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- PDB-8cv4: Peptide 4.2C in complex with BRD4.2 -

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Basic information

Entry
Database: PDB / ID: 8cv4
TitlePeptide 4.2C in complex with BRD4.2
Components
  • BRD4 protein
  • Peptide 4.2F
KeywordsTRANSCRIPTION / Cyclic Peptide Inhibitor Bromodomain
Function / homology
Function and homology information


chromosome / nucleus
Similarity search - Function
Brdt, bromodomain, repeat I / Brdt, bromodomain, repeat II / : / Bromodomain-like / Histone Acetyltransferase; Chain A / Bromodomain, conserved site / Bromodomain signature. / Bromodomain / Bromodomain profile. / bromo domain ...Brdt, bromodomain, repeat I / Brdt, bromodomain, repeat II / : / 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
ACETYL GROUP / AMINO GROUP / BRD4 protein
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.93 Å
AuthorsFranck, C. / Mackay, J.P.
Funding support Australia, 1items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia) Australia
CitationJournal: Structure / Year: 2023
Title: Discovery and characterization of cyclic peptides selective for the C-terminal bromodomains of BET family proteins.
Authors: Franck, C. / Patel, K. / Walport, L.J. / Christie, M. / Norman, A. / Passioura, T. / Suga, H. / Payne, R.J. / Mackay, J.P.
History
DepositionMay 18, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 24, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.3Dec 6, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _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.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: BRD4 protein
B: BRD4 protein
C: Peptide 4.2F
D: Peptide 4.2F
E: Peptide 4.2F
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,61311
Polymers33,4335
Non-polymers1806
Water2,126118
1
A: BRD4 protein
D: Peptide 4.2F
E: Peptide 4.2F
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,7237
Polymers17,6033
Non-polymers1204
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2740 Å2
ΔGint-22 kcal/mol
Surface area8630 Å2
MethodPISA
2
B: BRD4 protein
C: Peptide 4.2F
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,8904
Polymers15,8302
Non-polymers602
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1570 Å2
ΔGint-12 kcal/mol
Surface area7770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.575, 65.855, 76.395
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 BRD4 protein


Mass: 14058.205 Da / Num. of mol.: 2 / Fragment: BD2 (UNP residues 347-464)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BRD4 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5BJ26
#2: Protein/peptide Peptide 4.2F


Mass: 1772.163 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical ChemComp-ACE / ACETYL GROUP


Mass: 44.053 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H4O
#4: Chemical ChemComp-NH2 / AMINO GROUP


Mass: 16.023 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: NH2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 118 / 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: 2.02 Å3/Da / Density % sol: 38.97 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 0.1 M PCTPa, pH 4.0, 25% w/v PEG1500

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.953736 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 28, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.953736 Å / Relative weight: 1
ReflectionResolution: 1.93→43.86 Å / Num. obs: 20968 / % possible obs: 99.6 % / Redundancy: 13.1 % / Biso Wilson estimate: 26.48 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.079 / Rpim(I) all: 0.032 / Rrim(I) all: 0.085 / Net I/σ(I): 19.6
Reflection shellResolution: 1.93→1.97 Å / Rmerge(I) obs: 0.749 / Mean I/σ(I) obs: 3.4 / Num. unique obs: 1312 / CC1/2: 0.907 / Rpim(I) all: 0.311 / Rrim(I) all: 0.812 / % possible all: 94.4

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
PHENIX1.19.2_4158refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 5UVV

