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- PDB-6ytm: Human Brd2(BD2) L383V mutant in complex with ET-JQ1-OMe -

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Basic information

Entry
Database: PDB / ID: 6ytm
TitleHuman Brd2(BD2) L383V mutant in complex with ET-JQ1-OMe
ComponentsBromodomain-containing protein 2BRD2
KeywordsTRANSCRIPTION / Epigenetics / Bump and Hole / Brd2 / second bromodomain
Function / homology
Function and homology information


chromatin looping / acetylation-dependent protein binding / 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 / nuclear speck ...chromatin looping / acetylation-dependent protein binding / 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 / nuclear speck / protein phosphorylation / protein serine/threonine kinase activity / chromatin binding / chromatin / regulation of transcription by RNA polymerase II / nucleoplasm / nucleus / cytoplasm
Similarity search - Function
NET domain superfamily / NET domain profile. / Brdt, bromodomain, repeat II / Brdt, bromodomain, repeat I / NET domain / Bromodomain extra-terminal - transcription regulation / Bromodomain-like / Histone Acetyltransferase; Chain A / Bromodomain, conserved site / Bromodomain signature. ...NET domain superfamily / NET domain profile. / Brdt, bromodomain, repeat II / Brdt, bromodomain, repeat I / 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-PMW / Chem-PXN / Bromodomain-containing protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.56 Å
AuthorsBond, A.G. / Ciulli, A. / Cowan, A.D.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
European Research Council (ERC)ERC-2012-StG-311460-DrugE3CRLsEuropean Union
Citation
Journal: Org.Biomol.Chem. / Year: 2020
Title: Stereoselective synthesis of allele-specific BET inhibitors.
Authors: Bond, A.G. / Testa, A. / Ciulli, A.
#1: Journal: Chemrxiv / Year: 2020
Title: Stereoselective Synthesis of Allele-Specific BET Inhibitors
Authors: Bond, A.G. / Testa, A. / Ciulli, A.
History
DepositionApr 24, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 27, 2020Provider: repository / Type: Initial release
Revision 1.1Aug 19, 2020Group: Database references / Refinement description / Category: citation / citation_author / software / Item: _software.name
Revision 1.2Oct 14, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 2.0Sep 27, 2023Group: Advisory / Author supporting evidence ...Advisory / Author supporting evidence / Data collection / Database references / Derived calculations / Non-polymer description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / citation / database_2 / entity / pdbx_audit_support / pdbx_entity_nonpoly / pdbx_unobs_or_zero_occ_atoms
Item: _chem_comp.formula / _chem_comp.formula_weight ..._chem_comp.formula / _chem_comp.formula_weight / _chem_comp.name / _citation.journal_id_ISSN / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.formula_weight / _entity.pdbx_description / _pdbx_audit_support.country / _pdbx_entity_nonpoly.name
Revision 2.1Jan 24, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,3466
Polymers26,7232
Non-polymers1,6234
Water3,351186
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A: Bromodomain-containing protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,5414
Polymers13,3611
Non-polymers1,1803
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Bromodomain-containing protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,8042
Polymers13,3611
Non-polymers4431
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)34.050, 50.530, 130.490
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Bromodomain-containing protein 2 / BRD2 / O27.1.1 / Really interesting new gene 3 protein


Mass: 13361.383 Da / Num. of mol.: 2 / 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-PMW / methyl (2R)-2-[(9S)-7-(4-chlorophenyl)-4,5,13-trimethyl-3-thia-1,8,11,12-tetrazatricyclo[8.3.0.0^{2,6}]trideca-2(6),4,7,10,12-pentaen-9-yl]butanoate


Mass: 442.962 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C22H23ClN4O2S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-PXN / (2S)-1-[3-{[(2R)-2-hydroxypropyl]oxy}-2,2-bis({[(2R)-2-hydroxypropyl]oxy}methyl)propoxy]propan-2-ol / PENTAERYTHRITOL PROPOXYLATE (5/4 PO/OH)


