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- PDB-3svh: Crystal Structure of the bromdomain of human CREBBP in complex wi... -

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Basic information

Entry
Database: PDB / ID: 3svh
TitleCrystal Structure of the bromdomain of human CREBBP in complex with a 3,5-dimethylisoxazol ligand
ComponentsCREB-binding protein
KeywordsUNKNOWN FUNCTION / isoxazole / Bromodomain / Structural Genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


peptide lactyltransferase (CoA-dependent) activity / NFE2L2 regulating ER-stress associated genes / peptide N-acetyltransferase activity / Activation of the TFAP2 (AP-2) family of transcription factors / NFE2L2 regulating inflammation associated genes / regulation of smoothened signaling pathway / histone H3K18 acetyltransferase activity / LRR FLII-interacting protein 1 (LRRFIP1) activates type I IFN production / N-terminal peptidyl-lysine acetylation / histone H3K27 acetyltransferase activity ...peptide lactyltransferase (CoA-dependent) activity / NFE2L2 regulating ER-stress associated genes / peptide N-acetyltransferase activity / Activation of the TFAP2 (AP-2) family of transcription factors / NFE2L2 regulating inflammation associated genes / regulation of smoothened signaling pathway / histone H3K18 acetyltransferase activity / LRR FLII-interacting protein 1 (LRRFIP1) activates type I IFN production / N-terminal peptidyl-lysine acetylation / histone H3K27 acetyltransferase activity / NFE2L2 regulates pentose phosphate pathway genes / 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 / RUNX3 regulates NOTCH signaling / Regulation of FOXO transcriptional activity by acetylation / NOTCH4 Intracellular Domain Regulates Transcription / Regulation of gene expression by Hypoxia-inducible Factor / Nuclear events mediated by NFE2L2 / Regulation of NFE2L2 gene expression / negative regulation of transcription by RNA polymerase I / NOTCH3 Intracellular Domain Regulates Transcription / NFE2L2 regulating anti-oxidant/detoxification enzymes / TRAF6 mediated IRF7 activation / NFE2L2 regulating tumorigenic genes / peptide-lysine-N-acetyltransferase activity / FOXO-mediated transcription of cell death genes / embryonic digit morphogenesis / homeostatic process / protein acetylation / Notch-HLH transcription pathway / positive regulation of transforming growth factor beta receptor signaling pathway / Formation of paraxial mesoderm / non-canonical NF-kappaB signal transduction / Zygotic genome activation (ZGA) / stimulatory C-type lectin receptor signaling pathway / cellular response to nutrient levels / TP53 Regulates Transcription of Genes Involved in Cytochrome C Release / acetyltransferase activity / positive regulation of double-strand break repair via homologous recombination / histone acetyltransferase complex / Attenuation phase / regulation of cellular response to heat / histone acetyltransferase activity / histone acetyltransferase / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / RORA activates gene expression / NPAS4 regulates expression of target genes / Regulation of lipid metabolism by PPARalpha / CD209 (DC-SIGN) signaling / BMAL1:CLOCK,NPAS2 activates circadian gene expression / SUMOylation of transcription cofactors / Activation of gene expression by SREBF (SREBP) / Formation of the beta-catenin:TCF transactivating complex / Heme signaling / protein destabilization / Transcriptional activation of mitochondrial biogenesis / PPARA activates gene expression / Evasion by RSV of host interferon responses / Cytoprotection by HMOX1 / NOTCH1 Intracellular Domain Regulates Transcription / chromatin DNA binding / Pre-NOTCH Transcription and Translation / Constitutive Signaling by NOTCH1 PEST Domain Mutants / Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants / transcription coactivator binding / Transcriptional regulation of white adipocyte differentiation / Activation of anterior HOX genes in hindbrain development during early embryogenesis / positive regulation of protein localization to nucleus / transcription corepressor activity / cellular response to UV / rhythmic process / Circadian Clock / p53 binding / TRAF3-dependent IRF activation pathway / HATs acetylate histones / protein-containing complex assembly / DNA-binding transcription factor binding / Estrogen-dependent gene expression / RNA polymerase II-specific DNA-binding transcription factor binding / transcription regulator complex / damaged DNA binding / transcription coactivator activity / nuclear body / response to hypoxia / chromatin binding / regulation of DNA-templated transcription / chromatin / SARS-CoV-2 activates/modulates innate and adaptive immune responses / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / signal transduction / positive regulation of transcription by RNA polymerase II / zinc ion binding / nucleoplasm / nucleus / cytoplasm / cytosol
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. / 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-like / Histone Acetyltransferase; Chain A / Bromodomain, conserved site / Bromodomain signature. / Bromodomain / Bromodomain profile. / bromo domain / Bromodomain / Bromodomain-like superfamily / Zinc finger, RING/FYVE/PHD-type / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-KRG / CREB-binding protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.8 Å
AuthorsFilippakopoulos, P. / Picaud, S. / Felletar, I. / Hewings, S.D. / von Delft, F. / Arrowsmith, C.H. / Edwards, A.M. / Weigelt, J. / Bountra, C. / Conway, S.J. ...Filippakopoulos, P. / Picaud, S. / Felletar, I. / Hewings, S.D. / von Delft, F. / Arrowsmith, C.H. / Edwards, A.M. / Weigelt, J. / Bountra, C. / Conway, S.J. / Knapp, S. / Structural Genomics Consortium (SGC)
CitationJournal: To be Published
Title: Crystal Structure of the bromdomain of human CREBBP in complex with a 3,5-dimethylisoxazol ligand
Authors: Filippakopoulos, P. / Picaud, S. / Felletar, I. / Hewings, S.D. / von Delft, F. / Arrowsmith, C.H. / Edwards, A.M. / Weigelt, J. / Bountra, C. / Conway, S.J. / Knapp, S.
History
DepositionJul 12, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 10, 2011Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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_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

