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- PDB-8r6m: Crystal structure of Candida glabrata Bdf1 bromodomain 2 bound to... -

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Basic information

Entry
Database: PDB / ID: 8r6m
TitleCrystal structure of Candida glabrata Bdf1 bromodomain 2 bound to I-BET151
ComponentsCandida glabrata strain CBS138 chromosome C complete sequence
KeywordsTRANSCRIPTION / Bromodomain
Function / homology
Function and homology information


: / chromatin remodeling / regulation of DNA-templated transcription / chromatin / nucleus
Similarity search - Function
NET domain superfamily / NET domain profile. / : / NET domain / Bromodomain extra-terminal - transcription regulation / Bromodomain, conserved site / Bromodomain signature. / Bromodomain / bromo domain / Bromodomain ...NET domain superfamily / NET domain profile. / : / NET domain / Bromodomain extra-terminal - transcription regulation / Bromodomain, conserved site / Bromodomain signature. / Bromodomain / bromo domain / Bromodomain / Bromodomain (BrD) profile. / Bromodomain-like superfamily
Similarity search - Domain/homology
Chem-1GH / Candida glabrata strain CBS138 chromosome C complete sequence
Similarity search - Component
Biological speciesNakaseomyces glabratus (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsPetosa, C. / Wei, K. / McKenna, C.E. / Govin, J.
Funding support France, 1items
OrganizationGrant numberCountry
Agence Nationale de la Recherche (ANR) France
CitationJournal: Adv Sci / Year: 2025
Title: Humanized Candida and NanoBiT Assays Expedite Discovery of Bdf1 Bromodomain Inhibitors With Antifungal Potential.
Authors: Wei, K. / Arlotto, M. / Overhulse, J.M. / Dinh, T.A. / Zhou, Y. / Dupper, N.J. / Yang, J. / Kashemirov, B.A. / Dawi, H. / Garnaud, C. / Bourgine, G. / Mietton, F. / Champleboux, M. / Larabi, ...Authors: Wei, K. / Arlotto, M. / Overhulse, J.M. / Dinh, T.A. / Zhou, Y. / Dupper, N.J. / Yang, J. / Kashemirov, B.A. / Dawi, H. / Garnaud, C. / Bourgine, G. / Mietton, F. / Champleboux, M. / Larabi, A. / Hayat, Y. / Indorato, R.L. / Noirclerc-Savoye, M. / Skoufias, D. / Cornet, M. / Rabut, G. / McKenna, C.E. / Petosa, C. / Govin, J.
History
DepositionNov 22, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 30, 2024Provider: repository / Type: Initial release
Revision 1.1Jan 29, 2025Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Mar 26, 2025Group: Database references / Category: citation / Item: _citation.journal_volume

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Candida glabrata strain CBS138 chromosome C complete sequence
B: Candida glabrata strain CBS138 chromosome C complete sequence
C: Candida glabrata strain CBS138 chromosome C complete sequence
D: Candida glabrata strain CBS138 chromosome C complete sequence
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,15934
Polymers55,0944
Non-polymers4,06430
Water4,071226
1
A: Candida glabrata strain CBS138 chromosome C complete sequence
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,11812
Polymers13,7741
Non-polymers1,34411
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Candida glabrata strain CBS138 chromosome C complete sequence
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,8349
Polymers13,7741
Non-polymers1,0608
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Candida glabrata strain CBS138 chromosome C complete sequence
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,6507
Polymers13,7741
Non-polymers8766
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Candida glabrata strain CBS138 chromosome C complete sequence
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,5576
Polymers13,7741
Non-polymers7845
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)70.588, 88.426, 257.785
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11A-601-

HOH

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Components

#1: Protein
Candida glabrata strain CBS138 chromosome C complete sequence


Mass: 13773.615 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nakaseomyces glabratus (fungus) / Gene: CAGL0C02541g / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q6FWV7
#2: Chemical...
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 24 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-1GH / 7-(3,5-DIMETHYL-1,2-OXAZOL-4-YL)-8-METHOXY-1-[(1R)-1-(PYRIDIN-2-YL)ETHYL]-1H,2H,3H-IMIDAZO[4,5-C]QUINOLIN-2-ONE


Mass: 415.445 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C23H21N5O3 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 226 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 3.65 Å3/Da / Density % sol: 66.31 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: 0.9 M Ammonium Sulfate, 0.1 M Sodium Cacodylate pH 6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-3 / Wavelength: 0.9677 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Jun 17, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9677 Å / Relative weight: 1
ReflectionResolution: 1.95→55.2 Å / Num. obs: 28171 / % possible obs: 47.4 % / Redundancy: 7.4 % / Biso Wilson estimate: 24.29 Å2 / CC1/2: 0.99 / Rrim(I) all: 0.292 / Net I/σ(I): 6.7
Reflection shellResolution: 1.95→2.18 Å / Redundancy: 7.7 % / Mean I/σ(I) obs: 1.7 / Num. unique obs: 1410 / CC1/2: 0.601 / Rrim(I) all: 2.056 / % possible all: 8.5