Mass: 368.463 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H36O8
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 186 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.1 Å3/Da / Density % sol: 41.44 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.75
Details: 0.1 M Tris pH 8.75, 55% pentaerythiol propoxylate (5/4 PO/OH)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9686 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jan 25, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9686 Å / Relative weight: 1
ReflectionResolution: 1.56→65.24 Å / Num. obs: 32946 / % possible obs: 99 % / Redundancy: 12.3 % / CC1/2: 0.998 / Rmerge(I) obs: 0.185 / Rpim(I) all: 0.054 / Rrim(I) all: 0.193 / Net I/σ(I): 13.9 / Num. measured all: 405808 / Scaling rejects: 2547
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.56-1.6411.11.4895152646620.630.4631.5633.198
4.92-65.2410.40.0761256312090.9970.0240.0829.7100

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Processing

Software
NameVersionClassification
PHENIX1.17.1-3660refinement
autoPROCdata scaling
PHASERphasing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5O3D

5o3d


Resolution: 1.56→47.12 Å / SU ML: 0.1467 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.4285
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2037 1608 4.9 %
Rwork0.1727 31239 -
obs0.1743 32847 98.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 23.4 Å2
Refinement stepCycle: LAST / Resolution: 1.56→47.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1799 0 76 186 2061
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00871982
X-RAY DIFFRACTIONf_angle_d0.88792681
X-RAY DIFFRACTIONf_chiral_restr0.0499265
X-RAY DIFFRACTIONf_plane_restr0.0056342
X-RAY DIFFRACTIONf_dihedral_angle_d22.8029739
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.56-1.610.30051400.26592748X-RAY DIFFRACTION97.14
1.61-1.660.26831360.21212755X-RAY DIFFRACTION98.03
1.66-1.730.23131330.22789X-RAY DIFFRACTION97.53
1.73-1.810.25531330.18112802X-RAY DIFFRACTION98.16
1.81-1.90.20081390.17422801X-RAY DIFFRACTION98.49
1.9-2.020.24261510.17252823X-RAY DIFFRACTION98.87
2.02-2.180.18261580.15492814X-RAY DIFFRACTION99.2
2.18-2.40.17621540.16382833X-RAY DIFFRACTION99.43
2.4-2.750.18831490.17262873X-RAY DIFFRACTION99.28
2.75-3.460.20521550.17162921X-RAY DIFFRACTION99.64
3.46-47.120.18951600.16253080X-RAY DIFFRACTION99.94
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.967654200321.275169610462.294932705058.824042658471.153129586664.235142167860.0898262384654-0.7682130963040.2351527824650.263625688196-0.243079512836-0.335831295385-0.3138809232540.4710334776610.09205170409950.135933277993-0.0304432593388-0.008714905173390.281826968446-0.04297339799090.12664019502515.43666233863.42425402819-1.87231052974
24.05118976868-0.0675388122002-2.236660952134.340343766033.257759327768.87651481112-0.100448030455-0.425829643191-0.2180994517840.1923643685140.07251902675070.1514784144620.253984400181-0.07097658923880.04615390472870.0813980279308-0.00957990970829-0.003886696155650.1347910937360.05926845771990.1099179125975.16848038083-10.6537091337-5.80303017787
34.28908552538-0.03087234318921.027308624185.376168505741.426119845456.539777309490.07150103487930.268564688057-0.307394490149-0.232018082359-0.0841351150822-0.1633876437580.4111188670280.06483200711450.01825264772530.1453070683160.004061518346960.03817659926860.132177354347-0.02934662271110.13152254790811.7407694555-15.7083180147-21.6728519707
47.397541211214.871340485785.5811727283.7627644133.739325703668.338069391030.252313231501-0.456519652287-0.08146458194240.0732302177588-0.175161830119-0.5023859730080.07237505722930.318761673396-0.1056782002350.07400061875120.007273440102160.001756139789830.1773074200890.01309262936660.15334827655718.4600032078-6.81926834136-6.46653519321
