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- PDB-6dnq: HBZ77 in complex with KIX and c-Myb -

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Basic information

Entry
Database: PDB / ID: 6dnq
TitleHBZ77 in complex with KIX and c-Myb
Components
  • BZIP factor
  • CREB-binding protein
  • Transcriptional activator Myb
KeywordsTRANSCRIPTION / transcription coactivator / transcription factor / viral / eukaryotic / complex
Function / homology
Function and homology information


positive regulation of testosterone secretion / positive regulation of hepatic stellate cell proliferation / Activation of the TFAP2 (AP-2) family of transcription factors / Regulation of FOXO transcriptional activity by acetylation / myeloid cell development / TRAF6 mediated IRF7 activation / Nuclear events mediated by NFE2L2 / Attenuation phase / LRR FLII-interacting protein 1 (LRRFIP1) activates type I IFN production / RUNX1 regulates transcription of genes involved in differentiation of myeloid cells ...positive regulation of testosterone secretion / positive regulation of hepatic stellate cell proliferation / Activation of the TFAP2 (AP-2) family of transcription factors / Regulation of FOXO transcriptional activity by acetylation / myeloid cell development / TRAF6 mediated IRF7 activation / Nuclear events mediated by NFE2L2 / Attenuation phase / LRR FLII-interacting protein 1 (LRRFIP1) activates type I IFN production / 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 / Regulation of gene expression by Hypoxia-inducible Factor / cAMP response element binding protein binding / positive regulation of transforming growth factor beta production / Notch-HLH transcription pathway / Transcriptional and post-translational regulation of MITF-M expression and activity / positive regulation of hepatic stellate cell activation / negative regulation of hematopoietic progenitor cell differentiation / skeletal muscle cell proliferation / 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 / embryonic digestive tract development / peptide lactyltransferase (CoA-dependent) activity / outer kinetochore / myeloid cell differentiation / negative regulation of interferon-beta production / histone H3K18 acetyltransferase activity / N-terminal peptidyl-lysine acetylation / histone H3K27 acetyltransferase activity / MRF binding / cellular response to interleukin-6 / face morphogenesis / T-helper 2 cell differentiation / negative regulation of transcription by RNA polymerase I / protein-lysine-acetyltransferase activity / WD40-repeat domain binding / stem cell division / cellular response to hepatocyte growth factor stimulus / acetyltransferase activity / TFIIB-class transcription factor binding / positive regulation of collagen biosynthetic process / histone acetyltransferase complex / homeostasis of number of cells / positive regulation of glial cell proliferation / viral process / positive regulation of DNA-binding transcription factor activity / histone acetyltransferase activity / negative regulation of megakaryocyte differentiation / positive regulation of double-strand break repair via homologous recombination / histone acetyltransferase / spleen development / cellular response to retinoic acid / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / positive regulation of smooth muscle cell proliferation / thymus development / cellular response to leukemia inhibitory factor / B cell differentiation / response to ischemia / erythrocyte differentiation / RNA polymerase II transcription regulatory region sequence-specific DNA binding / G1/S transition of mitotic cell cycle / PML body / protein destabilization / cellular response to virus / positive regulation of miRNA transcription / RNA polymerase II transcription regulator complex / cellular response to hydrogen peroxide / disordered domain specific binding / cellular response to UV / calcium ion transport / rhythmic process / positive regulation of neuron apoptotic process / regulation of gene expression / DNA-binding transcription activator activity, RNA polymerase II-specific / transcription regulator complex / molecular adaptor activity / DNA-binding transcription factor binding / in utero embryonic development / damaged DNA binding / RNA polymerase II-specific DNA-binding transcription factor binding / transcription coactivator activity / response to hypoxia / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / protein domain specific binding / chromatin binding / positive regulation of gene expression / regulation of DNA-templated transcription / chromatin / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / protein-containing complex / DNA binding
Similarity search - Function
HTLV-1 basic zipper factor / Coactivator CBP, KIX domain / Transcription regulator Wos2-domain / LMSTEN motif / C-myb, C-terminal / C-myb, C-terminal / : / Nuclear receptor coactivator, CREB-bp-like, interlocking / Nuclear receptor coactivator, CREB-bp-like, interlocking domain superfamily / Creb binding ...HTLV-1 basic zipper factor / Coactivator CBP, KIX domain / Transcription regulator Wos2-domain / LMSTEN motif / C-myb, C-terminal / C-myb, C-terminal / : / 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 / Myb-type HTH DNA-binding domain profile. / Serum Albumin; Chain A, Domain 1 / Myb domain / 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. / Myb-like DNA-binding domain / SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains / SANT/Myb domain / Nuclear receptor coactivator, interlocking / Homeobox-like domain superfamily / Bromodomain, conserved site / Bromodomain signature. / Bromodomain / bromo domain / Bromodomain / Bromodomain (BrD) profile. / Bromodomain-like superfamily / Zinc finger, RING/FYVE/PHD-type / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Transcriptional activator Myb / Histone lysine acetyltransferase CREBBP / BZIP factor
Similarity search - Component
Biological speciesHuman T-lymphotropic virus 1
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsYang, K. / Wright, P.E. / Stanfield, R.L.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)CA214054 United States
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2018
Title: Structural basis for cooperative regulation of KIX-mediated transcription pathways by the HTLV-1 HBZ activation domain.
Authors: Yang, K. / Stanfield, R.L. / Martinez-Yamout, M.A. / Dyson, H.J. / Wilson, I.A. / Wright, P.E.
History
DepositionJun 7, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 19, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 3, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed ..._citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Oct 17, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
E: BZIP factor
C: Transcriptional activator Myb
D: CREB-binding protein
A: Transcriptional activator Myb
B: CREB-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,3816
Polymers37,3195
Non-polymers621
Water61334
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6290 Å2
ΔGint-30 kcal/mol
Surface area17890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)118.825, 51.166, 72.047
Angle α, β, γ (deg.)90.00, 126.41, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein BZIP factor


