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- PDB-8cv7: Peptide 2.2E in complex with BRD2-BD2 -

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Basic information

Entry
Database: PDB / ID: 8cv7
TitlePeptide 2.2E in complex with BRD2-BD2
Components
  • Isoform 3 of Bromodomain-containing protein 2
  • Peptide 2.2E
KeywordsTRANSCRIPTION / Bromodomain Cyclic peptides Acetyl-lysine
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 / 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 / bromo domain / Bromodomain / Bromodomain (BrD) profile. / Bromodomain-like superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
ACETYL GROUP / AMINO GROUP / Bromodomain-containing protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 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: Isoform 3 of Bromodomain-containing protein 2
B: Isoform 3 of Bromodomain-containing protein 2
C: Peptide 2.2E
D: Peptide 2.2E
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,0598
Polymers29,9384
Non-polymers1204
Water4,864270
1
A: Isoform 3 of Bromodomain-containing protein 2
D: Peptide 2.2E
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,0294
Polymers14,9692
Non-polymers602
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1560 Å2
ΔGint-13 kcal/mol
Surface area7140 Å2
MethodPISA
2
B: Isoform 3 of Bromodomain-containing protein 2
C: Peptide 2.2E
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,0294
Polymers14,9692
Non-polymers602
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1540 Å2
ΔGint-12 kcal/mol
Surface area7250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.948, 52.420, 55.993
Angle α, β, γ (deg.)90.000, 96.674, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

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


Mass: 13269.201 Da / Num. of mol.: 2 / Fragment: BD2 (UNP residues 300-408)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BRD2, KIAA9001, RING3 / Production host: Escherichia coli (E. coli) / References: UniProt: P25440
#2: Protein/peptide Peptide 2.2E


Mass: 1700.014 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical ChemComp-ACE / ACETYL GROUP


Mass: 44.053 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H4O
#4: Chemical ChemComp-NH2 / AMINO GROUP


Mass: 16.023 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: NH2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 270 / 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: 2.59 Å3/Da / Density % sol: 52.47 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.2 M sodium fluoride, 0.1 M Bis-Tris propane, pH 8.5, 20% w/v PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.953735 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 10, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.953735 Å / Relative weight: 1
ReflectionResolution: 1.6→40.64 Å / Num. obs: 39575 / % possible obs: 98.3 % / Redundancy: 7 % / Biso Wilson estimate: 16.88 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.054 / Rpim(I) all: 0.033 / Rrim(I) all: 0.064 / Net I/σ(I): 18.3
Reflection shellResolution: 1.6→1.63 Å / Redundancy: 7 % / Rmerge(I) obs: 0.427 / Mean I/σ(I) obs: 4.2 / Num. unique obs: 1893 / CC1/2: 0.933 / Rpim(I) all: 0.264 / Rrim(I) all: 0.503 / % possible all: 97

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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 3ONI

