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- PDB-9h02: Crystal structure of human CREBBP histone acetyltransferase domai... -

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Basic information

Entry
Database: PDB / ID: 9h02
TitleCrystal structure of human CREBBP histone acetyltransferase domain in complex with a bisubstrate inhibitor, Lys-CoA
ComponentsCREB-binding protein
KeywordsTRANSFERASE / Histone acetyltransferase
Function / homology
Function and homology information


peptide lactyltransferase (CoA-dependent) activity / NFE2L2 regulating ER-stress associated genes / Activation of the TFAP2 (AP-2) family of transcription factors / NFE2L2 regulating inflammation associated genes / histone H3K18 acetyltransferase activity / N-terminal peptidyl-lysine acetylation / histone H3K27 acetyltransferase activity / LRR FLII-interacting protein 1 (LRRFIP1) activates type I IFN production / NFE2L2 regulates pentose phosphate pathway genes / regulation of smoothened signaling pathway ...peptide lactyltransferase (CoA-dependent) activity / NFE2L2 regulating ER-stress associated genes / Activation of the TFAP2 (AP-2) family of transcription factors / NFE2L2 regulating inflammation associated genes / histone H3K18 acetyltransferase activity / N-terminal peptidyl-lysine acetylation / histone H3K27 acetyltransferase activity / LRR FLII-interacting protein 1 (LRRFIP1) activates type I IFN production / NFE2L2 regulates pentose phosphate pathway genes / regulation of smoothened signaling pathway / NFE2L2 regulating MDR associated enzymes / MRF binding / RUNX1 regulates transcription of genes involved in differentiation of myeloid cells / Regulation of gene expression in late stage (branching morphogenesis) pancreatic bud precursor cells / Regulation of FOXO transcriptional activity by acetylation / RUNX3 regulates NOTCH signaling / NOTCH4 Intracellular Domain Regulates Transcription / Nuclear events mediated by NFE2L2 / Regulation of NFE2L2 gene expression / Regulation of gene expression by Hypoxia-inducible Factor / NOTCH3 Intracellular Domain Regulates Transcription / negative regulation of transcription by RNA polymerase I / TRAF6 mediated IRF7 activation / NFE2L2 regulating tumorigenic genes / NFE2L2 regulating anti-oxidant/detoxification enzymes / embryonic digit morphogenesis / protein-lysine-acetyltransferase activity / protein acetylation / homeostatic process / Notch-HLH transcription pathway / Formation of paraxial mesoderm / acetyltransferase activity / positive regulation of transforming growth factor beta receptor signaling pathway / FOXO-mediated transcription of cell death genes / stimulatory C-type lectin receptor signaling pathway / Zygotic genome activation (ZGA) / TP53 Regulates Transcription of Genes Involved in Cytochrome C Release / histone acetyltransferase complex / canonical NF-kappaB signal transduction / Attenuation phase / histone acetyltransferase activity / cellular response to nutrient levels / histone acetyltransferase / positive regulation of double-strand break repair via homologous recombination / regulation of cellular response to heat / : / NPAS4 regulates expression of target genes / Regulation of lipid metabolism by PPARalpha / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / Transcriptional and post-translational regulation of MITF-M expression and activity / CD209 (DC-SIGN) signaling / BMAL1:CLOCK,NPAS2 activates circadian expression / SUMOylation of transcription cofactors / Activation of gene expression by SREBF (SREBP) / Heme signaling / Formation of the beta-catenin:TCF transactivating complex / Transcriptional activation of mitochondrial biogenesis / PPARA activates gene expression / Cytoprotection by HMOX1 / protein destabilization / Evasion by RSV of host interferon responses / chromatin DNA binding / NOTCH1 Intracellular Domain Regulates Transcription / Transcriptional regulation of white adipocyte differentiation / Pre-NOTCH Transcription and Translation / positive regulation of protein localization to nucleus / Constitutive Signaling by NOTCH1 PEST Domain Mutants / Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants / tau protein binding / transcription coactivator binding / Activation of anterior HOX genes in hindbrain development during early embryogenesis / cellular response to UV / p53 binding / : / rhythmic process / transcription corepressor activity / HATs acetylate histones / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / TRAF3-dependent IRF activation pathway / protein-containing complex assembly / transcription regulator complex / Estrogen-dependent gene expression / DNA-binding transcription factor binding / damaged DNA binding / RNA polymerase II-specific DNA-binding transcription factor binding / transcription coactivator activity / response to hypoxia / nuclear body / chromatin binding / regulation of DNA-templated transcription / chromatin / positive regulation of DNA-templated transcription / SARS-CoV-2 activates/modulates innate and adaptive immune responses / negative regulation of transcription by RNA polymerase II / signal transduction / positive regulation of transcription by RNA polymerase II / zinc ion binding / nucleoplasm / nucleus / 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-binding domain, present in Dystrophin, CREB-binding protein. / Zinc finger, ZZ type / 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
Chem-01K / CREB-binding protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.03 Å
AuthorsMechaly, A.E. / 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 human CREBBP histone acetyltransferase domain in complex with a bisubstrate inhibitor, Lys-CoA
Authors: Mechaly, A.E. / Cui, G. / Green, M.R. / Rodrigues-Lima, F.
History
DepositionOct 7, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 15, 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: CREB-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,8538
Polymers40,4861
Non-polymers1,3677
Water3,837213
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)75.010, 102.100, 51.480
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Space group name HallP22ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x+1/2,y+1/2,-z
#4: -x,-y,z