55.271627936031.614776344582.484291300722.79758047061.273152855413.522856378080.047680353856-0.0534823302481-0.0789623270932-0.08779045169880.00462247112517-0.156584221921-0.03905634586620.0207839244514-0.03493268838840.0575405979630.01361570759560.03053127140040.0761351294558-8.17224953322E-50.075680570017211.7364221988-3.50922903155-15.6365242908
65.399405373152.376407758711.963656877333.402941181853.256508071115.212431796710.0248735956956-0.1116297643490.176441342278-0.03022202113990.0221673567484-0.0583799285347-0.175148820696-0.0573568858871-0.002944048303810.07506921711620.01412965670750.00890525573410.1207831445460.003671381794420.07959979179083.853181561761.49425850261-10.1097372114
75.49111704483-1.78316720254-2.515747089512.605064616642.070982445754.11843503892-0.0893405776790.744408063990.0448088924162-0.5621924847180.0460200311537-0.4115197030850.1871457729160.1554649963890.01444502469320.3301398614810.04286236304390.0177379734680.290626826697-0.01232098016450.1888263083093.995945516555.39511957261-33.0481536789
84.765872186091.62300129031.564135330633.960446090231.422822249715.319797074230.0651752208128-0.00072404400720.304198615105-0.253844781283-0.1206170045080.197860254961-0.455697219829-0.2302300069270.09385247026750.1776236873150.0663449353851-0.001685884723570.1474778793140.006963896160860.126896014214-5.8149248069317.4379078103-19.9528389687
95.508063331380.0057793886145-1.007392602871.76371775002-1.598666810194.236895570520.1823663974690.2589196102490.349829051251-0.53865073044-0.0669862949219-0.217126024554-0.585378171020.19352130386-0.01762280748120.311173866037-0.007688081039470.06272143663330.09608659719750.02658305915740.1770281235185.3820562262319.3887980018-22.0479754473
106.435079973764.91837223929-3.342461369625.18884268666-1.502698603688.94633598393-0.2060278763910.283842958073-0.0624275845324-0.306769218641-0.124135547526-0.771553329799-0.8251804662890.7955954861670.2821404329480.4594543255380.02348014206090.2211082866390.3969380454140.1403831305470.32597968551713.677212419513.5694609839-32.7195173986
114.78816382377-2.70460871944-2.728610540184.796990833673.365133328947.472504982510.1940917875010.000241578899750.203073473184-0.0732929049993-0.0891022001096-0.0562932309122-0.230849723497-0.150024223216-0.09965230050920.140253075519-0.03820000038720.00350532232250.06487745376080.005049106892680.1066022031784.1803310375311.7693456843-15.6515623367
126.1456565518-3.72892982-3.909266877338.055447463114.657009915546.834584788950.2003493984770.0673711929191-0.0390684697227-0.279091606815-0.1514696414340.02509323138130.0015389070641-0.144313520363-0.02886204769840.0847980605863-0.018773378998-0.02924636228380.08530563108650.01332960399870.0585796277476-0.479175290643.6272228281-20.1005748562
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 345 through 360 )
2X-RAY DIFFRACTION2chain 'A' and (resid 361 through 377 )
3X-RAY DIFFRACTION3chain 'A' and (resid 378 through 395 )
4X-RAY DIFFRACTION4chain 'A' and (resid 396 through 404 )
5X-RAY DIFFRACTION5chain 'A' and (resid 405 through 433 )
6X-RAY DIFFRACTION6chain 'A' and (resid 434 through 454 )
7X-RAY DIFFRACTION7chain 'B' and (resid 347 through 360 )
8X-RAY DIFFRACTION8chain 'B' and (resid 361 through 385 )
9X-RAY DIFFRACTION9chain 'B' and (resid 386 through 404 )
10X-RAY DIFFRACTION10chain 'B' and (resid 405 through 410 )
11X-RAY DIFFRACTION11chain 'B' and (resid 411 through 433 )
12X-RAY DIFFRACTION12chain 'B' and (resid 434 through 454 )

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