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- PDB-9hku: Crystal structure of CREBBP histone acetyltransferase domain in c... -

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Basic information

Entry
Database: PDB / ID: 9hku
TitleCrystal structure of CREBBP histone acetyltransferase domain in complex with Acetyl-Coenzyme A
Componentshistone acetyltransferase
KeywordsTRANSFERASE / Histone acetyltransferase
Function / homology
Function and homology information


peptide lactyltransferase (CoA-dependent) activity / histone H3K18 acetyltransferase activity / histone H3K27 acetyltransferase activity / MRF binding / negative regulation of transcription by RNA polymerase I / positive regulation of transforming growth factor beta receptor signaling pathway / histone acetyltransferase complex / canonical NF-kappaB signal transduction / cellular response to nutrient levels / histone acetyltransferase ...peptide lactyltransferase (CoA-dependent) activity / histone H3K18 acetyltransferase activity / histone H3K27 acetyltransferase activity / MRF binding / negative regulation of transcription by RNA polymerase I / positive regulation of transforming growth factor beta receptor signaling pathway / histone acetyltransferase complex / canonical NF-kappaB signal transduction / cellular response to nutrient levels / histone acetyltransferase / positive regulation of double-strand break repair via homologous recombination / protein destabilization / positive regulation of protein localization to nucleus / transcription coactivator binding / p53 binding / cellular response to UV / transcription corepressor activity / rhythmic process / transcription regulator complex / RNA polymerase II-specific DNA-binding transcription factor binding / damaged DNA binding / transcription coactivator activity / nuclear body / chromatin binding / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / zinc ion binding / cytoplasm
Similarity search - Function
Nuclear receptor coactivator, CREB-bp-like, interlocking / Nuclear receptor coactivator, CREB-bp-like, interlocking domain superfamily / Creb binding / Zinc finger, TAZ-type / TAZ domain superfamily / TAZ zinc finger / Zinc finger TAZ-type profile. / TAZ zinc finger, present in p300 and CBP / : / Histone acetyltransferase p300-like, PHD domain ...Nuclear receptor coactivator, CREB-bp-like, interlocking / Nuclear receptor coactivator, CREB-bp-like, interlocking domain superfamily / Creb binding / Zinc finger, TAZ-type / TAZ domain superfamily / TAZ zinc finger / Zinc finger TAZ-type profile. / TAZ zinc finger, present in p300 and CBP / : / 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 / Zinc finger ZZ-type signature. / Zinc finger, ZZ type / Zinc-binding domain, present in Dystrophin, CREB-binding protein. / Zinc finger, ZZ-type / Zinc finger, ZZ-type superfamily / Zinc finger ZZ-type profile. / Nuclear receptor coactivator, interlocking / 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
ACETYL COENZYME *A / histone acetyltransferase
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.356 Å
AuthorsMechaly, A.E. / Zhang, W. / Cui, G. / Green, M.R. / Rodrigues-Lima, F.
Funding support France, United States, China, 3items
OrganizationGrant numberCountry
Centre National de la Recherche Scientifique (CNRS) France
National Institutes of Health/National Cancer Institute (NIH/NCI) United States
Chinese Scholarship Council China
CitationJournal: To Be Published
Title: Crystal structure of CREBBP histone acetyltransferase domain in complex with Acetyl-Coenzyme A
Authors: Mechaly, A.E. / Zhang, W. / Cui, G. / Green, M.R. / Rodrigues-Lima, F.
History
DepositionDec 4, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 17, 2025Provider: repository / Type: Initial release

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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)152,24712
Polymers150,1052
Non-polymers2,14210
Water4,918273
1
A: histone acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,1246
Polymers75,0521
Non-polymers1,0715
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: histone acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,1246
Polymers75,0521
Non-polymers1,0715
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)85.622, 139.928, 154.571
Angle α, β, γ (deg.)90, 90, 90
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein histone acetyltransferase


Mass: 75052.391 Da / Num. of mol.: 2 / Mutation: Y1503F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Crebbp / Production host: Escherichia coli (E. coli) / References: UniProt: F8VPR5, histone acetyltransferase
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-ACO / ACETYL COENZYME *A


Mass: 809.571 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C23H38N7O17P3S / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 273 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 3.08 Å3/Da / Density % sol: 60.12 %
Crystal growTemperature: 298 K / Method: vapor diffusion
Details: 0.2 M Sodium citrate tribasic dihydrate 20 % w/v Polyethylene glycol 3350 pH 8.2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97856 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 7, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 2.356→154.571 Å / Num. obs: 39974 / % possible obs: 94.4 % / Redundancy: 12.3 % / CC1/2: 0.948 / Rmerge(I) obs: 0.317 / Rpim(I) all: 0.093 / Rrim(I) all: 0.331 / Net I/σ(I): 7
Reflection shellResolution: 2.356→2.661 Å / Rmerge(I) obs: 1.82 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 1999 / CC1/2: 0.428 / Rpim(I) all: 0.576 / Rrim(I) all: 1.912

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Processing

Software
NameVersionClassification
BUSTER2.10.4refinement
autoPROCdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.356→154.57 Å / Cor.coef. Fo:Fc: 0.86 / Cor.coef. Fo:Fc free: 0.779 / SU R Cruickshank DPI: 1.19 / Cross valid method: THROUGHOUT / SU R Blow DPI: 1.278 / SU Rfree Blow DPI: 0.398 / SU Rfree Cruickshank DPI: 0.402
RfactorNum. reflection% reflectionSelection details
Rfree0.287 2017 -RANDOM
Rwork0.2455 ---
obs0.2476 39974 51.6 %-
Displacement parametersBiso mean: 58.93 Å2
Baniso -1Baniso -2Baniso -3
1--7.8956 Å20 Å20 Å2
2--11.2091 Å20 Å2
3----3.3136 Å2
Refine analyzeLuzzati coordinate error obs: 0.42 Å
Refinement stepCycle: LAST / Resolution: 2.356→154.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8765 0 110 273 9148
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0079136HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.9412366HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d3211SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes1529HARMONIC5
X-RAY DIFFRACTIONt_it9136HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion1117SEMIHARMONIC5
X-RAY DIFFRACTIONt_utility_distance28HARMONIC1
X-RAY DIFFRACTIONt_ideal_dist_contact7455SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion2.82
X-RAY DIFFRACTIONt_other_torsion20.12
LS refinement shellResolution: 2.36→2.53 Å
RfactorNum. reflection% reflection
Rfree0.4141 47 -
Rwork0.3015 --
obs0.3085 800 5.46 %
Refinement TLS params.

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)
12.13951.0132-1.34920.8251-0.71611.4401-0.1151-0.07080.0545-0.07080.2201-0.39960.0545-0.3996-0.1051-0.16080.0057-0.0490.20410.1472-0.056490.794641.391359.019
22.0676-0.9421-1.14130.47070.67091.19020.2017-0.0251-0.2218-0.0251-0.11380.1358-0.22180.1358-0.0878-0.1376-0.127-0.02590.4163-0.2078-0.147985.141538.408418.2929
30-1.15381.90752.70752.7661.878-0.0832-0.569-0.7871-0.5690.55950.1694-0.78710.1694-0.4763-0.0659-0.31660.01390.912-0.01710.037287.768344.302239.0506
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A1076 - 1746
2X-RAY DIFFRACTION1{ A|* }A1801 - 1804
3X-RAY DIFFRACTION2{ B|* }B1085 - 1746
4X-RAY DIFFRACTION2{ B|* }B1801 - 1804
5X-RAY DIFFRACTION3{ C|* }C1 - 2

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