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- PDB-8e1d: NMR-derived ensemble of the TAZ2 domain of p300 bound to the micr... -

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Basic information

Entry
Database: PDB / ID: 8e1d
TitleNMR-derived ensemble of the TAZ2 domain of p300 bound to the microphthalmia-associated transcription factor
Components
  • Histone acetyltransferase p300
  • Microphthalmia-associated transcription factor
KeywordsTRANSCRIPTION/TRANSFERASE / TAZ2 / MITF / METAL BINDING PROTEIN / TRANSCRIPTION-TRANSFERASE complex
Function / homology
Function and homology information


melanocyte apoptotic process / positive regulation of DNA-templated transcription initiation / behavioral defense response / protein propionyltransferase activity / peptidyl-lysine propionylation / histone lactyltransferase activity / peptidyl-lysine crotonylation / peptidyl-lysine butyrylation / histone butyryltransferase activity / histone H3K122 acetyltransferase activity ...melanocyte apoptotic process / positive regulation of DNA-templated transcription initiation / behavioral defense response / protein propionyltransferase activity / peptidyl-lysine propionylation / histone lactyltransferase activity / peptidyl-lysine crotonylation / peptidyl-lysine butyrylation / histone butyryltransferase activity / histone H3K122 acetyltransferase activity / swimming / peptide butyryltransferase activity / histone H2B acetyltransferase activity / thigmotaxis / regulation of RNA biosynthetic process / peptide 2-hydroxyisobutyryltransferase activity / histone crotonyltransferase activity / NOTCH2 intracellular domain regulates transcription / lysine N-acetyltransferase activity, acting on acetyl phosphate as donor / peptidyl-lysine acetylation / regulation of osteoclast differentiation / histone H4 acetyltransferase activity / melanocyte differentiation / histone H3 acetyltransferase activity / cellular response to L-leucine / bone remodeling / internal peptidyl-lysine acetylation / NFE2L2 regulating ER-stress associated genes / peptide N-acetyltransferase activity / STAT3 nuclear events downstream of ALK signaling / acetylation-dependent protein binding / Activation of the TFAP2 (AP-2) family of transcription factors / NFE2L2 regulating inflammation associated genes / NGF-stimulated transcription / camera-type eye development / Polo-like kinase mediated events / 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 / regulation of androgen receptor signaling pathway / NFE2L2 regulating MDR associated enzymes / positive regulation by host of viral transcription / regulation of mitochondrion organization / face morphogenesis / Regulation of gene expression in late stage (branching morphogenesis) pancreatic bud precursor cells / RUNX3 regulates NOTCH signaling / NOTCH4 Intracellular Domain Regulates Transcription / Regulation of FOXO transcriptional activity by acetylation / Regulation of gene expression by Hypoxia-inducible Factor / Nuclear events mediated by NFE2L2 / Regulation of NFE2L2 gene expression / NOTCH3 Intracellular Domain Regulates Transcription / regulation of glycolytic process / platelet formation / NFE2L2 regulating anti-oxidant/detoxification enzymes / nuclear androgen receptor binding / megakaryocyte development / TRAF6 mediated IRF7 activation / regulation of tubulin deacetylation / macrophage derived foam cell differentiation / peptide-lysine-N-acetyltransferase activity / FOXO-mediated transcription of cell death genes / NFE2L2 regulating tumorigenic genes / internal protein amino acid acetylation / STAT family protein binding / acyltransferase activity / fat cell differentiation / protein acetylation / Formation of paraxial mesoderm / RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known / E-box binding / positive regulation of transforming growth factor beta receptor signaling pathway / PI5P Regulates TP53 Acetylation / Zygotic genome activation (ZGA) / stimulatory C-type lectin receptor signaling pathway / acetyltransferase activity / cellular response to nutrient levels / RUNX3 regulates p14-ARF / SUMOylation of transcription factors / NF-kappaB binding / histone acetyltransferase complex / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / canonical NF-kappaB signal transduction / Attenuation phase / cell fate commitment / negative regulation of protein-containing complex assembly / negative regulation of gluconeogenesis / somitogenesis / pre-mRNA intronic binding / regulation of cellular response to heat / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / skeletal muscle tissue development / histone acetyltransferase activity / histone acetyltransferase / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / transcription initiation-coupled chromatin remodeling / Regulation of TP53 Activity through Acetylation
Similarity search - Function
MiT/TFE transcription factors, C-terminal / MiT/TFE transcription factors, N-terminal / Domain of unknown function (DUF3371) / MITF/TFEB/TFEC/TFE3 N-terminus / Helix-loop-helix DNA-binding 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 ...MiT/TFE transcription factors, C-terminal / MiT/TFE transcription factors, N-terminal / Domain of unknown function (DUF3371) / MITF/TFEB/TFEC/TFE3 N-terminus / Helix-loop-helix DNA-binding 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. / Coactivator CBP, KIX domain superfamily / Histone acetyltransferase Rtt109/CBP / Histone acetylation protein / Histone acetylation protein / 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. / Helix-loop-helix DNA-binding domain superfamily / helix loop helix domain / Myc-type, basic helix-loop-helix (bHLH) domain / Myc-type, basic helix-loop-helix (bHLH) domain 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
Similarity search - Domain/homology
Microphthalmia-associated transcription factor / Histone acetyltransferase p300
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsLangelaan, D.N. / Branch, M.
Funding support Canada, 1items
OrganizationGrant numberCountry
Other private Canada
CitationJournal: Biochim Biophys Acta Mol Cell Res / Year: 2023
Title: Structural basis of CBP/p300 recruitment by the microphthalmia-associated transcription factor.
Authors: Brown, A.D. / Vergunst, K.L. / Branch, M. / Blair, C.M. / Dupre, D.J. / Baillie, G.S. / Langelaan, D.N.
History
DepositionAug 10, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 21, 2023Provider: repository / Type: Initial release
Revision 1.1Jul 12, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._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 / _citation_author.name
Revision 1.2May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: Microphthalmia-associated transcription factor
A: Histone acetyltransferase p300
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,0245
Polymers13,8282
Non-polymers1963
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: NMR Distance Restraints, We observe intermolecular NOE contacts between the protein chains, homology, TAZ2 binds many different activation domains in a 1:1 manner, isothermal titration ...Evidence: NMR Distance Restraints, We observe intermolecular NOE contacts between the protein chains, homology, TAZ2 binds many different activation domains in a 1:1 manner, isothermal titration calorimetry, We observe 1:1 binding via ITC
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area1170 Å2
ΔGint-2 kcal/mol
Surface area9080 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide Microphthalmia-associated transcription factor / / Class E basic helix-loop-helix protein 32 / bHLHe32


