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- PDB-6sqc: Crystal structure of complex between nuclear coactivator binding ... -

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Entry
Database: PDB / ID: 6sqc
TitleCrystal structure of complex between nuclear coactivator binding domain of CBP and [1040-1086]ACTR containing alpha-methylated Leu1055 and Leu1076
Components
  • Maltose/maltodextrin-binding periplasmic protein,CREB-binding protein
  • Nuclear receptor coactivator 3
KeywordsPROTEIN BINDING / complex / unnatural amino acid
Function / homology
Function and homology information


: / cell dedifferentiation / regulation of stem cell division / peptide lactyltransferase (CoA-dependent) activity / NFE2L2 regulating ER-stress associated genes / protein N-acetyltransferase activity / Activation of the TFAP2 (AP-2) family of transcription factors / NFE2L2 regulating inflammation associated genes / positive regulation of keratinocyte differentiation / N-terminal peptidyl-lysine acetylation ...: / cell dedifferentiation / regulation of stem cell division / peptide lactyltransferase (CoA-dependent) activity / NFE2L2 regulating ER-stress associated genes / protein N-acetyltransferase activity / Activation of the TFAP2 (AP-2) family of transcription factors / NFE2L2 regulating inflammation associated genes / positive regulation of keratinocyte differentiation / N-terminal peptidyl-lysine acetylation / regulation of smoothened signaling pathway / LRR FLII-interacting protein 1 (LRRFIP1) activates type I IFN production / NFE2L2 regulates pentose phosphate pathway genes / NFE2L2 regulating MDR associated enzymes / MRF binding / RUNX1 regulates transcription of genes involved in differentiation of myeloid cells / vitamin D receptor signaling pathway / Regulation of FOXO transcriptional activity by acetylation / Regulation of gene expression in late stage (branching morphogenesis) pancreatic bud precursor cells / RUNX3 regulates NOTCH signaling / nuclear thyroid hormone receptor binding / Nuclear events mediated by NFE2L2 / NOTCH4 Intracellular Domain Regulates Transcription / 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 / protein-lysine-acetyltransferase activity / embryonic digit morphogenesis / protein acetylation / homeostatic process / Notch-HLH transcription pathway / Formation of paraxial mesoderm / detection of maltose stimulus / positive regulation of transforming growth factor beta receptor signaling pathway / histone acetyltransferase activity / acetyltransferase activity / FOXO-mediated transcription of cell death genes / maltose transport complex / stimulatory C-type lectin receptor signaling pathway / positive regulation of stem cell population maintenance / Zygotic genome activation (ZGA) / TP53 Regulates Transcription of Genes Involved in Cytochrome C Release / RNA polymerase II complex binding / carbohydrate transport / histone acetyltransferase complex / canonical NF-kappaB signal transduction / carbohydrate transmembrane transporter activity / maltose binding / maltose transport / maltodextrin transmembrane transport / cellular response to nutrient levels / Attenuation phase / positive regulation of double-strand break repair via homologous recombination / retinoic acid receptor signaling pathway / cellular response to hormone stimulus / 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 / regulation of cellular response to heat / histone acetyltransferase / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / : / Regulation of lipid metabolism by PPARalpha / NPAS4 regulates expression of target genes / 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 / ATP-binding cassette (ABC) transporter complex / SUMOylation of transcription cofactors / Activation of gene expression by SREBF (SREBP) / nuclear receptor binding / cell chemotaxis / cellular response to estradiol stimulus / Formation of the beta-catenin:TCF transactivating complex / Heme signaling / Transcriptional activation of mitochondrial biogenesis / transcription coactivator binding / PPARA activates gene expression / MAPK6/MAPK4 signaling / protein destabilization / Cytoprotection by HMOX1
Similarity search - Function
: / Creb-binding Protein; Chain: A / Nuclear receptor coactivator, CREB-bp-like, interlocking 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. ...: / Creb-binding Protein; Chain: A / Nuclear receptor coactivator, CREB-bp-like, interlocking 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. / Nuclear receptor coactivator 2/3, DUF4927 / Domain of unknown function (DUF4927) / Zinc finger, ZZ type / Zinc finger, ZZ-type / Zinc finger, ZZ-type superfamily / Zinc finger ZZ-type profile. / Nuclear receptor coactivator, DUF1518 / Nuclear receptor coactivator, Ncoa-type, interlocking / Nuclear receptor coactivator, Ncoa-type, interlocking domain superfamily / Nuclear receptor coactivator, DUF1518 / Nuclear receptor coactivator / DUF1518 / Nuclear receptor coactivator, receptor-binding domain / Nuclear receptor coactivator / : / Steroid receptor coactivator / Unstructured region on nuclear receptor coactivator protein / Nuclear receptor coactivators bHLH domain / Maltose/Cyclodextrin ABC transporter, substrate-binding protein / Solute-binding family 1, conserved site / Bacterial extracellular solute-binding proteins, family 1 signature. / PAS domain / Nuclear receptor coactivator, interlocking / Bacterial extracellular solute-binding protein / helix loop helix domain / Myc-type, basic helix-loop-helix (bHLH) domain / Myc-type, basic helix-loop-helix (bHLH) domain profile. / Helix-loop-helix DNA-binding domain superfamily / PAS fold / PAS fold / Bacterial extracellular solute-binding protein / PAS domain / PAS repeat profile. / PAS domain / PAS domain superfamily / 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
alpha-maltose / Maltose/maltodextrin-binding periplasmic protein / CREB-binding protein / Nuclear receptor coactivator 3
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.28 Å
AuthorsBauer, V. / Schmidtgall, B. / Gogl, G. / Dolenc, j. / Osz, J. / Kostmann, C. / Mitschler, A. / Cousido-Siah, A. / Rochel, N. / Trave, G. ...Bauer, V. / Schmidtgall, B. / Gogl, G. / Dolenc, j. / Osz, J. / Kostmann, C. / Mitschler, A. / Cousido-Siah, A. / Rochel, N. / Trave, G. / Kieffer, B. / Torbeev, V.
Funding support France, 3items
OrganizationGrant numberCountry
European Research Council (ERC)715062-HiChemSynPro France
Laboratories of Excellence (LabEx)ANR-10-LABX-0026_CSC France
ATIP-Avenir France
CitationJournal: Chem Sci / Year: 2020
Title: Conformational editing of intrinsically disordered protein by alpha-methylation.
Authors: Bauer, V. / Schmidtgall, B. / Gogl, G. / Dolenc, J. / Osz, J. / Nomine, Y. / Kostmann, C. / Cousido-Siah, A. / Mitschler, A. / Rochel, N. / Trave, G. / Kieffer, B. / Torbeev, V.
History
DepositionSep 3, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 30, 2020Provider: repository / Type: Initial release
Revision 1.1Apr 20, 2022Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Dec 14, 2022Group: Author supporting evidence / Category: pdbx_audit_support
Revision 1.3Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.4Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Maltose/maltodextrin-binding periplasmic protein,CREB-binding protein
B: Nuclear receptor coactivator 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,9576
Polymers51,4222
Non-polymers5354
Water2,810156
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3110 Å2
ΔGint-78 kcal/mol
Surface area20570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.180, 42.460, 113.790
Angle α, β, γ (deg.)90.000, 101.125, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