Downloads & links

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Assembly

Deposited unit
A: CREB-binding protein
B: CREB-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,5547
Polymers28,4472
Non-polymers1,1075
Water4,179232
1
A: CREB-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,8084
Polymers14,2231
Non-polymers5853
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: CREB-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,7463
Polymers14,2231
Non-polymers5232
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)42.360, 61.920, 58.420
Angle α, β, γ (deg.)90.000, 111.380, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein CREB-binding protein


Mass: 14223.349 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CBP, CREBBP / Plasmid: pNIC28-Bsa4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-R3 / References: UniProt: Q92793
#2: Chemical
ChemComp-KRG / 3-(3,5-dimethyl-1,2-oxazol-4-yl)-5-ethoxybenzoic acid


Mass: 261.273 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C14H15NO4
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 232 / Source method: isolated from a natural source / Formula: H2O

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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: 2.51 Å3/Da / Density % sol: 50.96 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.25M KSCN, 10% PEG 3350, 5% EtGly, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.52 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Feb 8, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.52 Å / Relative weight: 1
ReflectionRedundancy: 2.7 % / Av σ(I) over netI: 5.2 / Number: 67781 / Rsym value: 0.095 / D res high: 1.8 Å / D res low: 27.52 Å / Num. obs: 24922 / % possible obs: 95.4
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsRsym valueRedundancy
5.6927.5297.610.0840.0842.6
4.025.6998.510.0820.0822.7
3.294.029810.0770.0772.7
2.853.2997.510.0760.0762.7
2.552.8596.710.0770.0772.7
2.322.5596.110.0870.0872.7
2.152.3295.310.1030.1032.7
2.012.1594.410.1310.1312.7
1.92.0193.610.1990.1992.7
1.81.992.410.2650.2652.7
ReflectionResolution: 1.8→27.52 Å / Num. all: 26124 / Num. obs: 24922 / % possible obs: 95.4 % / Redundancy: 2.7 % / Biso Wilson estimate: 14 Å2 / Rmerge(I) obs: 0.095 / Rsym value: 0.095 / Net I/σ(I): 8.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.8-1.92.70.2652.9944635170.26592.4
1.9-2.012.70.1993.7918733770.19993.6
2.01-2.152.70.1315.4862331630.13194.4
2.15-2.322.70.1036.6823530090.10395.3
2.32-2.552.70.0877.4758827780.08796.1
2.55-2.852.70.0778.2694925350.07796.7
2.85-3.292.70.0767.9625722860.07697.5
3.29-4.022.70.0777.3520419070.07798
4.02-5.692.70.0826.7409215070.08298.5
5.69-27.522.60.0844.322008430.08497.6