Mass: 3720.123 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MITF, BHLHE32 / Production host: Escherichia coli (E. coli) / References: UniProt: O75030
#2: Protein Histone acetyltransferase p300 / p300 HAT / E1A-associated protein p300 / Histone butyryltransferase p300 / Histone ...p300 HAT / E1A-associated protein p300 / Histone butyryltransferase p300 / Histone crotonyltransferase p300 / Protein 2-hydroxyisobutyryltransferase p300 / Protein lactyltransferas p300 / Protein propionyltransferase p300


Mass: 10107.916 Da / Num. of mol.: 1 / Mutation: C1738A C1746A C1789A C1790A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EP300, P300 / Production host: Escherichia coli (E. coli)
References: UniProt: Q09472, histone acetyltransferase, Transferases; Acyltransferases; Transferring groups other than aminoacyl groups
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
Has ligand of interestN

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-15N HSQC
121isotropic12D 1H-13C HSQC
141isotropic13D HNCO
1111isotropic13D HCACO
1101isotropic13D HN(CA)CB
191isotropic13D CBCA(CO)NH
181isotropic13D C(CO)NH
171isotropic13D H(CCO)NH
161isotropic13D (H)CCH-COSY
151isotropic13D (H)CCH-TOCSY
131isotropic13D HBHA(CO)NH
1161isotropic13D 1H-13C NOESY aliphatic
1151isotropic13D 1H-15N NOESY
1142isotropic12D 1H-13C HSQC
1132isotropic12D 1H-15N HSQC
1122isotropic13D HNCO
1262isotropic13D HCACO
1252isotropic13D HN(CA)CB
1242isotropic13D CBCA(CO)NH
1232isotropic13D C(CO)NH
1222isotropic13D H(CCO)NH
1212isotropic13D (H)CCH-COSY
1202isotropic13D (H)CCH-TOCSY
1192isotropic13D HBHA(CO)NH
1182isotropic13D 1H-13C NOESY aliphatic
1172isotropic13D 1H-13C NOESY aromatic
1292isotropic13D 1H-15N NOESY

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution120 mM 2-(N-morpholino)ethanesulfonic acid (MES), 5 mM beta mercaptoethanol, 10 uM Zinc chloride, 1 mM [U-13C; U-15N] Microphthalmia-associated transcription factor, 1.2 mM TAZ2 domain of p300, 95% H2O/5% D2OMITF-labelled complex95% H2O/5% D2O
solution220 mM 2-(N-morpholino)ethanesulfonic acid (MES), 5 mM beta mercaptoethanol, 10 mM Zinc chloride, 1.15 mM Microphthalmia-associated transcription factor, 0.95 mM [U-13C; U-15N] TAZ2 domain of p300, 95% H2O/5% D2OTaz2-labelled complex95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
20 mM2-(N-morpholino)ethanesulfonic acid (MES)natural abundance1
5 mMbeta mercaptoethanolnatural abundance1
10 uMZinc chloridenatural abundance1
1 mMMicrophthalmia-associated transcription factor[U-13C; U-15N]1
1.2 mMTAZ2 domain of p300natural abundance1
20 mM2-(N-morpholino)ethanesulfonic acid (MES)natural abundance2
5 mMbeta mercaptoethanolnatural abundance2
10 mMZinc chloridenatural abundance2
1.15 mMMicrophthalmia-associated transcription factornatural abundance2
0.95 mMTAZ2 domain of p300[U-13C; U-15N]2
Sample conditionsIonic strength: 20 mM / Label: condition 1 / pH: 6.0 / Pressure: 1 atm / Temperature: 308 K

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NMR measurement

NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 600 MHz

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Processing

NMR software
NameDeveloperClassification
VnmrJVariancollection
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
CcpNmr AnalysisCCPNchemical shift assignment
ARIALinge, O'Donoghue and Nilgesrefinement
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
ARIALinge, O'Donoghue and Nilgesstructure calculation
RefinementMethod: simulated annealing / Software ordinal: 4
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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