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- PDB-8cv5: Peptide 4.2B in complex with BRD3.2 -

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Basic information

Entry
Database: PDB / ID: 8cv5
TitlePeptide 4.2B in complex with BRD3.2
Components
  • Bromodomain-containing protein 3
  • Peptide 4.2E
KeywordsTRANSCRIPTION / Cyclic Peptide Inhibitor Bromodomain
Function / homology
Function and homology information


lncRNA binding / endodermal cell differentiation / protein localization to chromatin / : / molecular condensate scaffold activity / histone binding / chromatin remodeling / protein serine/threonine kinase activity / chromatin binding / regulation of transcription by RNA polymerase II ...lncRNA binding / endodermal cell differentiation / protein localization to chromatin / : / molecular condensate scaffold activity / histone binding / chromatin remodeling / protein serine/threonine kinase activity / chromatin binding / regulation of transcription by RNA polymerase II / chromatin / positive regulation of transcription by RNA polymerase II / nucleus
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 / Bromodomain profile. / bromo domain / Bromodomain / Bromodomain-like superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
ACETYL GROUP / AMINO GROUP / Bromodomain-containing protein 3
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.47 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: Bromodomain-containing protein 3
B: Peptide 4.2E
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,0794
Polymers16,0182
Non-polymers602
Water2,846158
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: surface plasmon resonance
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1590 Å2
ΔGint-13 kcal/mol
Surface area7600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.066, 76.066, 57.907
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Space group name HallP322"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+2/3
#3: -x+y,-x,z+1/3
#4: x-y,-y,-z+1/3
#5: -x,-x+y,-z+2/3
#6: y,x,-z

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Components

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


Mass: 13784.844 Da / Num. of mol.: 1 / Fragment: BD2 (UNP residues 307-419)
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 Peptide 4.2E


Mass: 2233.630 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical ChemComp-ACE / ACETYL GROUP


Mass: 44.053 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H4O
#4: Chemical ChemComp-NH2 / AMINO GROUP


Mass: 16.023 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: NH2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 158 / 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: 3.02 Å3/Da / Density % sol: 59.26 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 0.2 M sodium sulfate, 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: 0.953736 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: 1.47→43.49 Å / Num. obs: 33328 / % possible obs: 99.9 % / Redundancy: 20.3 % / Biso Wilson estimate: 14.67 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.083 / Rpim(I) all: 0.027 / Rrim(I) all: 0.087 / Χ2: 1.01 / Net I/σ(I): 22.8
Reflection shellResolution: 1.47→1.49 Å / Redundancy: 19.7 % / Rmerge(I) obs: 0.906 / Mean I/σ(I) obs: 3.5 / Num. unique obs: 1627 / CC1/2: 0.882 / Rpim(I) all: 0.294 / Rrim(I) all: 0.954 / Χ2: 1.02 / % possible all: 99

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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 3S92

3s92


Resolution: 1.47→31.79 Å / SU ML: 0.1204 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 19.7739
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1967 1755 5.27 %
Rwork0.18 31537 -
obs0.1809 33292 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 18.72 Å2
Refinement stepCycle: LAST / Resolution: 1.47→31.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1086 0 4 158 1248
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00591119
X-RAY DIFFRACTIONf_angle_d1.04531504
X-RAY DIFFRACTIONf_chiral_restr0.0782149
X-RAY DIFFRACTIONf_plane_restr0.0093193
X-RAY DIFFRACTIONf_dihedral_angle_d7.4876161
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.47-1.510.24551450.20322338X-RAY DIFFRACTION99.4
1.51-1.550.18881320.18552411X-RAY DIFFRACTION99.92
1.55-1.60.17521290.18112402X-RAY DIFFRACTION99.96
1.6-1.660.18361310.17562421X-RAY DIFFRACTION100
1.66-1.730.18521580.18632372X-RAY DIFFRACTION99.92
1.73-1.810.2141290.17772425X-RAY DIFFRACTION100
1.81-1.90.19341070.17722433X-RAY DIFFRACTION100
1.9-2.020.21741110.17982428X-RAY DIFFRACTION100
2.02-2.180.19711480.17442426X-RAY DIFFRACTION100
2.18-2.390.19761190.18612446X-RAY DIFFRACTION100
2.4-2.740.2031490.19662431X-RAY DIFFRACTION100
2.74-3.450.20971530.18892447X-RAY DIFFRACTION100
3.45-31.790.17671440.16252557X-RAY DIFFRACTION99.96
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)
10.07674934639970.02712367606620.03976280807940.1009703189410.03266012517670.04103958994820.0364347009746-0.5183555466520.2336589552830.339052400893-0.0988352836599-0.339407755054-0.08797721496770.4297953197770.009580991956040.179699297591-0.0387920312377-0.05309798348080.3836566045910.05486217224260.187179124861-10.521451964325.75249171486.71721268727
20.337132926650.0638286791413-0.1942819098930.129750431282-0.1987558644740.319480705373-0.00395913022509-0.0242626957664-0.05928074828220.04167963937150.0234407918064-0.01961085155850.013159394026-0.002862424502510.0004229023782660.126177765314-0.009914531443660.002507724962350.116476588896-0.006555177045490.116283468974-31.310721266323.1379443359-1.59818146083
30.3428028470850.302047087577-0.1499790305080.104888206209-0.004350180774110.282865945201-0.0529421591682-0.0605520441304-0.07039133955780.01872095206380.00104201192186-0.0345141886826-0.01304736858930.0412451592504-0.0008837085337160.1142780631520.0010231786199-0.003288985487460.1147376952650.01866055015840.128804108255-21.212571474522.1866634216-2.66437798777
40.17039047940.0614715322537-0.2324101121990.4205189680120.05995963183710.3570329588190.0560800678776-0.04755102158140.05852590775460.0165973584607-0.0527710489985-0.0713336441946-0.1093245265590.04414932233850.02809240646370.125934261227-0.02784106186310.005316386296980.1215995128360.004610089907630.147236023671-17.275512675932.7666605358-3.26319781962
50.06423151415820.0181889523728-0.05163135059670.03532361534970.06636914183450.167577113761-0.000334995781583-0.2295894593640.2512475614730.03402311453-0.01087876389250.0616695398596-0.311750982532-0.281342251476-0.0006946204389550.1294389375690.02553901136710.002798566358480.2010137215710.009118482527750.14229884533-45.158610479426.9547560721-1.84121377231
60.05973038157-0.00192973527871-0.03775308423770.00312643742291-0.00226596736790.0130874150265-0.01292328944-0.2760998642910.1859973658650.0352728217538-0.0567745372960.0375747265113-0.112433383311-0.180443087613-0.0001993961715360.1621686552720.0140632041247-0.01702728626110.167058141754-0.03715592218510.165973168134-40.090898930729.8604716812-3.87464700891
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 307 through 322 )AA307 - 3221 - 16
22chain 'A' and (resid 323 through 357 )AA323 - 35717 - 51
33chain 'A' and (resid 358 through 395 )AA358 - 39552 - 89
44chain 'A' and (resid 396 through 418 )AA396 - 41890 - 112
55chain 'B' and (resid 1 through 10 )BC1 - 102 - 11
66chain 'B' and (resid 11 through 17 )BC11 - 1712 - 18

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