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
AutoProcessdata reduction
STARANISOdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.95→43.58 Å / SU ML: 0.2053 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.852
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2405 1407 5 %
Rwork0.1951 26757 -
obs0.1974 28164 47.44 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 36.3 Å2
Refinement stepCycle: LAST / Resolution: 1.95→43.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3753 0 278 226 4257
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00274125
X-RAY DIFFRACTIONf_angle_d0.55015563
X-RAY DIFFRACTIONf_chiral_restr0.0418538
X-RAY DIFFRACTIONf_plane_restr0.0041696
X-RAY DIFFRACTIONf_dihedral_angle_d12.40551481
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.95-2.020.3439140.3085192X-RAY DIFFRACTION3.5
2.02-2.10.3797310.2842499X-RAY DIFFRACTION9.08
2.1-2.190.2496410.2718796X-RAY DIFFRACTION14.34
2.19-2.310.2924350.28151085X-RAY DIFFRACTION19.18
2.31-2.450.2634740.27911435X-RAY DIFFRACTION25.33
2.45-2.640.29871180.28192212X-RAY DIFFRACTION39.77
2.64-2.910.30511840.26563876X-RAY DIFFRACTION68.55
2.91-3.330.29062910.23785161X-RAY DIFFRACTION90.96
3.33-4.20.22342990.1655604X-RAY DIFFRACTION98.84
4.2-43.580.19433200.14685897X-RAY DIFFRACTION99.89
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)
16.776180732472.139479248878.504368574816.312723228811.657783112312.03411022959-0.3704235253230.6103839913980.3087212741640.114473108388-0.0331179811708-0.183392540860.448157538670.9940903386140.3144945932930.226857764097-0.0261526481840.03899084303890.2852206106060.04702744912960.18004618630743.5493323839-5.6333342489353.723762318
25.33996954592-4.36970996111-2.954658854146.995682848156.522462543856.6728173527-0.2212109321810.216011625223-0.0439423138408-0.5534702134920.176207772673-0.365489433771-0.2914528058080.08910543230720.06986574327350.209367803054-0.03516958930520.05011913570130.2974941936470.05579158745730.12898008954934.3427038032-6.7502787803339.242205871
38.29746395701-1.96278726606-0.2380254180745.83209047935-2.714547223437.02949836235-0.2554554295040.1502439608940.5578558798220.08309956310990.05256859216050.250275133433-1.1867294575-0.3069098720420.2706275518920.4680920802220.0324617412807-0.0467207336960.1952557581490.007562670741630.1896527285422.31668810316.0951085507142.0171872336
42.076866617552.823885366488.38692889797.701632512734.339257980837.037730203750.08324311797480.6944167917630.621013673141-0.111771300017-0.190411613749-0.38655239627-1.182313337070.5176118319970.1753981858140.279696926925-0.0969555909431-0.03014807113970.2487040093260.02064751873350.21143188706640.39080955313.6971058156651.5871726082
510.01144431780.1234280545747.226486500260.611942633489-0.5183189958512.40140140098-0.17704719802-0.8772049404390.2771761486650.113384295295-0.1207669987270.162117474371-0.869315528911-1.138860202660.3381408864020.242741185585-0.02652450006580.008032022226530.261233802031-0.01849379709490.1441189284127.8268631464-2.1009407484952.4750420632
64.23509259616-0.5101765291124.266046139133.49945983973-1.481753321859.122400428560.232801327357-0.161892645834-0.430122117269-0.1761860378710.08339934217250.03698526996430.64732022715-0.972959752418-0.3122673543120.200818656578-0.05186933133460.03348284838990.209252162602-0.03986053719250.11870328876528.0612359106-11.680134098447.3985276949
78.063149749935.027491077391.440940380638.332728370381.292165627742.05737189233-0.1315922997190.09886372287090.03576500457670.7143415394850.0580183046666-1.05272560786-0.06786840671731.456871959910.0682848287680.2552587547980.0444178333169-0.05842617300490.30023723269-0.01586638165970.30707299461242.3057595806-8.6091777059567.0716220039
82.040188926351.68597115146-1.591962833296.39515172551-6.305650820918.55584640861-0.2418316600620.2771561444290.8537353330340.554473606798-0.0766123419282-0.272517647565-2.00565292238-0.3048677355130.3322548100890.6724686299550.0248084096607-0.1162342023020.3511548347730.04933890111810.33955727969724.28782333798.8655343779410.3090639444