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Components

#1: Protein CREB-binding protein / Histone lysine acetyltransferase CREBBP / Protein lactyltransferas CREBBP / Protein-lysine ...Histone lysine acetyltransferase CREBBP / Protein lactyltransferas CREBBP / Protein-lysine acetyltransferase CREBBP


Mass: 40485.988 Da / Num. of mol.: 1 / Mutation: Y1503F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CREBBP, CBP / Production host: Escherichia coli (E. coli)
References: UniProt: Q92793, histone acetyltransferase, Transferases; Acyltransferases; Transferring groups other than aminoacyl groups
#2: Chemical ChemComp-01K / [(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-4-hydroxy-3-(phosphonooxy)tetrahydrofuran-2-yl]methyl (3R,20R)-20-carbamoyl-3-hydroxy-2,2-dimethyl-4,8,14,22-tetraoxo-12-thia-5,9,15,21-tetraazatricos-1-yl dihydrogen diphosphate / Lysine-COENZYME A derivative


Mass: 994.794 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C31H53N10O19P3S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 213 / 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: 2.43 Å3/Da / Density % sol: 49.48 %
Crystal growTemperature: 291 K / Method: vapor diffusion
Details: 0.1M (NH4)2SO4, 0.1 Na3 cit 5.6pH, 30% w/v PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.9793 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 6, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.03→45.97 Å / Num. obs: 48684 / % possible obs: 99 % / Redundancy: 7 % / Biso Wilson estimate: 33.06 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.1696 / Rpim(I) all: 0.06943 / Rrim(I) all: 0.1835 / Net I/σ(I): 8.35
Reflection shellResolution: 2.03→2.11 Å / Redundancy: 6.8 % / Rmerge(I) obs: 1.3 / Mean I/σ(I) obs: 1.53 / Num. unique obs: 5109 / CC1/2: 0.58 / Rpim(I) all: 0.5273 / Rrim(I) all: 1.405 / % possible all: 93.83

