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- PDB-8cv6: Peptide 4.2B in complex with BRD4.2 -

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Basic information

Entry
Database: PDB / ID: 8cv6
TitlePeptide 4.2B in complex with BRD4.2
Components
  • BRD4 protein
  • Peptide 4.2E
KeywordsTRANSCRIPTION / Cyclic Peptide Inhibitor Bromodomain
Function / homology
Function and homology information


Brdt, bromodomain, repeat I / Brdt, bromodomain, repeat II / : / Bromodomain-like / Histone Acetyltransferase; Chain A / Bromodomain, conserved site / Bromodomain signature. / Bromodomain / bromo domain / Bromodomain ...Brdt, bromodomain, repeat I / Brdt, bromodomain, repeat II / : / 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 / BRD4 protein
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)16,3524
Polymers16,2922
Non-polymers602
Water1,838102
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: surface plasmon resonance
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1540 Å2
ΔGint-13 kcal/mol
Surface area8540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)29.442, 59.636, 36.269
Angle α, β, γ (deg.)90.000, 100.606, 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 BRD4 protein


Mass: 14058.205 Da / Num. of mol.: 1 / 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 4.2E


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.: 102 / 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: 1.91 Å3/Da / Density % sol: 35.47 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 0.1 M HEPES, pH 7.5, 30% w/v PEG1000

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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: 1.7→35.65 Å / Num. obs: 13420 / % possible obs: 97.8 % / Redundancy: 7.1 % / Biso Wilson estimate: 16.68 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.073 / Rpim(I) all: 0.044 / Rrim(I) all: 0.085 / Χ2: 1.02 / Net I/σ(I): 15.9
Reflection shellResolution: 1.7→1.73 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.566 / Mean I/σ(I) obs: 3 / Num. unique obs: 4431 / CC1/2: 0.851 / Rpim(I) all: 0.355 / Rrim(I) all: 0.67 / % possible all: 93

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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 3UVV

3uvv


Resolution: 1.7→35.65 Å / SU ML: 0.1807 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.1758
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2222 625 4.66 %
Rwork0.1813 12777 -
obs0.1832 13402 97.61 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 19.23 Å2
Refinement stepCycle: LAST / Resolution: 1.7→35.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1089 0 4 102 1195
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00661120
X-RAY DIFFRACTIONf_angle_d1.03691501
X-RAY DIFFRACTIONf_chiral_restr0.0558151
X-RAY DIFFRACTIONf_plane_restr0.0055190
X-RAY DIFFRACTIONf_dihedral_angle_d16.4737162
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.870.28661420.20843141X-RAY DIFFRACTION96.13
1.87-2.140.2311510.18553181X-RAY DIFFRACTION97.4
2.14-2.690.24431590.18593203X-RAY DIFFRACTION97.99
2.69-35.650.19951730.17193252X-RAY DIFFRACTION98.9

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