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- PDB-6u8h: BRD2-BD1 in complex with the cyclic peptide 3.2_2 -

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Basic information

Entry
Database: PDB / ID: 6u8h
TitleBRD2-BD1 in complex with the cyclic peptide 3.2_2
Components
  • Bromodomain-containing protein 2
  • cyclic peptide 3.2_2
KeywordsTRANSCRIPTION/INHIBITOR / BET / bromodomain / macrocyclic peptide / BRD2 / inhibitor / RaPID / TRANSCRIPTION-INHIBITOR complex / TRANSCRIPTION
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 / chromosome / chromatin organization / 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, conserved site / Bromodomain signature. / Bromodomain ...Brdt, bromodomain, repeat I / Brdt, bromodomain, repeat II / 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
IODIDE ION / AMINO GROUP / Chem-PE3 / Bromodomain-containing protein 2 / Bromodomain-containing protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.07 Å
AuthorsPatel, K. / Walshe, J.L. / Walport, L.J. / Mackay, J.P.
Funding support Australia, 1items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia)APP1161623 Australia
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2020
Title: Cyclic peptides can engage a single binding pocket through highly divergent modes.
Authors: Patel, K. / Walport, L.J. / Walshe, J.L. / Solomon, P.D. / Low, J.K.K. / Tran, D.H. / Mouradian, K.S. / Silva, A.P.G. / Wilkinson-White, L. / Norman, A. / Franck, C. / Matthews, J.M. / Guss, ...Authors: Patel, K. / Walport, L.J. / Walshe, J.L. / Solomon, P.D. / Low, J.K.K. / Tran, D.H. / Mouradian, K.S. / Silva, A.P.G. / Wilkinson-White, L. / Norman, A. / Franck, C. / Matthews, J.M. / Guss, J.M. / Payne, R.J. / Passioura, T. / Suga, H. / Mackay, J.P.
History
DepositionSep 5, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 19, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2021Group: 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
Revision 1.2Oct 11, 2023Group: 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
Revision 1.3Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Bromodomain-containing protein 2
C: cyclic peptide 3.2_2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,15112
Polymers17,5542
Non-polymers1,59610
Water2,324129
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: surface plasmon resonance
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3020 Å2
ΔGint-15 kcal/mol
Surface area9220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.587, 89.587, 71.592
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Space group name HallP4abw2nw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/4
#3: y+1/2,-x+1/2,z+3/4
#4: x+1/2,-y+1/2,-z+3/4
#5: -x+1/2,y+1/2,-z+1/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2
Components on special symmetry positions
IDModelComponents
11A-201-

IOD

21A-379-

HOH

31C-201-

HOH

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Components

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Protein / Protein/peptide , 2 types, 2 molecules AC

#1: Protein Bromodomain-containing protein 2


Mass: 15893.472 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BRD2 / Production host: Escherichia coli (E. coli) / References: UniProt: H0Y6K2, UniProt: P25440*PLUS
#2: Protein/peptide cyclic peptide 3.2_2


Mass: 1660.979 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)

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Non-polymers , 5 types, 139 molecules

#3: Chemical
ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: I
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-NH2 / AMINO GROUP


Mass: 16.023 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: NH2
#6: Chemical ChemComp-PE3 / 3,6,9,12,15,18,21,24,27,30,33,36,39-TRIDECAOXAHENTETRACONTANE-1,41-DIOL / POLYETHYLENE GLYCOL


Mass: 634.751 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C28H58O15
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 129 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 4.3 Å3/Da / Density % sol: 71.39 %
Crystal growTemperature: 100 K / Method: vapor diffusion, sitting drop
Details: 0.2 M Sodium iodide 0.1 M Bis-Tris propane 7.5 20 % w/v PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 30, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.07→47.77 Å / Num. obs: 18193 / % possible obs: 99.7 % / Redundancy: 12.2 % / Biso Wilson estimate: 27.56 Å2 / CC1/2: 0.999 / Net I/σ(I): 25
Reflection shellResolution: 2.07→2.13 Å / Num. unique obs: 1350 / CC1/2: 0.971

