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- PDB-5mqk: Crystal structure of CREBBP bromodomain complexed with CBP019 -

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Basic information

Entry
Database: PDB / ID: 5mqk
TitleCrystal structure of CREBBP bromodomain complexed with CBP019
ComponentsCREB-binding protein
KeywordsTRANSCRIPTION / CREBBP bromodomain / Inhibitor
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 / Regulation of FOXO transcriptional activity by acetylation / RUNX3 regulates NOTCH signaling / Regulation of gene expression by Hypoxia-inducible Factor / Nuclear events mediated by NFE2L2 / NOTCH4 Intracellular Domain Regulates Transcription / 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 / Transcriptional and post-translational regulation of MITF-M expression and activity / Notch-HLH transcription pathway / positive regulation of transforming growth factor beta receptor signaling pathway / Formation of paraxial mesoderm / stimulatory C-type lectin receptor signaling pathway / Zygotic genome activation (ZGA) / 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 / cellular response to nutrient levels / regulation of cellular response to heat / canonical NF-kappaB signal transduction / 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 / Cytoprotection by HMOX1 / Evasion by RSV of host interferon responses / NOTCH1 Intracellular Domain Regulates Transcription / chromatin DNA binding / transcription coactivator binding / Constitutive Signaling by NOTCH1 PEST Domain Mutants / Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants / Pre-NOTCH Transcription and Translation / Transcriptional regulation of white adipocyte differentiation / positive regulation of protein localization to nucleus / Activation of anterior HOX genes in hindbrain development during early embryogenesis / transcription corepressor activity / cellular response to UV / Circadian Clock / p53 binding / rhythmic process / 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 / response to hypoxia / nuclear body / chromatin binding / chromatin / regulation of DNA-templated transcription / 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
1-(1-methylindol-3-yl)ethanone / CREB-binding protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.53 Å
AuthorsZhu, J. / Spiliotopoulos, D. / Caflisch, A.
CitationJournal: Bioorg. Med. Chem. Lett. / Year: 2017
Title: Virtual screen to NMR (VS2NMR): Discovery of fragment hits for the CBP bromodomain.
Authors: Spiliotopoulos, D. / Zhu, J. / Wamhoff, E.C. / Deerain, N. / Marchand, J.R. / Aretz, J. / Rademacher, C. / Caflisch, A.
History
DepositionDec 20, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 19, 2017Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2017Group: Database references
Revision 1.2May 10, 2017Group: Structure summary
Revision 1.3May 17, 2017Group: Database references
Revision 1.4Oct 16, 2019Group: Data collection / Category: reflns_shell
Revision 1.5May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)28,7934
Polymers28,4472
Non-polymers3462
Water3,801211
1
A: CREB-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,3972
Polymers14,2231
Non-polymers1731
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: CREB-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,3972
Polymers14,2231
Non-polymers1731
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)122.356, 122.356, 40.368
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

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Components

#1: Protein CREB-binding protein


Mass: 14223.349 Da / Num. of mol.: 2 / Fragment: bromodomain, UNP residues 1081-1197
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CREBBP, CBP / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q92793, histone acetyltransferase
#2: Chemical ChemComp-QPR / 1-(1-methylindol-3-yl)ethanone


Mass: 173.211 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H11NO
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 211 / 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: 2.04 Å3/Da / Density % sol: 39.83 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / Details: 0.15 M KSCN, 20% PEG3350, 10% EG

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.99998 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 26, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99998 Å / Relative weight: 1
ReflectionResolution: 1.53→37.72 Å / Num. obs: 33860 / % possible obs: 99.6 % / Redundancy: 5.1 % / Rmerge(I) obs: 0.041 / Net I/σ(I): 16.5

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.53→37.72 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.98 / Phase error: 24.68
RfactorNum. reflection% reflection
Rfree0.2102 2007 5.93 %
Rwork0.1839 --
obs0.1854 33854 99.59 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.53→37.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1922 0 26 211 2159
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072063
X-RAY DIFFRACTIONf_angle_d0.9152816
X-RAY DIFFRACTIONf_dihedral_angle_d8.9081737
X-RAY DIFFRACTIONf_chiral_restr0.053290
X-RAY DIFFRACTIONf_plane_restr0.007368
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.53-1.56830.27491410.27822258X-RAY DIFFRACTION100
1.5683-1.61070.31451450.26232330X-RAY DIFFRACTION100
1.6107-1.65810.31281430.25682221X-RAY DIFFRACTION99
1.6581-1.71160.30871430.25432295X-RAY DIFFRACTION99
1.7116-1.77280.31641430.23992275X-RAY DIFFRACTION100
1.7728-1.84380.24961450.22632315X-RAY DIFFRACTION100
1.8438-1.92770.24661410.22092260X-RAY DIFFRACTION100
1.9277-2.02930.29221450.21882275X-RAY DIFFRACTION100
2.0293-2.15650.25021440.20952285X-RAY DIFFRACTION100
2.1565-2.32290.20751420.20842259X-RAY DIFFRACTION99
2.3229-2.55670.23171420.19672269X-RAY DIFFRACTION100
2.5567-2.92650.20821470.18792281X-RAY DIFFRACTION100
2.9265-3.68660.18041430.16682268X-RAY DIFFRACTION99
3.6866-37.73470.1641430.1412256X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 5.446 Å / Origin y: -20.0062 Å / Origin z: 4.0986 Å
111213212223313233
T0.2083 Å2-0.0572 Å20.0088 Å2-0.3196 Å20.0045 Å2--0.2501 Å2
L1.5055 °21.2696 °20.2429 °2-0.697 °20.2185 °2---0.4123 °2
S0.0268 Å °-0.1005 Å °-0.1199 Å °0.0095 Å °-0.0179 Å °-0.0703 Å °-0.0463 Å °0.1162 Å °-0.0032 Å °
Refinement TLS groupSelection details: all

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