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- PDB-5o3d: Human Brd2(BD2) mutant in complex with 9-ET -

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Basic information

Entry
Database: PDB / ID: 5o3d
TitleHuman Brd2(BD2) mutant in complex with 9-ET
ComponentsBromodomain-containing protein 2
KeywordsTRANSCRIPTION / The Bromodomain and Extra-Terminal Domain (BET) Family Chromatin binding protein
Function / homology
Function and homology information


histone H4K12ac reader activity / histone H4K5ac reader activity / histone H3K14ac reader activity / acetylation-dependent protein binding / chromatin looping / RUNX3 regulates p14-ARF / positive regulation of T-helper 17 cell lineage commitment / protein localization to chromatin / neural tube closure / nucleosome assembly ...histone H4K12ac reader activity / histone H4K5ac reader activity / histone H3K14ac reader activity / acetylation-dependent protein binding / chromatin looping / RUNX3 regulates p14-ARF / positive regulation of T-helper 17 cell lineage commitment / protein localization to chromatin / neural tube closure / nucleosome assembly / spermatogenesis / histone binding / nuclear speck / chromatin remodeling / protein serine/threonine kinase activity / chromatin binding / regulation of transcription by RNA polymerase II / chromatin / nucleoplasm / nucleus / cytoplasm
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
Chem-9J5 / (2~{S})-1-[(2~{S})-2-oxidanylpropoxy]propan-2-ol / Bromodomain-containing protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsChan, K.-H. / Runcie, A.C. / Ciulli, A.
Funding support United Kingdom, 3items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research CouncilBB/J001201/2 United Kingdom
Biotechnology and Biological Sciences Research CouncilBB/G023123/2 United Kingdom
European Research CouncilERC-2012-StG-311460 DrugE3CRLs
CitationJournal: Chem Sci / Year: 2018
Title: Optimization of a "bump-and-hole" approach to allele-selective BET bromodomain inhibition.
Authors: Runcie, A.C. / Zengerle, M. / Chan, K.H. / Testa, A. / van Beurden, L. / Baud, M.G.J. / Epemolu, O. / Ellis, L.C.J. / Read, K.D. / Coulthard, V. / Brien, A. / Ciulli, A.
History
DepositionMay 23, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 14, 2018Provider: repository / Type: Initial release
Revision 1.1May 16, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_id_ISSN / _citation.journal_volume ..._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_author.name
Revision 2.0Jan 17, 2024Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Refinement description
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_special_symmetry
Item: _atom_site.occupancy / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Bromodomain-containing protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,9704
Polymers13,3611
Non-polymers6093
Water3,945219
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area110 Å2
ΔGint-7 kcal/mol
Surface area6540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.407, 71.830, 32.003
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-502-

CL

21A-503-

DQW

31A-818-

HOH

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Components

#1: Protein Bromodomain-containing protein 2 / O27.1.1 / Really interesting new gene 3 protein


Mass: 13361.383 Da / Num. of mol.: 1 / Mutation: L383V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BRD2, KIAA9001, RING3 / Plasmid: pNIC28-Bsa4 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: P25440
#2: Chemical ChemComp-9J5 / methyl (2~{R})-2-[(4~{S})-6-(4-chlorophenyl)-9-methoxy-1-methyl-4~{H}-[1,2,4]triazolo[4,3-a][1,4]benzodiazepin-4-yl]butanoate


Mass: 438.907 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H23ClN4O3
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-DQW / (2~{S})-1-[(2~{S})-2-oxidanylpropoxy]propan-2-ol


Mass: 134.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 219 / 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: 2.29 Å3/Da / Density % sol: 46.26 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.25
Details: 0.1M Tris pH8.25 55% Pentaerythritol propoxylate (5/4 PO/OH) 0.2M Imidazole

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Nov 19, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.6→32.003 Å / Num. obs: 16364 / % possible obs: 98.83 % / Redundancy: 10.3 % / CC1/2: 0.999 / Rmerge(I) obs: 0.05236 / Net I/σ(I): 32.7
Reflection shellResolution: 1.6→1.657 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.07519 / Num. unique obs: 1536 / CC1/2: 0.994 / % possible all: 94.76

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
iMOSFLMdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4QEU

4qeu


Resolution: 1.6→32.003 Å / SU ML: 0.1 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 15.2 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1703 808 4.94 %Random
Rwork0.1473 ---
obs0.1484 16363 98.82 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.6→32.003 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms922 0 41 219 1182
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091018
X-RAY DIFFRACTIONf_angle_d1.0561373
X-RAY DIFFRACTIONf_dihedral_angle_d10.813381
X-RAY DIFFRACTIONf_chiral_restr0.038136
X-RAY DIFFRACTIONf_plane_restr0.005174
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.70030.15481400.12872411X-RAY DIFFRACTION95
1.7003-1.83150.17841390.14352525X-RAY DIFFRACTION98
1.8315-2.01580.17971400.15232600X-RAY DIFFRACTION100
2.0158-2.30740.16921420.14112584X-RAY DIFFRACTION100
2.3074-2.90680.17731210.15452659X-RAY DIFFRACTION100
2.9068-32.00930.16431260.152776X-RAY DIFFRACTION100

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