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Processing

Software
NameVersionClassification
PHENIX1.21.1_5286refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.03→45.97 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 22.5667
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2241 1294 5 %
Rwork0.1748 24591 -
obs0.1773 25885 99.01 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 40.02 Å2
Refinement stepCycle: LAST / Resolution: 2.03→45.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2618 0 88 213 2919
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00762793
X-RAY DIFFRACTIONf_angle_d1.03273770
X-RAY DIFFRACTIONf_chiral_restr0.0578388
X-RAY DIFFRACTIONf_plane_restr0.0086478
X-RAY DIFFRACTIONf_dihedral_angle_d19.30811060
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.03-2.110.31671340.22922543X-RAY DIFFRACTION93.9
2.11-2.210.33171410.22342689X-RAY DIFFRACTION99.3
2.21-2.330.25631420.20262705X-RAY DIFFRACTION99.27
2.33-2.470.22581420.18522711X-RAY DIFFRACTION99.69
2.47-2.660.26531430.19772714X-RAY DIFFRACTION99.65
2.66-2.930.22831450.1812747X-RAY DIFFRACTION99.79
2.93-3.360.23171450.16992757X-RAY DIFFRACTION99.9
3.36-4.230.16751480.1482803X-RAY DIFFRACTION99.97
4.23-45.970.21381540.16722922X-RAY DIFFRACTION99.55
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)
12.685742631830.453386487727-0.1983897466543.66560195125-0.5144667424193.49642982068-0.166729444168-0.06925348380410.01732034424450.3698196095110.061525276526-0.349260500685-0.1740041983520.3135754148490.03698523957540.259503416123-0.0268232940174-0.07268196066420.278105181674-0.03342737950160.30381203852210.19997446331.773148626-8.85687801145
22.416272288760.6953952465550.2630604118433.219315924910.3199094272871.238672740520.03379409413810.02247670194880.6647362431570.02599360724550.115661426011-0.089624170044-0.1816544048940.155186424044-0.2075956798110.164203696360.0106034389413-0.07699474450320.2244298865690.004748523814370.158120369964.0287514810530.4391647763-12.3751780572
31.571559031850.677069863091-0.286730946471.805754166640.06658312284211.35547053267-0.02544363043550.07469544243070.0394251562588-0.04220017491510.0449059152070.0604994179448-0.0966441348952-0.0239408829299-0.02433723405630.1615675073110.0121159791156-0.01099543493770.170486318047-0.001213315707740.162060425831-4.8623605667719.8668368132-15.1206991612
43.76611840208-4.25461362635-3.403061040584.923625018363.226405106946.313087268160.146754704530.639107518879-0.8073536110490.0182081417996-0.4288108486620.5302602111820.150784419599-0.6256770667630.2869853682550.292504093732-0.0137660900127-0.04788731937120.334108317172-0.04864154621340.386760496153-22.22969906529.00922888275-19.0075186424
51.9979189811-0.01300572778360.4704113152223.503469772390.14113337132.986277816090.0420882772384-0.162635186825-0.1149985836740.385171779220.09030785014590.07721360722070.194132581356-0.0517059810718-0.1160449989290.184997833637-0.0007504696171720.02629573048140.2145888577470.03407199897030.190908279688-2.6258338560214.4894861206-6.37108422913
66.731288120090.03006853114250.7745608966595.715483854491.619355093135.64628709322-0.0816176454397-0.2561041020270.566408809318-0.112806205917-0.06259421061280.200155119754-0.52560342236-0.4423743705520.1774706116030.311802221440.0402960776826-0.02617555975190.156228801214-0.02171715049490.295360300439-5.6665312649242.776847284-15.8372519903
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: B

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 1323 through 1348 )1323 - 13482 - 27
22chain 'A' and (resid 1349 through 1370 )1349 - 137028 - 49
33chain 'A' and (resid 1371 through 1543 )1371 - 154350 - 222
44chain 'A' and (resid 1544 through 1626 )1544 - 1626223 - 247
55chain 'A' and (resid 1627 through 1657 )1627 - 1657248 - 278
66chain 'A' and (resid 1658 through 1699 )1658 - 1699279 - 320

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