Mass: 8728.772 Da / Num. of mol.: 1 / Fragment: residues 3-77
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human T-lymphotropic virus 1 / Gene: HBZ / Production host: Escherichia coli (E. coli) / References: UniProt: Q2Q067
#2: Protein/peptide Transcriptional activator Myb / Proto-oncogene c-Myb


Mass: 3810.263 Da / Num. of mol.: 2 / Fragment: residues 284-315
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Myb / Production host: Escherichia coli (E. coli) / References: UniProt: P06876
#3: Protein CREB-binding protein


Mass: 10485.053 Da / Num. of mol.: 2 / Fragment: residues 586-672
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Crebbp, Cbp / Production host: Escherichia coli (E. coli) / References: UniProt: P45481, histone acetyltransferase
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


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


Mass: 18.015 Da / Num. of mol.: 34 / 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: 2.36 Å3/Da / Density % sol: 47.92 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: PEG 3350, calcium chloride

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 16, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.35→50 Å / Num. obs: 14320 / % possible obs: 97.1 % / Redundancy: 4.5 % / Biso Wilson estimate: 38 Å2 / CC1/2: 0.87 / Rmerge(I) obs: 0.12 / Rpim(I) all: 0.06 / Rrim(I) all: 0.13 / Net I/σ(I): 13.7
Reflection shellResolution: 2.35→2.39 Å

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Processing

Software
NameVersionClassification
PHENIX(1.10_2155)refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2AGH

2agh


Resolution: 2.35→36.019 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.54
RfactorNum. reflection% reflection
Rfree0.2289 628 4.39 %
Rwork0.1988 --
obs0.2001 14314 96.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.35→36.019 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2243 0 4 34 2281
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0042301
X-RAY DIFFRACTIONf_angle_d0.7213087
X-RAY DIFFRACTIONf_dihedral_angle_d20.0991449
X-RAY DIFFRACTIONf_chiral_restr0.037340
X-RAY DIFFRACTIONf_plane_restr0.006399
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3479-2.58410.28171600.25643338X-RAY DIFFRACTION95
2.5841-2.95790.26551490.23443422X-RAY DIFFRACTION98
2.9579-3.7260.26421500.1983421X-RAY DIFFRACTION97
3.726-36.02320.18761690.17563505X-RAY DIFFRACTION97

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