98.59728106255-1.23699576082-7.331582762824.647286383222.212248261577.7496511359-0.803149794684-0.1975742199280.5574273407570.1602179014250.5039163847410.207585382769-0.8899080170050.4131839434330.2841717034280.4214787933740.00249757233643-0.09217720180190.2426637568010.05123767899030.18048757931424.67973221760.99651232489225.645922531
104.8256130766-0.9589510717061.979804957984.15873208189-4.037662262124.848630840480.1329938956920.396630288333-0.0891932935484-0.867100064311-0.0647292825443-0.1925967926660.2232038436090.7138137700120.0004425352751390.339296139626-0.03294273674950.03199801263320.33393353369-0.04107722797860.1599707325238.3058297376-10.224513905822.6337537501
112.021100418543.26410340019-4.764144463838.18112091295-5.949225640496.27090479445-0.6761891564680.450396480690.7114402119970.0119889540207-0.55272622243-1.22632501666-1.922182073080.4702441726921.021166485490.711777315239-0.167959982668-0.1316025441110.390963147420.1421600015940.342152107534.00526777496.6317325098312.1809633249
121.48671025161-2.900799958253.379021580136.02752176666-6.336585145787.4684537750.1224172547310.2088955836430.0626328775285-0.84842015893-0.256950581634-0.1267866419540.6588953495450.513900909130.1003913689410.49513426985-0.041976166119-0.00137666614940.261634568098-0.008564326315660.15489938767528.9395945682-6.2010404075712.6720150399
132.76020954743-1.76737918752-0.507797362623.27477723801-1.212354867951.543552200580.1465327296560.0551919318559-0.0929842623074-0.1458581487910.05677831810610.2927384536430.210477072311-0.37428040836-0.1841091763270.337161815689-0.117708116717-0.01744909626850.2667458375940.02020603769330.14784377730719.7997530388-6.2156168728718.5435509303
142.05015403036-2.12928486222-2.133427520222.23047938047-1.19864273152.008010578480.396660659972-0.2067246395490.3748502272170.263764873197-0.213641073969-0.503748039087-0.4477579159190.84622242826-0.2083973759970.444531141598-0.05210364597860.02214986049430.2500459053380.04863341806720.23966800538723.16989739556.67452014701-1.28701026241
155.35634177081-1.51605520038-2.053707841977.99436774049-4.426990033994.087249162560.161865072643-0.606295527901-0.7495464852081.536382907430.4057178358030.4377214283330.0910066532777-0.548649917415-0.4237520489180.581911095089-0.209541046789-0.03074392753140.4525299424470.1784024960760.3400199617918.8551707319-34.773067476157.6817654348
169.50524545746-3.95908541393-1.102018418432.128625053740.5514834058873.20662931309-0.417116165680.008042713188980.145645920505-0.2547993209880.3266161854170.7109931402690.153002732517-1.011586493110.02376821020840.238191188519-0.0367613041986-0.01217030739980.4019008383730.08828900050970.24033406380315.2634357676-25.067334295243.8382836505
175.1800904076-0.8910048271790.04117321909013.849193795540.4090963644286.044750042090.05748903048230.390931345917-0.358238148928-0.7134337181280.0237098908091-0.4798834514990.6162563155250.129273673554-0.04884699148110.400807851277-0.04563733928260.06183944689880.200606799595-0.03750056009160.31496478359225.3953173813-33.247868973431.5992183149
186.670272102046.46849734652-8.201765745758.994752692951.945258403592.01002225199-0.108527603561-0.112624708232-1.22437772114-0.5055944326060.0598153180409-0.1668926770310.64172902782-0.873252877991-0.1118246667830.316452857222-0.120737873849-0.1378131352550.3170017615290.2059919602050.45047237699818.9085978143-40.857445219749.6815176596
190.122143305361-0.693093019717-0.1706513811272.12661724012-0.2771920977514.033733082040.0892670974835-0.20395313082-0.6369057234610.1473768898150.114291765453-0.496916250479-0.2650483462120.564942830908-0.1262971829140.166247363967-0.02980203234320.007362069152420.3238297237250.07109436516770.5358774899828.8787659908-32.318123257745.4904600424
203.00737035619-0.443232914054-0.1308442457973.8959664959-1.151716322763.573649841980.0599165945614-0.366457858237-0.01085731115240.361877283521-0.0424153047192-0.06365978234050.1213661728510.075664997239-0.02518514192910.258762378474-0.0840945270622-0.04385624604690.1618299462880.001709247792630.22567204753425.4896531372-21.994000791247.3963981821
216.72081721233-5.376240415995.747147655154.36107274697-4.243129309576.488444095061.042882924260.864642922535-1.225487098080.7212059582250.1528846650920.127403323760.5748151222060.168083868725-1.102340489550.223355622216-0.354248621238-0.6061885389160.7966022822430.2350095458490.8872158755728.7144464722-34.839406826464.4138869691