5uvv


Resolution: 1.93→41.56 Å / SU ML: 0.2446 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.6282
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2545 1056 5.06 %
Rwork0.209 19825 -
obs0.2112 20881 99.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 29.39 Å2
Refinement stepCycle: LAST / Resolution: 1.93→41.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2259 0 12 118 2389
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00712331
X-RAY DIFFRACTIONf_angle_d1.00263130
X-RAY DIFFRACTIONf_chiral_restr0.0507308
X-RAY DIFFRACTIONf_plane_restr0.0089394
X-RAY DIFFRACTIONf_dihedral_angle_d14.7465329
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.93-2.020.35721350.26182365X-RAY DIFFRACTION97.35
2.02-2.120.29681130.23342485X-RAY DIFFRACTION99.92
2.12-2.260.29361480.22622408X-RAY DIFFRACTION99.96
2.26-2.430.27131090.22012492X-RAY DIFFRACTION99.77
2.43-2.670.27521270.22332469X-RAY DIFFRACTION99.73
2.67-3.060.25821440.23582470X-RAY DIFFRACTION99.69
3.06-3.860.27121340.20252519X-RAY DIFFRACTION99.85
3.86-41.560.19491460.17492617X-RAY DIFFRACTION99.71
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)
12.84553161211.292566155051.068983468582.453465379773.637421426225.94611989784-0.02504047474170.214078737717-0.409992152318-0.02702367502830.00784605590901-0.1965308114290.618448958554-0.2522779862730.04437857129230.294265407433-0.01015083428130.04859130253540.199560577429-0.0119337312010.23461857899.721361124557.03242263595.92951009178
21.95135186450.391101603412-0.03065436524881.26688004889-0.6203279091853.86387425478-0.117204094422-0.2084289781340.1373281072670.00973035365808-0.0394809833609-0.224956810436-0.1471492867290.2117239345320.1620603555140.17938380251-0.00435935224071-0.01129058443440.207060756296-0.01072252360570.191223283315.728147267421.686485278315.1665793235
31.60281542111-1.864444856931.911570826632.2037984587-2.223474297723.465300912440.337791381746-0.1129280780750.0367655425219-0.17246843712-0.351663105352-0.224639095887-0.0328799153680.8755375992090.177334659780.2150689035140.05494924239190.01468158532760.283133672014-0.0007677989426620.27578121214720.815235137614.364958242723.1753890734
41.164008380590.455701357855-0.2324639576221.437011572210.818469353094.315103388610.0366254727146-0.155461496417-0.1847003376290.0999752009959-0.0448745069444-0.14205185120.3999117789170.299005724881-0.01510242110070.207735706790.0560169643713-0.0111821600740.247643127570.04547332664920.2679182856916.72850237649.3959381848426.8937706492
55.05738863153-1.787006430033.313874441954.140008980931.570025990544.353640887760.207598102615-0.395962494453-1.28699660582-0.07736174227580.0770054147691-1.018565391220.7425561074820.0461834676759-0.2395187436330.4630692434-0.009656671351960.04160796165170.1970615657220.02948694314350.57241382587410.9528806391-1.7382742297112.9141065434
61.63023726024-0.0317750980930.8597082448193.544276465292.839577277243.685289793110.071881141568-0.0604583903044-0.174177462911-0.15387020754-0.132875625959-0.1379613284980.0464969736302-0.2911557869370.0956758566390.216723888331-0.003582456862580.03201406414430.2516321513630.02968195283820.200845303657.3136650680410.480461476822.0394661712
72.09508305318-1.182101683241.298123166552.58863509941-3.445021250184.63407218871-0.376200106963-0.4867153964440.4838003509741.16940043290.252870794615-0.339979841167-0.510171465217-0.2833264641040.1538316467540.3251157494880.0376243297693-0.00140244660820.261532798418-0.04576552245690.2423552029948.2700930670923.725069937531.7452727644
