å / Num. obs: 38396 / % possible obs: 99.6 % / Redundancy: 8.2 % / Biso Wilson estimate: 24.84 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.129 / Rpim(I) all: 0.069 / Rrim(I) all: 0.147 / Net I/σ(I): 11.3
Reflection shellResolution: 1.93→1.98 Å / Redundancy: 8.1 % / Rmerge(I) obs: 1.118 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 2398 / CC1/2: 0.636 / Rpim(I) all: 0.603 / Rrim(I) all: 1.274 / % possible all: 94.4

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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: 1.93→49.64 Å / SU ML: 0.2321 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.8532
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2506 2027 5.29 %
Rwork0.2013 36292 -
obs0.2039 38319 99.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 27.42 Å2
Refinement stepCycle: LAST / Resolution: 1.93→49.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4089 0 12 156 4257
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00724434
X-RAY DIFFRACTIONf_angle_d0.85416002
X-RAY DIFFRACTIONf_chiral_restr0.0478642
X-RAY DIFFRACTIONf_plane_restr0.0053756
X-RAY DIFFRACTIONf_dihedral_angle_d10.7404576
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.93-1.980.32741350.26122420X-RAY DIFFRACTION94.73
1.98-2.040.30871150.24222579X-RAY DIFFRACTION100
2.04-2.10.28121460.23092585X-RAY DIFFRACTION99.93
2.1-2.160.26851380.22042554X-RAY DIFFRACTION100
2.16-2.240.26551770.2092532X-RAY DIFFRACTION100
2.24-2.330.28741570.21792580X-RAY DIFFRACTION99.96
2.33-2.440.2851320.21572550X-RAY DIFFRACTION100
2.44-2.570.28141530.20982599X-RAY DIFFRACTION99.96
2.57-2.730.29341330.21552577X-RAY DIFFRACTION100
2.73-2.940.28891470.21622610X-RAY DIFFRACTION99.96
2.94-3.230.26331400.21862622X-RAY DIFFRACTION99.96
3.23-3.70.22831360.19362631X-RAY DIFFRACTION100
3.7-4.660.18891610.15862666X-RAY DIFFRACTION100
4.66-49.640.23291570.1872787X-RAY DIFFRACTION99.83

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