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3ONI

3oni


Resolution: 2.07→47.44 Å / SU ML: 0.1689 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 20.5018
RfactorNum. reflection% reflection
Rfree0.2232 898 4.95 %
Rwork0.1819 --
obs0.1839 18148 99.65 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 34.99 Å2
Refinement stepCycle: LAST / Resolution: 2.07→47.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1172 0 62 129 1363
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0021258
X-RAY DIFFRACTIONf_angle_d0.46491680
X-RAY DIFFRACTIONf_chiral_restr0.0376172
X-RAY DIFFRACTIONf_plane_restr0.0037204
X-RAY DIFFRACTIONf_dihedral_angle_d11.8188756
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.07-2.20.23481630.18572763X-RAY DIFFRACTION98.49
2.2-2.370.23241490.18972815X-RAY DIFFRACTION99.87
2.37-2.610.25431510.19942839X-RAY DIFFRACTION100
2.61-2.990.21511330.19282892X-RAY DIFFRACTION100
2.99-3.770.23031470.18612900X-RAY DIFFRACTION100
3.77-47.440.20661550.16743041X-RAY DIFFRACTION99.56
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)
17.67156686526-2.138060418882.52284307983.60464466593-1.026979224151.48348586278-0.325848283514-0.270872365560.1431450137910.06940803049730.191820688818-0.227610834864-0.173426824504-0.01677424456590.1397366793070.181444797898-0.006128240802330.007741196470880.243093274813-0.006028522444460.185145182485-12.878103469721.0567544662-6.9981792137
28.363961492910.808058282979-3.174557309922.01698737928-0.4647361647169.947629026040.0146931829802-0.375601321731-0.1964309563330.2889074230010.2616728566550.05199200997650.595024804167-0.353559818101-0.2778000868460.264867721406-0.0305345058341-0.01653625339870.2661829854780.05956906071440.2510309197583.7764849802612.5440133937-1.71404386325
35.021270326540.424029452287-1.063171242793.09561784608-1.889889790556.986718360070.04576175122741.236663338090.0856100237172-0.3083647258080.0415224867985-0.3765946707140.107018330132-0.431597194765-0.0591558671350.172890142772-0.018764353175-0.01602264825640.407345337652-0.005430150291540.2718931576488.9337622597916.389388009-16.7134037123
47.04335397798-4.44835188033-4.270337810189.248553155076.5012925735.023739799550.2530464460240.8787035311470.0465888136895-0.537941117920.270642459965-0.245913840521-0.344539698992-0.642714140613-0.4465944806390.268723477269-0.0578664166882-0.02452914085560.4541629706290.06945355456690.2445412650450.66017347720913.0664987274-20.8041614582
55.90504853168-5.004307058691.026781518685.596880422561.155670068753.3011538326-0.132315450499-0.6787800236770.9499844843230.3658239165930.0205700236205-0.591708346267-0.1290034698580.4844702693960.09412266475770.218035559702-0.04592488763330.01244161001380.3685506991590.01648440650260.286388697895-6.3363935298121.9656568208-8.60842863151
69.08955786824-5.68686463158-0.6802841995625.639249720590.6080847967760.0667455945379-0.02959219429060.305687790202-0.1694140421220.07607247382960.004817411362920.183846028339-0.00459405948749-0.01794355528990.02341063533610.189204291522-0.0119381422638-0.02247428688520.2889921493170.01354768016280.170501083996-8.6377019688113.4029266756-12.6961265084
72.493732948974.087461816010.3205683617148.25062494435-1.391596818382.484739049380.3457757610491.09148777711-1.92314392417-0.02646216879120.0157301289391-1.031676775160.3058462180080.0440339340176-0.4053139969740.3933039158990.0331383270126-0.08993047349310.358268847728-0.1217567391440.542522641277.618894785760.112663759123-13.2490511921
87.04612153469-3.78985591129-6.928150788953.426516967313.489633635638.16642913432-0.2626559972740.0990819209094-0.9994606767420.3545053932190.1278175403330.120809983610.33095050276-0.2386632046370.1164504969590.283480573957-0.01430157374790.002871923531430.2142335417290.02940688018910.253337239466-3.834850883845.48593206888-3.17613903377
94.01813389629-5.123726634-0.5518590640686.550824893530.4267192729498.84285265281-0.142887581401-0.331678770206-0.701197898036-0.5303388734270.3265301719360.3127669739790.264840914646-0.245922578565-0.1907344337950.173460811065-0.002027278221630.03595555966810.474531207990.12042717210.41079536839-24.023019791719.1676778183-2.62307289789
106.210419131213.848420605572.763635590428.172569011771.364142583174.659341737950.1084213131230.681869281999-0.2817527732940.1008514935940.155497640956-0.6897841481440.3468239561410.407694635468-0.324349287090.1529076119250.007455002755520.006869326860450.2428530603610.01222162524220.18933114442414.547004334613.3784060485-8.94610248345
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 63 through 91 )
2X-RAY DIFFRACTION2chain 'A' and (resid 92 through 99 )
3X-RAY DIFFRACTION3chain 'A' and (resid 100 through 112 )
4X-RAY DIFFRACTION4chain 'A' and (resid 113 through 122 )
5X-RAY DIFFRACTION5chain 'A' and (resid 123 through 131 )
6X-RAY DIFFRACTION6chain 'A' and (resid 132 through 155 )
7X-RAY DIFFRACTION7chain 'A' and (resid 156 through 160 )
8X-RAY DIFFRACTION8chain 'A' and (resid 161 through 179 )
9X-RAY DIFFRACTION9chain 'A' and (resid 180 through 190 )
10X-RAY DIFFRACTION10chain 'C' and (resid 1 through 12 )

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