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 41.38 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å27.52 Å
Translation2.5 Å27.52 Å

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Processing

Software
NameVersionClassificationNB
SCALA3.3.16data scaling
PHASER2.1.4phasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
CrystalCleardata collection
MOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3DWY

3dwy


Resolution: 1.8→27.52 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.905 / WRfactor Rfree: 0.2409 / WRfactor Rwork: 0.1976 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8884 / SU B: 4.164 / SU ML: 0.074 / SU R Cruickshank DPI: 0.1394 / SU Rfree: 0.1304 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.13 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED.
RfactorNum. reflection% reflectionSelection details
Rfree0.2243 1279 5.1 %RANDOM
Rwork0.1874 ---
all0.1893 26210 --
obs0.1893 24905 95.02 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 65.24 Å2 / Biso mean: 12.2571 Å2 / Biso min: 2.49 Å2
Baniso -1Baniso -2Baniso -3
1--0.3 Å20 Å20.01 Å2
2---0.18 Å20 Å2
3---0.48 Å2
Refinement stepCycle: LAST / Resolution: 1.8→27.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1964 0 80 232 2276
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0222127
X-RAY DIFFRACTIONr_bond_other_d0.0010.021487
X-RAY DIFFRACTIONr_angle_refined_deg1.6112.0222892
X-RAY DIFFRACTIONr_angle_other_deg0.9173.0023590
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4675240
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.91224.231104
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.69715371
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.1951515
X-RAY DIFFRACTIONr_chiral_restr0.0890.2291
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0212311
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02414
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.29 84 -
Rwork0.255 1665 -
all-1749 -
obs--91.86 %
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)
15.3464-1.3758-4.64070.88850.87244.2795-0.0658-0.16370.3357-0.1510.215-0.12530.16130.0694-0.14920.094-0.0311-0.01160.07630.02170.221214.031726.0508-5.5626
20.23040.0866-0.01010.10490.00120.4855-0.0013-0.01260.03270.01330.01450.0009-0.0155-0.0042-0.01320.0580.0004-0.01010.03840.0010.075312.649920.702216.8034
30.3479-0.03570.09980.1454-0.3093.6691-0.02570.0027-0.04190.0168-0.0148-0.02930.0450.00460.04050.05540.0052-0.00490.03810.00640.080116.453910.323215.0436
41.35860.31910.25630.3147-0.11850.18320.0787-0.0988-0.0183-0.0287-0.04790.0380.05950.0003-0.03080.07730.0068-0.00510.050.01540.0744-9.83638.668118.0873
50.1560.1561-0.18320.28480.02260.7215-0.03090.0247-0.0318-0.02710.03070.00370.037-0.01210.00020.0547-0.0087-0.00440.0465-0.00160.0702-8.073310.9178-2.3042
60.22970.1048-0.13570.2343-0.19482.82490.0050.0110.04760.00890.027-0.0074-0.0483-0.0358-0.0320.0454-0.0034-0.00380.050.00630.0741-4.978621.37772.0964
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1081 - 1089
2X-RAY DIFFRACTION2A1090 - 1168
3X-RAY DIFFRACTION3A1169 - 1197
4X-RAY DIFFRACTION4B1081 - 1096
5X-RAY DIFFRACTION5B1097 - 1168
6X-RAY DIFFRACTION6B1169 - 1197

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