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- PDB-5o3b: Human Brd2(BD2) mutant in complex with AL -

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Basic information

Entry
Database: PDB / ID: 5o3b
TitleHuman Brd2(BD2) mutant in complex with AL
ComponentsBromodomain-containing protein 2
KeywordsTRANSCRIPTION / The Bromodomain and Extra-Terminal Domain (BET) Family Chromatin binding protein
Function / homology
Function and homology information


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 / lysine-acetylated histone binding / nucleosome assembly / spermatogenesis / histone binding ...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 / lysine-acetylated histone binding / 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 / Bromodomain profile. / bromo domain / Bromodomain / Bromodomain-like superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-9HZ / Bromodomain-containing protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsRuncie, A.C. / Chan, K.-H. / 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 1.2Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _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
B: Bromodomain-containing protein 2
C: Bromodomain-containing protein 2
D: Bromodomain-containing protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,2498
Polymers53,4464
Non-polymers1,8044
Water10,070559
1
A: Bromodomain-containing protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,8122
Polymers13,3611
Non-polymers4511
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Bromodomain-containing protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,8122
Polymers13,3611
Non-polymers4511
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Bromodomain-containing protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,8122
Polymers13,3611
Non-polymers4511
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Bromodomain-containing protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,8122
Polymers13,3611
Non-polymers4511
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)88.075, 101.893, 123.534
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-701-

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.: 4 / Mutation: L383V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BRD2, KIAA9001, RING3 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: P25440
#2: Chemical
ChemComp-9HZ / methyl (2~{R})-2-[(4~{S})-6-(4-chlorophenyl)-8-methoxy-1-methyl-4~{H}-[1,2,4]triazolo[4,3-a][1,4]benzodiazepin-4-yl]pent-4-enoate


Mass: 450.917 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C24H23ClN4O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 559 / 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: 2.59 Å3/Da / Density % sol: 52.56 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1M Tris pH 7.5 60% Pentaerythritol propoxylate (5/4 PO/OH) 0.2M Imidazole pH 8.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9174 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Nov 24, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9174 Å / Relative weight: 1
ReflectionResolution: 1.95→44.04 Å / Num. obs: 40791 / % possible obs: 99.92 % / Redundancy: 8.6 % / CC1/2: 0.984 / Rmerge(I) obs: 0.2827 / Net I/σ(I): 10.54
Reflection shellResolution: 1.95→2.02 Å / Redundancy: 7.8 % / Rmerge(I) obs: 0.9697 / Num. unique obs: 4007 / CC1/2: 0.535 / % possible all: 99.98

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Processing

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

4qeu


Resolution: 1.95→44.038 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.59 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2439 2002 4.92 %
Rwork0.2007 --
obs0.2028 40702 99.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.95→44.038 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3613 0 128 559 4300
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093853
X-RAY DIFFRACTIONf_angle_d1.0435205
X-RAY DIFFRACTIONf_dihedral_angle_d12.4171412
X-RAY DIFFRACTIONf_chiral_restr0.042516
X-RAY DIFFRACTIONf_plane_restr0.005664
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.95-1.99880.33821460.27742724X-RAY DIFFRACTION100
1.9988-2.05280.32391510.2722728X-RAY DIFFRACTION100
2.0528-2.11320.31881390.27112716X-RAY DIFFRACTION99
2.1132-2.18140.26651330.23162743X-RAY DIFFRACTION100
2.1814-2.25940.30971300.26462720X-RAY DIFFRACTION99
2.2594-2.34990.26011220.21672770X-RAY DIFFRACTION100
2.3499-2.45680.2781550.20682734X-RAY DIFFRACTION100
2.4568-2.58630.24661350.20282765X-RAY DIFFRACTION100
2.5863-2.74830.27221350.21392771X-RAY DIFFRACTION100
2.7483-2.96050.24031490.20072746X-RAY DIFFRACTION100
2.9605-3.25830.26441440.19572780X-RAY DIFFRACTION100
3.2583-3.72960.22371450.17482767X-RAY DIFFRACTION100
3.7296-4.69810.17921610.15422814X-RAY DIFFRACTION100
4.6981-44.04890.20261570.16642922X-RAY DIFFRACTION100

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