82.225427021231.249061392712.578438154662.345489148361.572130369195.576082900880.0526426416409-0.1222627181160.1597274445770.0985296168106-0.07025807798120.2801252144850.00983860471435-0.3176461886280.05560175603830.1497194467580.01104622381120.02725212194630.134411637928-0.005527453468650.2151483722545.9159368296619.438409888216.912007609
93.933857148521.96439169821.879058018446.09399875519-2.278931531595.39213582425-0.1744676918070.763883050066-1.981996254560.2478709010210.380801386568-0.268675483941.1839858234-0.719706324141-0.1976759307640.540508589848-0.239289446641-0.02963895843580.640787577342-0.0341257593630.7037996500141.151023855775.7605687140.551997763458
102.42201687776-0.6341062893111.097525099932.19147873832-0.6033810099593.70927828361-0.0137266736098-0.271975156818-0.01552561781550.222423033705-0.0785287290204-0.002579934374280.0352180657915-0.2772989639330.08257685403050.156355427087-0.04622771033890.01138069337770.204597901989-0.01104704808320.158365245883-12.203277238413.606746635626.0446118236
112.131367841860.2505790296360.5647067216741.45031802976-0.3154424078333.659204091680.08081423928460.0832261716928-0.0625894795177-0.0532114015489-0.0447563809479-0.01825464375840.2226951021620.0716382787319-0.03721290812110.1356589336190.022003286926-0.006431680009430.138633633907-0.01970402744990.15905591786-8.9616751441211.87595251815.9451193909
129.363393206162.7215234032-1.474166527773.17684298683.301755764636.00808850156-0.712906822276-0.613485073304-1.828960472040.4349756888010.988323207563-0.3462438031070.7065146102410.493268935575-0.2115669606810.426524156690.0989994243074-0.008220152251930.4868166723310.1077904063840.5707577113240.8560637318665.6567142741637.5026443298
134.18688636166-0.77032262937-2.484375460862.417881304990.5525642242046.327303770260.06079843444240.05695922628730.430326983994-0.05124928237130.204354144366-0.0553607451069-0.195234373923-0.231310931225-0.2375765360950.2237008654420.0247561983694-0.00820783057840.218410229773-0.003915060624870.265047896785-20.432393140424.410900663314.1839010843
143.765778659250.359852307072-1.288463043833.5340687538-0.5923437672276.081464359520.0306886956379-0.05173624646070.1670304700650.34167407120.0729457237029-0.388032053483-0.1857515482720.326280976837-0.0821048012210.189346755505-0.0126885590718-0.01969592527490.208225135518-0.002812657808570.20778057117522.2818796124.661993233324.2512747603
151.23228734735-0.505750364873-0.0743686004194.43863394503-1.610753740666.816385706990.4396723987850.5859055691661.34656261178-0.496619115473-0.401723105568-0.613031002944-1.124206296630.465200409203-0.1994038239340.4527925444-0.0005873422389840.06816500842840.3665200235050.1597059242930.59200097580922.288871183635.902396766320.2773819659
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-IDEnd label seq-ID
11chain 'A' and (resid 348 through 364 )AA348 - 3641 - 17
22chain 'A' and (resid 365 through 376 )AA365 - 37618 - 29
33chain 'A' and (resid 377 through 381 )AA377 - 38130 - 34
44chain 'A' and (resid 382 through 408 )AA382 - 40835 - 61
55chain 'A' and (resid 409 through 414 )AA409 - 41462 - 67
66chain 'A' and (resid 415 through 432 )AA415 - 43268 - 85
77chain 'A' and (resid 433 through 437 )AA433 - 43786 - 90
88chain 'A' and (resid 438 through 455 )AA438 - 45591 - 108
99chain 'A' and (resid 456 through 463 )AA456 - 463109 - 116
1010chain 'B' and (resid 349 through 381 )BB349 - 3811 - 33
1111chain 'B' and (resid 382 through 455 )BB382 - 45534 - 107
1212chain 'B' and (resid 456 through 463 )BB456 - 463108 - 115
1313chain 'C' and (resid 0 through 11 )CC - D0 - 1112
1414chain 'D' and (resid 0 through 11 )DF - G0 - 1112
1515chain 'E' and (resid 0 through 11 )EJ - K0 - 1112

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