222.10915033593-0.1690948083673.429778978532.670438751591.601231887536.7297907695-0.2247724444891.6357320262-0.689560413711-0.9822965589620.3897650540850.7106046340310.907352399615-0.194589223627-0.2200572802660.803207038569-0.394221964589-0.1654487202460.870486721333-0.08755874664940.4830889736292.68325735829-23.654403298912.120520419
232.17140480648-3.82780625261-3.164249602658.598364839634.092574000416.64762486882-0.1803436630060.0053525060685-0.541958611406-0.6629888652920.3091225465690.1605477074190.0519369675535-0.262941218775-0.1235088263010.355103929742-0.110937879317-0.07371547505990.2697272699450.06128890877590.29546993301312.462702741-23.046752983125.7165111765
248.11478102003-3.455260661894.349056548488.72560048483-2.303393803987.00628127922-0.178391900963-1.10140356992-0.2155371733340.1381237935980.6950728450051.33479028873-0.14070405743-1.48943450872-0.4730710570280.187310854388-0.008873257883220.02096563478980.5312003291660.06510393206180.4247958604471.13989316666-16.842928655737.8766026032
252.020558676681.090990587912.268964031635.367600522111.72660341831.733999356340.0009781758474210.259108621695-0.202881434698-0.1631910706130.07546850550881.011253762081.39133836999-1.22832130654-0.0730287328890.743465655692-0.392000008532-0.1375200141170.6767206236640.001508012690.551767359103-3.2438342189-25.836230882119.7547058154
265.504706127591.034057906381.459326723392.658056628712.379846105875.53378383162-0.2401791699110.01160263978330.175002141491-0.9531735540570.3209205307530.871645837236-0.88234446573-1.34093711343-0.0002464009114360.4285729020250.00077451821983-0.2213147992760.4146568626460.07766167223030.5152819334850.597429345011-13.21828034723.9665186588
275.70237197585-0.8998927683985.341039459622.335098752111.991976596532.08431398511-0.6621752575590.7814821663970.325159156893-1.016021529740.8297677922660.258971511624-0.953457313640.778327114656-0.1269844857980.51449881073-0.255645020874-0.1250589068140.5044192338190.09244168525350.28311785562711.4426464838-12.24001139222.103499208
281.99507239427-5.35704598788.287893243047.65625766393-3.818851214182.001747595140.9327347547121.87274077708-0.663742995989-2.315294492650.6514563916892.959058098661.76965821784-2.67840971688-1.458990071180.931868848771-0.14527374931-0.3878608874681.135749667040.1572130987820.930102216561-1.2633470699-14.1916052645.08425017149
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 301 through 318)AA301 - 3181 - 18
22chain 'A' and (resid 319 through 332)AA319 - 33219 - 32
33chain 'A' and (resid 333 through 352)AA333 - 35233 - 52
44chain 'A' and (resid 353 through 365)AA353 - 36553 - 65
55chain 'A' and (resid 366 through 387)AA366 - 38766 - 87
66chain 'A' and (resid 388 through 409)AA388 - 40988 - 109
77chain 'A' and (resid 410 through 416)AA410 - 416110 - 116
88chain 'B' and (resid 301 through 318)BN301 - 3181 - 18
99chain 'B' and (resid 319 through 332)BN319 - 33219 - 32
1010chain 'B' and (resid 333 through 352)BN333 - 35233 - 52
1111chain 'B' and (resid 353 through 365)BN353 - 36553 - 65
1212chain 'B' and (resid 366 through 387)BN366 - 38766 - 87
1313chain 'B' and (resid 388 through 409)BN388 - 40988 - 109
1414chain 'B' and (resid 410 through 417)BN410 - 417110 - 117
1515chain 'C' and (resid 301 through 318)CX301 - 3181 - 18
1616chain 'C' and (resid 319 through 332)CX319 - 33219 - 32
1717chain 'C' and (resid 333 through 352)CX333 - 35233 - 52
1818chain 'C' and (resid 353 through 365)CX353 - 36553 - 65
1919chain 'C' and (resid 366 through 387)CX366 - 38766 - 87
2020chain 'C' and (resid 388 through 409)CX388 - 40988 - 109
2121chain 'C' and (resid 410 through 413)CX410 - 413110 - 113
2222chain 'D' and (resid 301 through 318)DD301 - 3181 - 18
2323chain 'D' and (resid 319 through 332)DD319 - 33219 - 32
2424chain 'D' and (resid 333 through 352)DD333 - 35233 - 52
2525chain 'D' and (resid 353 through 365)DD353 - 36553 - 65
2626chain 'D' and (resid 366 through 387)DD366 - 38766 - 87
2727chain 'D' and (resid 388 through 409)DD388 - 40988 - 109
2828chain 'D' and (resid 410 through 413)DD410 - 413110 - 113

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