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- PDB-4i9o: Crystal Structure of GACKIX L664C Tethered to 1-10 -

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Basic information

Entry
Database: PDB / ID: 4i9o
TitleCrystal Structure of GACKIX L664C Tethered to 1-10
ComponentsCREB-binding protein
KeywordsTRANSFERASE / KIX domain / Transcriptional Coactivator
Function / homology
Function and homology information


Activation of the TFAP2 (AP-2) family of transcription factors / Regulation of FOXO transcriptional activity by acetylation / TRAF6 mediated IRF7 activation / Nuclear events mediated by NFE2L2 / Attenuation phase / LRR FLII-interacting protein 1 (LRRFIP1) activates type I IFN production / Regulation of gene expression by Hypoxia-inducible Factor / RUNX1 regulates transcription of genes involved in differentiation of myeloid cells / Formation of the beta-catenin:TCF transactivating complex / NOTCH1 Intracellular Domain Regulates Transcription ...Activation of the TFAP2 (AP-2) family of transcription factors / Regulation of FOXO transcriptional activity by acetylation / TRAF6 mediated IRF7 activation / Nuclear events mediated by NFE2L2 / Attenuation phase / LRR FLII-interacting protein 1 (LRRFIP1) activates type I IFN production / Regulation of gene expression by Hypoxia-inducible Factor / RUNX1 regulates transcription of genes involved in differentiation of myeloid cells / Formation of the beta-catenin:TCF transactivating complex / NOTCH1 Intracellular Domain Regulates Transcription / RUNX3 regulates NOTCH signaling / cAMP response element binding protein binding / Notch-HLH transcription pathway / Transcriptional and post-translational regulation of MITF-M expression and activity / germ-line stem cell population maintenance / negative regulation of viral process / Regulation of lipid metabolism by PPARalpha / Cytoprotection by HMOX1 / Estrogen-dependent gene expression / CD209 (DC-SIGN) signaling / peptide lactyltransferase (CoA-dependent) activity / outer kinetochore / negative regulation of interferon-beta production / N-terminal peptidyl-lysine acetylation / MRF binding / face morphogenesis / negative regulation of transcription by RNA polymerase I / protein-lysine-acetyltransferase activity / cellular response to hepatocyte growth factor stimulus / histone acetyltransferase activity / acetyltransferase activity / TFIIB-class transcription factor binding / histone acetyltransferase complex / positive regulation of double-strand break repair via homologous recombination / histone H4K16 acetyltransferase activity / histone H3K56 acetyltransferase activity / histone H3K23 acetyltransferase activity / histone H2AK5 acetyltransferase activity / histone H2AK9 acetyltransferase activity / histone H2BK5 acetyltransferase activity / histone H2BK12 acetyltransferase activity / histone H3K4 acetyltransferase activity / histone H3K27 acetyltransferase activity / histone H3K36 acetyltransferase activity / histone H3K122 acetyltransferase activity / histone H3K18 acetyltransferase activity / histone H3K9 acetyltransferase activity / histone H3K14 acetyltransferase activity / histone H4K5 acetyltransferase activity / histone H4K8 acetyltransferase activity / histone H4K12 acetyltransferase activity / histone acetyltransferase / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / positive regulation of DNA-binding transcription factor activity / RNA polymerase II transcription regulatory region sequence-specific DNA binding / protein destabilization / PML body / cellular response to virus / RNA polymerase II transcription regulator complex / disordered domain specific binding / cellular response to UV / rhythmic process / DNA-binding transcription factor binding / molecular adaptor activity / transcription regulator complex / RNA polymerase II-specific DNA-binding transcription factor binding / damaged DNA binding / transcription coactivator activity / protein domain specific binding / chromatin binding / positive regulation of gene expression / regulation of DNA-templated transcription / chromatin / positive regulation of DNA-templated transcription / positive regulation of transcription by RNA polymerase II / protein-containing complex / DNA binding / zinc ion binding / nucleoplasm / nucleus / cytoplasm
Similarity search - Function
Coactivator CBP, KIX 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 / 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 / Serum Albumin; Chain A, Domain 1 / 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 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-KI1 / Histone lysine acetyltransferase CREBBP
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å
AuthorsWang, N. / Meagher, J.L. / Stuckey, J.A. / Mapp, A.K.
CitationJournal: J.Am.Chem.Soc. / Year: 2013
Title: Ordering a dynamic protein via a small-molecule stabilizer.
Authors: Wang, N. / Majmudar, C.Y. / Pomerantz, W.C. / Gagnon, J.K. / Sadowsky, J.D. / Meagher, J.L. / Johnson, T.K. / Stuckey, J.A. / Brooks, C.L. / Wells, J.A. / Mapp, A.K.
History
DepositionDec 5, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 6, 2013Provider: repository / Type: Initial release
Revision 1.1Apr 17, 2013Group: Database references
Revision 1.2Nov 15, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software
Revision 1.3Nov 6, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_unobs_or_zero_occ_atoms / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CREB-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,6314
Polymers12,1391
Non-polymers4923
Water48627
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: CREB-binding protein
hetero molecules

