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- PDB-8cmz: Crystal structure of CREBBP-R1446C histone acetyltransferase doma... -

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Basic information

Entry
Database: PDB / ID: 8cmz
TitleCrystal structure of CREBBP-R1446C histone acetyltransferase domain in complex with Coenzyme A
Componentshistone acetyltransferase
KeywordsTRANSFERASE / histone acetyltransferase
Function / homology
Function and homology information


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 / non-canonical NF-kappaB signal transduction / cellular response to nutrient levels / histone acetyltransferase complex / histone acetyltransferase / protein destabilization ...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 / non-canonical NF-kappaB signal transduction / cellular response to nutrient levels / histone acetyltransferase complex / histone acetyltransferase / protein destabilization / transcription coactivator binding / positive regulation of protein localization to nucleus / transcription corepressor activity / cellular response to UV / rhythmic process / p53 binding / 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 / Coactivator CBP, KIX domain / CREB-binding protein/p300, atypical RING 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 / 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. / Coactivator CBP, KIX domain superfamily / Histone acetyltransferase Rtt109/CBP / Histone acetylation protein / Histone acetylation protein / 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 / Bromodomain profile. / bromo domain / Bromodomain / Bromodomain-like superfamily / Zinc finger, RING/FYVE/PHD-type
Similarity search - Domain/homology
COENZYME A / histone acetyltransferase
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.252 Å
AuthorsMechaly, A.E. / Zhang, W. / Haouz, A. / Green, M. / Rodrigues-Lima, F.
Funding support1items
OrganizationGrant numberCountry
Other government
CitationJournal: To Be Published
Title: Crystal structure of CREBBP-R1446C histone acetyltransferase domain in complex with Coenzyme A
Authors: Mechaly, A.E. / Zhang, W. / Haouz, A. / Green, M. / Rodrigues-Lima, F.
History
DepositionFeb 21, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 6, 2024Provider: 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,0286
Polymers74,9981
Non-polymers1,0295
Water25214
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1190 Å2
ΔGint-34 kcal/mol
Surface area28070 Å2
Unit cell
Length a, b, c (Å)87.181, 145.095, 154.783
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

#1: Protein histone acetyltransferase /


Mass: 74998.336 Da / Num. of mol.: 1
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.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-COA / COENZYME A / Coenzyme A


Mass: 767.534 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H36N7O16P3S / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 14 / 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: 3.26 Å3/Da / Density % sol: 62.31 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 7
Details: 0,1 M Ammonium citrate tribasic pH 7.0 12 % w/v Polyethylene glycol 3,350

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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: Dec 7, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 2.252→105.857 Å / Num. obs: 23161 / % possible obs: 93.5 % / Redundancy: 13.4 % / CC1/2: 0.998 / Rmerge(I) obs: 0.121 / Rpim(I) all: 0.034 / Rrim(I) all: 0.125 / Net I/σ(I): 12.2
Reflection shellResolution: 2.252→2.539 Å / Rmerge(I) obs: 1.39 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 1158 / CC1/2: 0.687 / Rpim(I) all: 0.409 / Rrim(I) all: 1.451

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Processing

Software
NameClassification
autoBUSTERrefinement
PHASERphasing
autoPROCdata processing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.252→53.76 Å / SU ML: 0.32 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 45.14 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2972 1183 5.11 %
Rwork0.2393 --
obs0.2424 23155 49.48 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.252→53.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4409 0 52 14 4475
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0114592
X-RAY DIFFRACTIONf_angle_d1.3596215
X-RAY DIFFRACTIONf_dihedral_angle_d10.957621
X-RAY DIFFRACTIONf_chiral_restr0.066641
X-RAY DIFFRACTIONf_plane_restr0.008809
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.252-2.350.648460.4743179X-RAY DIFFRACTION3
2.35-2.480.416320.3932528X-RAY DIFFRACTION10
2.48-2.630.3637500.37011127X-RAY DIFFRACTION20
2.63-2.840.42081150.36161949X-RAY DIFFRACTION36
2.84-3.120.3821560.33213024X-RAY DIFFRACTION54
3.12-3.570.31431960.26944102X-RAY DIFFRACTION74
3.57-4.50.2833310.21035265X-RAY DIFFRACTION95
4.5-53.760.27912970.22245798X-RAY DIFFRACTION100
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)
11.2845-0.5241-0.531.1555-0.79431.2930.1540.88270.371-0.24520.09670.29270.0825-0.6095-0.28210.27940.0066-0.01440.61380.45460.3649-9.937438.663521.1462
20.3402-0.082-0.01020.1535-0.2360.27590.10980.68270.4011-0.23980.21290.5391-0.0621-0.7083-0.0770.350.2346-0.07950.81440.84060.4394-12.45445.225121.531
30.24730.3793-0.47451.4629-0.14751.73980.57260.0396-0.97380.02220.03940.90420.7906-1.4583-0.63441.0908-0.4918-0.38921.70370.52451.72560.456718.660633.8768
40.67720.30080.00333.3868-0.99852.7262-0.0612-0.2457-0.33180.2677-0.3506-0.48390.17540.69280.3640.33690.0530.05550.80650.35030.13835.623556.66729.4357
50.76990.34040.01181.9053-0.85451.9493-0.0576-0.0627-0.0518-0.0366-0.2176-0.1635-0.14990.35440.06740.23350.26110.04440.58450.43410.018527.613951.685112.9416
65.9639-0.8796-0.55660.3509-0.51431.6292-0.05660.4086-1.2801-0.361-0.2603-0.28710.88610.3623-0.09980.64490.20260.08870.44610.25630.66610.741327.830522.789
74.0859-1.004-0.43773.3025-0.33281.147-0.03670.40320.1073-0.08610.36250.7321-0.2173-0.6866-0.21990.40480.03980.01980.41790.38620.5098-14.858441.845329.3455
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|1389-1483}A1389 - 1483
2X-RAY DIFFRACTION2{ A|1484-1698}
3X-RAY DIFFRACTION3{ A|1699-1745}
4X-RAY DIFFRACTION4{ A|1076-1135}
5X-RAY DIFFRACTION5{ A|1136-1296}
6X-RAY DIFFRACTION6{ A|1297-1349}
7X-RAY DIFFRACTION7{ A|1350-1388}

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