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- PDB-6ulp: BRD3-BD2 in complex with the cyclic peptide 3.2_3 -

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Basic information

Entry
Database: PDB / ID: 6ulp
TitleBRD3-BD2 in complex with the cyclic peptide 3.2_3
Components
  • Bromodomain-containing protein 3
  • Cyclic peptide 3.2_3
KeywordsTRANSCRIPTION/INHIBITOR / BET / bromodomain / macrocyclic peptide / BRD3 / inhibitor / RaPID / Transcription-Inhibitor complex / TRANSCRIPTION
Function / homology
Function and homology information


lncRNA binding / endodermal cell differentiation / protein localization to chromatin / molecular condensate scaffold activity / lysine-acetylated histone binding / chromatin organization / chromatin binding / regulation of transcription by RNA polymerase II / nucleus
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, conserved site / Bromodomain signature. / Bromodomain / Bromodomain profile. ...NET domain superfamily / NET domain profile. / Brdt, bromodomain, repeat II / Brdt, bromodomain, repeat I / NET domain / Bromodomain extra-terminal - transcription regulation / Bromodomain, conserved site / Bromodomain signature. / Bromodomain / Bromodomain profile. / bromo domain / Bromodomain / Bromodomain-like superfamily
Similarity search - Domain/homology
Bromodomain-containing protein 3
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 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
DepositionOct 8, 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: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
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 3
B: Bromodomain-containing protein 3
C: Cyclic peptide 3.2_3


Theoretical massNumber of molelcules
Total (without water)29,5173
Polymers29,5173
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: surface plasmon resonance
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)97.568, 97.568, 77.748
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number79
Space group name H-MI4
Space group name HallI4
Symmetry operation#1: x,y,z
#2: -y,x,z
#3: y,-x,z
#4: -x,-y,z
#5: x+1/2,y+1/2,z+1/2
#6: -y+1/2,x+1/2,z+1/2
#7: y+1/2,-x+1/2,z+1/2
#8: -x+1/2,-y+1/2,z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11LEULEUMETMET(chain 'A' and (resid 308 through 356 or resid 358...AA308 - 3568 - 56
12LEULEUARGARG(chain 'A' and (resid 308 through 356 or resid 358...AA358 - 40258 - 102
13LEULEUMETMET(chain 'A' and (resid 308 through 356 or resid 358...AA404 - 410104 - 110
14PHEPHEMETMET(chain 'A' and (resid 308 through 356 or resid 358...AA412 - 415112 - 115
21LEULEUMETMET(chain 'B' and (resid 308 through 356 or resid 358...BB308 - 3568 - 56
22LEULEUARGARG(chain 'B' and (resid 308 through 356 or resid 358...BB358 - 40258 - 102
23LEULEUMETMET(chain 'B' and (resid 308 through 356 or resid 358...BB404 - 410104 - 110
24PHEPHEMETMET(chain 'B' and (resid 308 through 356 or resid 358...BB412 - 415112 - 115

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Components

#1: Protein Bromodomain-containing protein 3 / / RING3-like protein


Mass: 13912.973 Da / Num. of mol.: 2 / Fragment: second bromodomain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BRD3, KIAA0043, RING3L / Production host: Escherichia coli (E. coli) / References: UniProt: Q15059
#2: Protein/peptide Cyclic peptide 3.2_3


Mass: 1691.070 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
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: 3.13 Å3/Da / Density % sol: 60.76 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 0.2 M Calcium chloride dihydrate, 0.1 M Tris 8.0, 20 % w/v PEG 6000

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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: Oct 18, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.8→38.87 Å / Num. obs: 9024 / % possible obs: 99.8 % / Redundancy: 14 % / Biso Wilson estimate: 96.43 Å2 / CC1/2: 1 / Net I/σ(I): 29.9
Reflection shellResolution: 2.8→2.96 Å / Num. unique obs: 1304 / CC1/2: 0.916

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3S92

3s92


Resolution: 2.8→38.05 Å / SU ML: 0.5285 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 31.3778
RfactorNum. reflection% reflection
Rfree0.2477 426 4.72 %
Rwork0.2102 --
obs0.2121 9017 99.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 110.06 Å2
Refinement stepCycle: LAST / Resolution: 2.8→38.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1935 0 1 0 1936
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00231993
X-RAY DIFFRACTIONf_angle_d0.55922679
X-RAY DIFFRACTIONf_chiral_restr0.0383266
X-RAY DIFFRACTIONf_plane_restr0.004343
X-RAY DIFFRACTIONf_dihedral_angle_d10.48091214
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-3.210.37371380.32642818X-RAY DIFFRACTION99.36
3.21-4.040.2931720.25572842X-RAY DIFFRACTION100
4.04-38.050.20241160.17662931X-RAY DIFFRACTION99.9
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)
19.15311059797-5.37972002565-2.794406737985.469452037623.83324048343.19623661879-1.01755402167-1.461643191690.0005734993955152.492568770430.5953760481220.85711984655-0.0742082176261-0.5354385790920.306860532041.38744261812-0.07636663227240.02838568198551.154644050280.0758359196660.957357962911-12.410665369338.573431375916.7486243314
29.470148856772.39787289171-0.2111094813718.11094523289-0.5101016206916.143404046170.06639765808350.30115341817-0.0154749953106-0.00200010437010.0440587518435-1.06085179281-0.01753306496980.571399018832-0.1031568992050.923051113820.000845460297142-0.09879238425670.830643778028-0.007387050474910.923077714088-5.4527836464735.26069053942.63203746646
32.556373640860.01147400667940.6028468494243.26782390692-1.992027836824.59845005540.6244659124952.404697652740.381202291356-1.43202476845-0.3180861920660.433288468701-0.04788305142030.516224314231-0.2161718336441.396960184850.0938830394051-0.06693286468611.467355997690.1901746624550.93940860406728.028147693522.4932066604-13.8852362112
47.82166048683-4.097883771483.065314296447.095253427622.61602353746.65092479205-0.0797101338696-0.5526231030511.707203253210.2538168254370.309133412214-0.305962629734-0.994065039089-0.278375740854-0.2604821684720.9917513352380.03605485656290.134190945530.839945826550.1210494634281.2414211762625.876700445528.76394723361.9855769398
56.91010760221-5.805126868732.418739575277.798126168751.575748831345.52115627801-0.0810656127811-0.0658264659418-1.22456155924-0.795607940632-0.02322557410711.499302498171.006803148-0.1515586424860.1051363223111.08982265752-0.0781555241839-0.05690316191020.883685926490.1474702642390.8733962385725.017460486315.8737383448-3.62254058611
64.95751253016-3.84280208523-3.75195279186.95309115981-0.8867535413636.39921244616-0.123275630235-0.5538113975471.064181665880.2027612069640.917166415765-0.6163353804680.613821687504-0.402219100284-0.7571859169081.192830574090.1516617589750.113772554951.46899031736-0.0974729162721.1111902315110.027518312529.50019636212.579229694
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 307 through 323 )
2X-RAY DIFFRACTION2chain 'A' and (resid 324 through 416 )
3X-RAY DIFFRACTION3chain 'B' and (resid 308 through 327 )
4X-RAY DIFFRACTION4chain 'B' and (resid 328 through 395 )
5X-RAY DIFFRACTION5chain 'B' and (resid 396 through 416 )
6X-RAY DIFFRACTION6chain 'C' and (resid 1 through 12 )

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