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- PDB-8fvs: Bromodomain of CBP liganded with CCS1477int -

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Basic information

Entry
Database: PDB / ID: 8fvs
TitleBromodomain of CBP liganded with CCS1477int
ComponentsHistone acetyltransferase
KeywordsTRANSFERASE / bromodomain / complex / TRANSCRIPTION
Function / homology
Function and homology information


histone acetyltransferase activity / histone acetyltransferase / transcription coregulator activity / nuclear body / regulation of DNA-templated transcription / nucleoplasm
Similarity search - Function
: / Histone acetyltransferase p300-like, PHD domain / Coactivator CBP, KIX domain / CREB-binding protein/p300, atypical RING domain / CBP/p300-type histone acetyltransferase domain / CBP/p300, atypical RING domain superfamily / KIX domain / CREB-binding protein/p300, atypical RING domain / KIX domain profile. / CBP/p300-type histone acetyltransferase (HAT) domain profile. ...: / Histone acetyltransferase p300-like, PHD domain / Coactivator CBP, KIX domain / CREB-binding protein/p300, atypical RING domain / CBP/p300-type histone acetyltransferase domain / CBP/p300, atypical RING domain superfamily / KIX domain / CREB-binding protein/p300, atypical RING domain / KIX domain profile. / CBP/p300-type histone acetyltransferase (HAT) domain profile. / Histone acetyltransferase Rtt109/CBP / Histone acetylation protein / Histone acetylation protein / Coactivator CBP, KIX domain superfamily / Bromodomain, conserved site / Bromodomain signature. / Bromodomain / bromo domain / Bromodomain / Bromodomain (BrD) profile. / Bromodomain-like superfamily / Zinc finger, RING/FYVE/PHD-type
Similarity search - Domain/homology
Chem-YBE / histone acetyltransferase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsSchonbrunn, E. / Bikowitz, M.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Nat Commun / Year: 2024
Title: Group 3 medulloblastoma transcriptional networks collapse under domain specific EP300/CBP inhibition.
Authors: Shendy, N.A.M. / Bikowitz, M. / Sigua, L.H. / Zhang, Y. / Mercier, A. / Khashana, Y. / Nance, S. / Liu, Q. / Delahunty, I.M. / Robinson, S. / Goel, V. / Rees, M.G. / Ronan, M.A. / Wang, T. / ...Authors: Shendy, N.A.M. / Bikowitz, M. / Sigua, L.H. / Zhang, Y. / Mercier, A. / Khashana, Y. / Nance, S. / Liu, Q. / Delahunty, I.M. / Robinson, S. / Goel, V. / Rees, M.G. / Ronan, M.A. / Wang, T. / Kocak, M. / Roth, J.A. / Wang, Y. / Freeman, B.B. / Orr, B.A. / Abraham, B.J. / Roussel, M.F. / Schonbrunn, E. / Qi, J. / Durbin, A.D.
History
DepositionJan 19, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 24, 2024Provider: repository / Type: Initial release
Revision 1.1May 8, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _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: Histone acetyltransferase
B: Histone acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,9849
Polymers27,6962
Non-polymers1,2887
Water6,233346
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)35.070, 79.190, 46.130
Angle α, β, γ (deg.)90.00, 93.85, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Histone acetyltransferase


Mass: 13847.882 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CREBBP / Plasmid: pNIC28-Bsa4 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): RIL / References: UniProt: I3L466, histone acetyltransferase
#2: Chemical ChemComp-YBE / tert-butyl [(1R,4s)-4-{(5M)-5-(3,5-dimethyl-1,2-oxazol-4-yl)-2-[(2S)-6-oxopiperidin-2-yl]-1H-benzimidazol-1-yl}cyclohexyl]carbamate


Mass: 507.624 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C28H37N5O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 346 / 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: 2.31 Å3/Da / Density % sol: 46.7 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.2M Magnesium chloride hexahydrate, 0.1 M Tris 8.5, 25 % w/v Polyethylene glycol 3,350

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Data collection

DiffractionMean temperature: 93 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 11, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.75→39.79 Å / Num. obs: 25279 / % possible obs: 99.6 % / Redundancy: 7.3 % / Biso Wilson estimate: 18.6 Å2 / CC1/2: 0.994 / Rrim(I) all: 0.244 / Net I/σ(I): 16.2
Reflection shellResolution: 1.75→1.8 Å / Mean I/σ(I) obs: 6.1 / Num. unique obs: 1817 / CC1/2: 0.931 / Rrim(I) all: 0.574 / % possible all: 98.8

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Processing

Software
NameVersionClassification
PHENIX1.20.1-4487refinement
XDSJan 10, 2022data reduction
XSCALEJan 10, 2022data scaling
PHENIX1.20.1-4487phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.75→39.79 Å / SU ML: 0.13 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 17.82 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1809 1263 5 %
Rwork0.1524 --
obs0.1538 25274 99.61 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.75→39.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1946 0 91 346 2383
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007
X-RAY DIFFRACTIONf_angle_d1.113
X-RAY DIFFRACTIONf_dihedral_angle_d15.306289
X-RAY DIFFRACTIONf_chiral_restr0.06302
X-RAY DIFFRACTIONf_plane_restr0.008381
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.75-1.820.19821370.17942609X-RAY DIFFRACTION99
1.82-1.90.20041400.16422660X-RAY DIFFRACTION99
1.9-20.20371400.14982661X-RAY DIFFRACTION99
2-2.130.19881380.15412629X-RAY DIFFRACTION99
2.13-2.290.18291420.14792691X-RAY DIFFRACTION100
2.29-2.520.21631400.15662666X-RAY DIFFRACTION100
2.52-2.890.1661420.15832686X-RAY DIFFRACTION100
2.89-3.640.16571410.14832682X-RAY DIFFRACTION100
3.64-39.790.15841430.1422727X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 1.0762 Å / Origin y: -3.8265 Å / Origin z: -11.4598 Å
111213212223313233
T0.0374 Å2-0.0067 Å20.016 Å2-0.057 Å2-0.0019 Å2--0.0681 Å2
L0.2681 °20.0015 °20.0045 °2-0.2056 °2-0.0539 °2--1.5253 °2
S-0.0152 Å °-0.008 Å °0.0005 Å °0.0061 Å °-0.0002 Å °0.0056 Å °0.0052 Å °-0.0025 Å °0.0135 Å °
Refinement TLS groupSelection details: all

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