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- PDB-6gyr: Transcription factor dimerization activates the p300 acetyltransferase -

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Basic information

Entry
Database: PDB / ID: 6gyr
TitleTranscription factor dimerization activates the p300 acetyltransferase
ComponentsHistone acetyltransferase p300
KeywordsGENE REGULATION / P300 / CBP / acetyltransferase / Chromatin / transcriptional regulation
Function / homology
Function and homology information


behavioral defense response / peptidyl-lysine propionylation / peptidyl-lysine crotonylation / peptidyl-lysine butyrylation / histone butyryltransferase activity / swimming / peptide butyryltransferase activity / histone H2B acetyltransferase activity / thigmotaxis / internal protein amino acid acetylation ...behavioral defense response / peptidyl-lysine propionylation / peptidyl-lysine crotonylation / peptidyl-lysine butyrylation / histone butyryltransferase activity / swimming / peptide butyryltransferase activity / histone H2B acetyltransferase activity / thigmotaxis / internal protein amino acid acetylation / peptide 2-hydroxyisobutyryltransferase activity / histone crotonyltransferase activity / protein propionyltransferase activity / histone H4K16 propionyltransferase activity / NOTCH2 intracellular domain regulates transcription / peptidyl-lysine acetylation / positive regulation of TORC2 signaling / L-lysine N-acetyltransferase activity, acting on acetyl phosphate as donor / internal peptidyl-lysine acetylation / histone H4 acetyltransferase activity / cellular response to L-leucine / histone H3 acetyltransferase 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 / acetylation-dependent protein binding / NGF-stimulated transcription / histone lactyltransferase (CoA-dependent) activity / N-terminal peptidyl-lysine acetylation / LRR FLII-interacting protein 1 (LRRFIP1) activates type I IFN production / NFE2L2 regulates pentose phosphate pathway genes / STAT3 nuclear events downstream of ALK signaling / Polo-like kinase mediated events / NFE2L2 regulating MDR associated enzymes / TGFBR3 expression / positive regulation by host of viral transcription / regulation of androgen receptor signaling pathway / regulation of mitochondrion organization / 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 events mediated by NFE2L2 / NOTCH4 Intracellular Domain Regulates Transcription / face morphogenesis / Regulation of NFE2L2 gene expression / Regulation of gene expression by Hypoxia-inducible Factor / regulation of glycolytic process / platelet formation / NOTCH3 Intracellular Domain Regulates Transcription / TRAF6 mediated IRF7 activation / NFE2L2 regulating tumorigenic genes / megakaryocyte development / NFE2L2 regulating anti-oxidant/detoxification enzymes / regulation of tubulin deacetylation / protein-lysine-acetyltransferase activity / STAT family protein binding / nuclear androgen receptor binding / acyltransferase activity / protein acetylation / histone acetyltransferase activity / positive regulation of transforming growth factor beta receptor signaling pathway / Formation of paraxial mesoderm / PI5P Regulates TP53 Acetylation / fat cell differentiation / acetyltransferase activity / FOXO-mediated transcription of cell death genes / RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known / stimulatory C-type lectin receptor signaling pathway / Zygotic genome activation (ZGA) / RUNX3 regulates p14-ARF / histone acetyltransferase complex / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / canonical NF-kappaB signal transduction / NF-kappaB binding / negative regulation of gluconeogenesis / negative regulation of protein-containing complex assembly / cellular response to nutrient levels / somitogenesis / pre-mRNA intronic binding / Attenuation phase / positive regulation of T-helper 17 cell lineage commitment / 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 / regulation of cellular response to heat / histone H3K18 acetyltransferase activity / histone H3K9 acetyltransferase activity / histone H3K14 acetyltransferase activity / histone H4K5 acetyltransferase activity / histone H4K8 acetyltransferase activity / histone H4K12 acetyltransferase activity
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, conserved site / Bromodomain signature. / Bromodomain / Bromodomain profile. / bromo domain / Bromodomain / Bromodomain-like superfamily / Zinc finger, RING/FYVE/PHD-type
Similarity search - Domain/homology
Chem-01K / Histone acetyltransferase p300
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsPanne, D. / Ortega, E.
CitationJournal: Nature / Year: 2018
Title: Transcription factor dimerization activates the p300 acetyltransferase.
Authors: Ortega, E. / Rengachari, S. / Ibrahim, Z. / Hoghoughi, N. / Gaucher, J. / Holehouse, A.S. / Khochbin, S. / Panne, D.
History
DepositionJul 1, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 17, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 24, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_ASTM ..._citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Nov 14, 2018Group: Author supporting evidence / Data collection / Database references
Category: citation / citation_author / pdbx_audit_support
Item: _citation.journal_abbrev / _citation.journal_id_ASTM ..._citation.journal_abbrev / _citation.journal_id_ASTM / _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
Revision 1.3Jan 17, 2024Group: 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_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Histone acetyltransferase p300
B: Histone acetyltransferase p300
C: Histone acetyltransferase p300
D: Histone acetyltransferase p300
hetero molecules