3oni


Resolution: 1.6→32.12 Å / SU ML: 0.1377 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.0878
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1983 1758 4.45 %
Rwork0.1744 37787 -
obs0.1756 39545 98.05 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 23.94 Å2
Refinement stepCycle: LAST / Resolution: 1.6→32.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2042 0 8 270 2320
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00692123
X-RAY DIFFRACTIONf_angle_d1.0252860
X-RAY DIFFRACTIONf_chiral_restr0.054279
X-RAY DIFFRACTIONf_plane_restr0.0088365
X-RAY DIFFRACTIONf_dihedral_angle_d12.3634296
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.640.2391240.19912850X-RAY DIFFRACTION97.03
1.64-1.690.22091180.19522878X-RAY DIFFRACTION97.02
1.69-1.750.23561210.18382864X-RAY DIFFRACTION97.1
1.75-1.810.22281260.17762880X-RAY DIFFRACTION97.31
1.81-1.880.21991330.18372866X-RAY DIFFRACTION97.69
1.88-1.970.18481310.18222912X-RAY DIFFRACTION97.72
1.97-2.070.21481210.17832909X-RAY DIFFRACTION97.87
2.07-2.20.1981170.17572926X-RAY DIFFRACTION98.38
2.2-2.370.20831400.17482895X-RAY DIFFRACTION98.32
2.37-2.610.22311400.18632922X-RAY DIFFRACTION98.62
2.61-2.990.2081210.18272968X-RAY DIFFRACTION99.04
2.99-3.760.20071920.16912920X-RAY DIFFRACTION99.3
3.76-32.120.16491740.15672997X-RAY DIFFRACTION99.28
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)
12.362542913020.2352972493972.436688742431.000318939140.339036087914.03146154735-0.0110206349336-0.01369947714150.0675561899672-0.0422024673173-0.00995595385397-0.0351542251703-0.05539975447690.001321116627880.02718939052020.1420136386910.001059486387160.003416239668140.0967899219510.01714479235230.144794312154-14.110422098114.4738931325-14.2119669612
24.49790541832-0.436422066902-2.210079880556.585256644350.3657661683716.78601697140.07212978056530.8274320726330.125561976239-0.9296510238270.026180484439-0.420316740502-0.376191211330.671623523953-0.179888218930.245109456724-0.0341510198020.03285143552820.3244927401050.002749290775660.178855001983-9.5338248661213.7764846232-26.2269096657
32.27630509188-0.1527950523831.880684800882.471862635760.8073856263246.220408200990.255361834950.0865788632983-0.1431886563160.02869226057930.0683810482331-0.08018538622640.440887801108-0.00453146321794-0.3110999424350.122329585516-0.00515280444768-0.03330347418010.08867772486910.004423124175090.171330274687-10.29006996837.97022805282-10.3933090188
42.600594656970.1815802026251.202958910683.778541406621.891169563864.484985194890.20409114591-0.00534428514071-0.323726013906-0.0927896904259-0.04949340269710.1423803811030.573401947044-0.246646404441-0.1389766792670.178706519421-0.0264231227361-0.05053915612140.1007501102640.03777173847110.174666255624-19.24372520423.49278675438-14.8833412384
52.364307634632.61993252913-2.027280530775.12698658942-0.09474882911353.99150924708-0.07162717581550.1695138903310.291304981836-0.0803762092912-0.107779012436-0.19765833534-0.2182313189250.3620351660790.1471861309110.2082583062570.00414311702492-0.06764778759790.2090216777470.05095413152760.222464094440.574561216389-6.21042354501-5.54492465252
63.661780612120.8122988155211.933248793022.81624057781.116316006625.480997195350.231106374306-0.349634636882-0.2249584120940.133483013888-0.0996721588103-0.009758575626710.175853367861-0.271484986134-0.1320334877170.160018613774-0.0127363465268-0.006944759681710.1572630298070.03279927035690.162316660502-14.1299367789-15.616889464-5.75575837043
73.36817834944-0.02881043247861.562780990993.62985103848-3.101538243397.209185172540.169348478118-0.0649843374137-0.547372190776-0.2564394752920.04831583378340.08565075444830.770131347206-0.145230724149-0.1835329389370.254213661323-0.0451975044097-0.04749376036680.1229026104180.004639807356830.213837811755-23.0795761915-21.9674304761-20.5509171508
85.136273452080.6153161691473.857990831251.779948227851.497679000274.452258719440.05096693123140.489621815749-0.177187148173-0.2177246290650.170419429723-0.115058582472-0.006511825919970.521683404435-0.2121672437020.216252918929-0.004788694862970.004417143772680.188777833918-0.02232030014690.147299622733-15.0542076483-14.2827759137-23.1308491893
99.378156158710.945782005427-0.7735629851377.2730747034-0.3316039737565.705313122780.1277815902590.295497492441-0.872417074906-0.04252726838180.131535301983-0.8090883509540.3798763683850.945937785763-0.2176830111450.2072021002720.0625585791715-0.02721794287080.256287955844-0.08116147009330.265776670346-2.0553965086-15.344351132-12.4915136306
105.70249572864-3.70681456793-1.157960689976.262706183082.584595160653.58166877046-0.04885769377380.647525700667-0.419794785406-0.5180219390720.146318357646-0.914043086821-0.2076485091041.15794569310.03169746738350.280380877776-0.007012126980360.1132583233530.666296928777-0.05026618605660.4048523014234.73274505136-9.60096770722-16.2237223526
115.284916615361.312169778682.529926958752.839865155810.4378929792083.39449787249-0.4178611885180.1208897198190.329312643873-0.186691044320.0651889162617-0.0163042171236-0.3289957276240.2704811182890.3554586133230.196188866601-0.0210554316862-0.02891886556280.1153401777460.01248946049040.129735130366-11.2664330502-6.61750901273-16.2688148838
122.57573599013.58244329156-1.330371715664.98643868319-1.902469563576.381830257710.200570794551-0.4868746638320.555075144360.0161120158137-0.1159225027060.781178117836-0.397148169758-1.29172342225-0.096647640260.2287801676910.0686878487115-0.02415702841780.325525653247-0.05428918877080.235363199442-27.7854384104-8.66588396583-14.5380842853
137.081861010163.418612206111.773684813544.551835687530.5757729921292.61847781134-0.111743540356-0.3034952889710.4842803391090.181361271308-0.1088824184950.0432236392155-0.261000240592-0.1783954058190.2375813539510.1935804201060.0442976516052-0.03256806523860.133166131001-0.03196544906970.148160683223-12.6608498358-3.05158172307-6.37024119225
141.68351355958-0.868113552183-0.5517046066532.4285202050.9470458193042.093783564270.0998721109217-0.647570074623-0.2772535244080.525099835299-0.2129419018790.3816029074570.551916890111-0.8969565551270.05094099803380.260816064734-0.1210026141110.04049709644180.4225363074270.002625800001250.211221884782-26.6663582547-17.6454181441-6.78562296359
154.288262023730.4926001136220.5377397260322.36387828312-0.06936185564771.722380912760.0817399405407-0.4118238042750.2870354002840.412966632308-0.05592651054620.28493754786-0.195051604278-0.567335529672-0.04534178449960.194356413920.01544341766750.04464161811920.261887826837-0.03218107575030.15371708672-21.554123053918.2544045191-0.387538563889
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 347 through 395 )AA347 - 3951 - 49
22chain 'A' and (resid 396 through 410 )AA396 - 41050 - 64
33chain 'A' and (resid 411 through 433 )AA411 - 43365 - 87
44chain 'A' and (resid 434 through 455 )AA434 - 45588 - 109
55chain 'B' and (resid 346 through 360 )BB346 - 3601 - 15
66chain 'B' and (resid 361 through 377 )BB361 - 37716 - 32
77chain 'B' and (resid 378 through 385 )BB378 - 38533 - 40
88chain 'B' and (resid 386 through 395 )BB386 - 39541 - 50
99chain 'B' and (resid 396 through 404 )BB396 - 40451 - 59
1010chain 'B' and (resid 405 through 410 )BB405 - 41060 - 65
1111chain 'B' and (resid 411 through 428 )BB411 - 42866 - 83
1212chain 'B' and (resid 429 through 433 )BB429 - 43384 - 88
1313chain 'B' and (resid 434 through 454 )BB434 - 45489 - 109
1414chain 'C' and (resid 1 through 12 )CD1 - 122 - 13
1515chain 'D' and (resid 1 through 12 )DG1 - 122 - 13

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