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- PDB-8b5a: Human BRD3 bromodomain 2 in complex with a H4 peptide containing ... -

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Basic information

Entry
Database: PDB / ID: 8b5a
TitleHuman BRD3 bromodomain 2 in complex with a H4 peptide containing ApmTri (H4K20ApmTri)
Components
  • Bromodomain-containing protein 3
  • H4K20ApmTri
KeywordsPEPTIDE BINDING PROTEIN / ApmTri / acetyl-lysine mimic / BET-Bromodomain / histone-peptide
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)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.92 Å
AuthorsBraun, M.B. / Bartlick, N. / Stehle, T.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)SCHW 1163/9-1 Germany
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2023
Title: Synthesis, Biochemical Characterization, and Genetic Encoding of a 1,2,4-Triazole Amino Acid as an Acetyllysine Mimic for Bromodomains of the BET Family.
Authors: Kirchgassner, S. / Braun, M.B. / Bartlick, N. / Koc, C. / Reinkemeier, C.D. / Lemke, E.A. / Stehle, T. / Schwarzer, D.
History
DepositionSep 22, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 11, 2023Provider: repository / Type: Initial release
Revision 1.1Feb 15, 2023Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Mar 15, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.identifier_ORCID
Revision 1.3Mar 22, 2023Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 2.0May 24, 2023Group: Non-polymer description / Category: chem_comp / Item: _chem_comp.formula
Revision 2.1Feb 7, 2024Group: Data collection / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_conn
Item: _struct_conn.pdbx_leaving_atom_flag
Revision 2.2Oct 23, 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

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Assembly

Deposited unit
A: Bromodomain-containing protein 3
B: H4K20ApmTri


Theoretical massNumber of molelcules
Total (without water)14,3022
Polymers14,3022
Non-polymers00
Water1,36976
1
A: Bromodomain-containing protein 3
B: H4K20ApmTri

A: Bromodomain-containing protein 3
B: H4K20ApmTri


Theoretical massNumber of molelcules
Total (without water)28,6034
Polymers28,6034
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_555x,x-y,-z+1/61
Buried area3250 Å2
ΔGint-24 kcal/mol
Surface area12350 Å2
Unit cell
Length a, b, c (Å)79.610, 79.610, 95.300
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122
Space group name HallP612(x,y,z+5/12)
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/6
#3: y,-x+y,z+5/6
#4: -y,x-y,z+1/3
#5: -x+y,-x,z+2/3
#6: x-y,-y,-z
#7: -x,-x+y,-z+2/3
#8: -x,-y,z+1/2
#9: y,x,-z+1/3
#10: -y,-x,-z+5/6
#11: -x+y,y,-z+1/2
#12: x,x-y,-z+1/6
Components on special symmetry positions
IDModelComponents
11A-506-

HOH

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Components

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


Mass: 13032.073 Da / Num. of mol.: 1
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 H4K20ApmTri


Mass: 1269.436 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 76 / 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: 3.05 Å3/Da / Density % sol: 59.64 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 200 mM potassium sodium tatrate 100 mM sodium citrate pH 5.6 2 M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.99989 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: May 11, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99989 Å / Relative weight: 1
ReflectionResolution: 1.92→50 Å / Num. obs: 14001 / % possible obs: 98.9 % / Redundancy: 25.2 % / Biso Wilson estimate: 41.79 Å2 / CC1/2: 1 / Net I/σ(I): 31.84
Reflection shellResolution: 1.92→1.97 Å / Num. unique obs: 1012 / CC1/2: 0.776 / % possible all: 97.7

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2OO1

2oo1


Resolution: 1.92→36.73 Å / SU ML: 0.2888 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 29.3417
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2496 1248 8.99 %
Rwork0.2136 12633 -
obs0.2168 13881 98.11 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 48.24 Å2
Refinement stepCycle: LAST / Resolution: 1.92→36.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms954 0 0 76 1030
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0045988
X-RAY DIFFRACTIONf_angle_d0.63231339
X-RAY DIFFRACTIONf_chiral_restr0.0421139
X-RAY DIFFRACTIONf_plane_restr0.0033173
X-RAY DIFFRACTIONf_dihedral_angle_d2.0212810
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.92-20.47541250.49511282X-RAY DIFFRACTION91.36
2-2.090.25091360.24491387X-RAY DIFFRACTION99.48
2.09-2.20.32271330.25881337X-RAY DIFFRACTION96.33
2.2-2.340.39511340.34631352X-RAY DIFFRACTION95.87
2.34-2.520.24961380.22331404X-RAY DIFFRACTION100
2.52-2.770.25351410.20581415X-RAY DIFFRACTION99.94
2.77-3.170.26341420.21871437X-RAY DIFFRACTION99.81
3.17-40.22231440.19021459X-RAY DIFFRACTION99.81
4-36.730.21871550.18621560X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -23.5585414241 Å / Origin y: -28.110201011 Å / Origin z: 3.23749531333 Å
111213212223313233
T0.264955933953 Å2-0.0122397986889 Å2-0.0535009753031 Å2-0.342632148701 Å2-0.0698993232227 Å2--0.32728359151 Å2
L1.93575924773 °2-0.0642272406748 °2-0.127877957285 °2-3.77981258243 °2-0.337430747161 °2--3.99491272561 °2
S0.115106652953 Å °-0.189310537885 Å °-0.0625313590602 Å °0.171655941338 Å °0.142045482631 Å °-0.26912490488 Å °0.111423705429 Å °0.28555134317 Å °-0.230660722139 Å °
Refinement TLS groupSelection details: all

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