Theoretical massNumber of molelcules
Total (without water)279,50422
Polymers274,6094
Non-polymers4,89518
Water00
1
A: Histone acetyltransferase p300
hetero molecules

C: Histone acetyltransferase p300
hetero molecules


Theoretical massNumber of molelcules
Total (without water)139,75211
Polymers137,3042
Non-polymers2,4479
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_655x+1,y,z1
Buried area1120 Å2
ΔGint-158 kcal/mol
Surface area61680 Å2
MethodPISA
2
B: Histone acetyltransferase p300
D: Histone acetyltransferase p300
hetero molecules


Theoretical massNumber of molelcules
Total (without water)139,75211
Polymers137,3042
Non-polymers2,4479
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1260 Å2
ΔGint-36 kcal/mol
Surface area61110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.826, 146.717, 116.477
Angle α, β, γ (deg.)90.00, 91.75, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: 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 propionyltransferase p300


Mass: 68652.242 Da / Num. of mol.: 4 / Mutation: Y1467F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EP300, P300 / Production host: Trichoplusia (butterflies/moths)
References: UniProt: Q09472, histone acetyltransferase, Transferases; Acyltransferases; Transferring groups other than aminoacyl groups
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-01K / [(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-4-hydroxy-3-(phosphonooxy)tetrahydrofuran-2-yl]methyl (3R,20R)-20-carbamoyl-3-hydroxy-2,2-dimethyl-4,8,14,22-tetraoxo-12-thia-5,9,15,21-tetraazatricos-1-yl dihydrogen diphosphate / Lysine-COENZYME A derivative


Mass: 994.794 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C31H53N10O19P3S

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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: 3.14 Å3/Da / Density % sol: 60.78 %
Crystal growTemperature: 277 K / Method: vapor diffusion
Details: 100 mM HEPES, pH 7.5, 18-22% polyethylene glycol 3350, 0.2 M NaCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.282 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Nov 17, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.282 Å / Relative weight: 1
ReflectionResolution: 3.1→50 Å / Num. obs: 106462 / % possible obs: 99 % / Redundancy: 1.9 % / Net I/σ(I): 7.48
Reflection shellResolution: 3.1→3.25 Å

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4BHW

4bhw


Resolution: 3.1→50 Å / SU ML: 0.46 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.11
RfactorNum. reflection% reflection
Rfree0.2646 2967 4.79 %
Rwork0.2087 --
obs0.2113 61949 99.03 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.1→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19100 0 270 0 19370
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00819866
X-RAY DIFFRACTIONf_angle_d1.24226882
X-RAY DIFFRACTIONf_dihedral_angle_d14.03112121
X-RAY DIFFRACTIONf_chiral_restr0.0762809
X-RAY DIFFRACTIONf_plane_restr0.0063489
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.0825-3.1330.3771510.31622807X-RAY DIFFRACTION99
3.133-3.18710.35561460.30712789X-RAY DIFFRACTION99
3.1871-3.2450.41251670.28552806X-RAY DIFFRACTION99
3.245-3.30740.36651330.28162762X-RAY DIFFRACTION99
3.3074-3.37490.33091300.26362787X-RAY DIFFRACTION98
3.3749-3.44830.28581050.23822859X-RAY DIFFRACTION99
3.4483-3.52850.31931560.23492783X-RAY DIFFRACTION100
3.5285-3.61680.30131600.242802X-RAY DIFFRACTION100
3.6168-3.71460.28351530.22392805X-RAY DIFFRACTION99
3.7146-3.82390.2691180.20732810X-RAY DIFFRACTION99
3.8239-3.94730.31021210.20092819X-RAY DIFFRACTION99
3.9473-4.08840.28841390.20172809X-RAY DIFFRACTION99
4.0884-4.2520.25111230.19542808X-RAY DIFFRACTION98
4.252-4.44550.24271490.18612773X-RAY DIFFRACTION98
4.4455-4.67990.21551490.18122800X-RAY DIFFRACTION99
4.6799-4.9730.23751530.18852777X-RAY DIFFRACTION99
4.973-5.35690.24471490.19912849X-RAY DIFFRACTION99
5.3569-5.89580.23791350.19582809X-RAY DIFFRACTION99
5.8958-6.74850.29261430.21562825X-RAY DIFFRACTION99
6.7485-8.50050.24391470.20182837X-RAY DIFFRACTION99
8.5005-75.09620.19671400.17862866X-RAY DIFFRACTION98

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