A: CREB-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,2628
Polymers24,2782
Non-polymers9846
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_665-y+1,-x+1,-z+1/21
Buried area2600 Å2
ΔGint-9 kcal/mol
Surface area9150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.330, 48.330, 85.464
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-820-

HOH

21A-822-

HOH

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Components

#1: Protein CREB-binding protein


Mass: 12139.228 Da / Num. of mol.: 1 / Fragment: UNP residues 562-672, GACKIX domain / Mutation: L664C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Crebbp, Cbp / Plasmid: pRSET-b / Production host: Escherichia coli (E. coli) / Strain (production host): Rossetta pLysS (DE3) / References: UniProt: P45481, histone acetyltransferase
#2: Chemical ChemComp-KI1 / 1-{4-[4-chloro-3-(trifluoromethyl)phenyl]-4-hydroxypiperidin-1-yl}-3-sulfanylpropan-1-one


Mass: 367.814 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H17ClF3NO2S
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 27 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.06 Å3/Da / Density % sol: 40.16 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 1.8 M (NH4)2SO4, 0.1 M Tris-HCl, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97852 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 13, 2012
RadiationMonochromator: Diamond [111] / Protocol: SAD / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97852 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. all: 7383 / Num. obs: 7383 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 20.8 % / Rmerge(I) obs: 0.067 / Χ2: 1.188 / Net I/σ(I): 15.7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2-2.0321.20.2333490.9231100
2.03-2.0721.80.2233590.9171100
2.07-2.1121.30.2023550.9381100
2.11-2.1521.40.1973640.9181100
2.15-2.221.50.1643570.9351100
2.2-2.2521.50.153490.9641100
2.25-2.3121.20.1173740.9571100
2.31-2.3721.80.1063500.9361100
2.37-2.4421.20.0983680.9541100
2.44-2.5221.40.1023641.0621100
2.52-2.6121.20.113501.3051100
2.61-2.7121.30.13661.4231100
2.71-2.8421.30.093661.3791100
2.84-2.99210.0773691.3011100
2.99-3.1720.80.0673721.3691100
3.17-3.4220.70.063781.2151100
3.42-3.7620.50.0543701.2451100
3.76-4.3119.70.0513851.441100
4.31-5.4318.80.0493981.5481100
5.43-5016.50.0614402.111199.8

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
BUSTER-TNTrefinement
PDB_EXTRACT3.11data extraction
MD2data collection
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
BUSTER2.10.0refinement
RefinementMethod to determine structure: SAD / Resolution: 2→42.07 Å / Cor.coef. Fo:Fc: 0.9403 / Cor.coef. Fo:Fc free: 0.9233 / Occupancy max: 1 / Occupancy min: 0 / SU R Cruickshank DPI: 0.161 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.2329 340 4.65 %RANDOM
Rwork0.2064 ---
obs0.2076 7312 99.99 %-
Displacement parametersBiso max: 106.96 Å2 / Biso mean: 35.8758 Å2 / Biso min: 15.05 Å2
Baniso -1Baniso -2Baniso -3
1--2.2045 Å20 Å20 Å2
2---2.2045 Å20 Å2
3---4.409 Å2
Refine analyzeLuzzati coordinate error obs: 0.22 Å
Refinement stepCycle: LAST / Resolution: 2→42.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms626 0 31 27 684
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d322SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes15HARMONIC2
X-RAY DIFFRACTIONt_gen_planes109HARMONIC5
X-RAY DIFFRACTIONt_it684HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion83SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact821SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d684HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg926HARMONIC20.87
X-RAY DIFFRACTIONt_omega_torsion2.89
X-RAY DIFFRACTIONt_other_torsion3.02
LS refinement shellResolution: 2→2.24 Å / Total num. of bins used: 5
RfactorNum. reflection% reflection
Rfree0.2159 84 4.19 %
Rwork0.1742 1919 -
all0.176 2003 -
obs--99.99 %
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)
11.2620.3496-0.84941.0224-1.71150.6653-0.0114-0.04940.0534-0.01620.00870.02570.0127-0.00230.0027-0.02730.0077-0.00440.0318-0.003-0.048628.207514.299124.8765
20.65180.08480.63291.53530.13070.452-0.0195-0.0136-0.02920.01840.02890.0579-0.02190.0031-0.0094-0.0398-0.0297-0.03110.00150.01080.016121.721111.477120.7678
30.2838-0.78330.10171.7927-1.78680.58380.0053-0.0467-0.029-0.0294-0.00340.01790.0358-0.0031-0.00190.08230.0217-0.0269-0.06930.0052-0.046929.54884.66329.1708
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{A|588 - 619}A588 - 619
2X-RAY DIFFRACTION2{A|620 - 644}A620 - 644
3X-RAY DIFFRACTION3{A|645 - 665}A645 - 665

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