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Protein / Protein/peptide / Sugars , 3 types, 3 molecules AB

#1: Protein Maltose/maltodextrin-binding periplasmic protein,CREB-binding protein / MMBP / Maltodextrin-binding protein / Maltose-binding protein / MBP


Mass: 46290.527 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria), (gene. exp.) Homo sapiens (human)
Strain: K12 / Gene: malE, b4034, JW3994, CREBBP, CBP / Production host: Escherichia coli (E. coli)
References: UniProt: P0AEX9, UniProt: Q92793, histone acetyltransferase
#2: Protein/peptide Nuclear receptor coactivator 3 / NCoA-3 / ACTR / Amplified in breast cancer 1 protein / AIB-1 / CBP-interacting protein / pCIP / ...NCoA-3 / ACTR / Amplified in breast cancer 1 protein / AIB-1 / CBP-interacting protein / pCIP / Class E basic helix-loop-helix protein 42 / bHLHe42 / Receptor-associated coactivator 3 / RAC-3 / Steroid receptor coactivator protein 3 / SRC-3 / Thyroid hormone receptor activator molecule 1 / TRAM-1


Mass: 5131.617 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q9Y6Q9, histone acetyltransferase
#3: Polysaccharide alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose / alpha-maltose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: alpha-maltose
DescriptorTypeProgram
DGlcpa1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1a_1-5]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][a-D-Glcp]{}}LINUCSPDB-CARE

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Non-polymers , 3 types, 159 molecules

#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 156 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
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: 2.39 Å3/Da / Density % sol: 48.63 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / Details: 20% PEG6000, 100 mM Tris pH 8 and 10 mM ZnCl2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1.00003 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Apr 4, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00003 Å / Relative weight: 1
ReflectionResolution: 2.28→41.72 Å / Num. obs: 21924 / % possible obs: 97.23 % / Redundancy: 3.4 % / Biso Wilson estimate: 33.76 Å2 / CC1/2: 0.995 / Net I/σ(I): 9.58
Reflection shellResolution: 2.28→2.362 Å / Mean I/σ(I) obs: 1.94 / Num. unique obs: 2175 / CC1/2: 0.745

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5H7Q

5h7q


Resolution: 2.28→41.72 Å / SU ML: 0.3392 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 31.9254
RfactorNum. reflection% reflection
Rfree0.2741 1100 5.03 %
Rwork0.2277 --
obs0.23 21875 97.25 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 50.72 Å2
Refinement stepCycle: LAST / Resolution: 2.28→41.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3589 0 6 156 3751
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00563677
X-RAY DIFFRACTIONf_angle_d0.64784989
X-RAY DIFFRACTIONf_chiral_restr0.0411561
X-RAY DIFFRACTIONf_plane_restr0.0033645
X-RAY DIFFRACTIONf_dihedral_angle_d17.89581343
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.28-2.380.34641310.29432586X-RAY DIFFRACTION97.49
2.38-2.510.30791390.27882604X-RAY DIFFRACTION98.21
2.51-2.670.40961400.29782546X-RAY DIFFRACTION96.51
2.67-2.870.36731280.28672533X-RAY DIFFRACTION96.48
2.87-3.160.2931380.2572640X-RAY DIFFRACTION99.29
3.16-3.620.29121430.23952550X-RAY DIFFRACTION95.8
3.62-4.560.26721430.19882562X-RAY DIFFRACTION95.45
4.56-41.720.16861380.17142754X-RAY DIFFRACTION98.8

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