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- PDB-3p57: Crystal structure of the p300 TAZ2 domain bound to MEF2 on DNA -

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Basic information

Entry
Database: PDB / ID: 3p57
TitleCrystal structure of the p300 TAZ2 domain bound to MEF2 on DNA
Components
  • DNA (5'-D(*A*AP*AP*CP*TP*AP*TP*TP*TP*AP*TP*AP*AP*GP*A)-3')
  • DNA (5'-D(*TP*TP*CP*TP*TP*AP*TP*AP*AP*AP*TP*AP*GP*TP*T)-3')
  • Histone acetyltransferase p300
  • Myocyte-specific enhancer factor 2A
KeywordsTRANSFERASE/TRANSCRIPTION ACTIVATOR/DNA / protein-DNA complex / transcription factor / transcriptional activation / p300 / zinc finger / TRANSFERASE-TRANSCRIPTION ACTIVATOR-DNA complex
Function / homology
Function and homology information


ERK5 cascade / ventricular cardiac myofibril assembly / mitochondrion distribution / behavioral defense response / protein propionyltransferase activity / peptidyl-lysine propionylation / histone lactyltransferase activity / peptidyl-lysine crotonylation / peptidyl-lysine butyrylation / histone butyryltransferase activity ...ERK5 cascade / ventricular cardiac myofibril assembly / mitochondrion distribution / 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 / 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 / histone H3 acetyltransferase activity / histone H4 acetyltransferase activity / cardiac conduction / mitochondrial genome maintenance / cellular response to L-leucine / internal peptidyl-lysine acetylation / NFE2L2 regulating ER-stress associated genes / peptide N-acetyltransferase activity / acetylation-dependent protein binding / STAT3 nuclear events downstream of ALK signaling / Activation of the TFAP2 (AP-2) family of transcription factors / NFE2L2 regulating inflammation associated genes / NGF-stimulated transcription / histone H3K27 acetyltransferase activity / histone H3K18 acetyltransferase activity / Polo-like kinase mediated events / N-terminal peptidyl-lysine acetylation / LRR FLII-interacting protein 1 (LRRFIP1) activates type I IFN production / 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 / dendrite morphogenesis / Regulation of gene expression in late stage (branching morphogenesis) pancreatic bud precursor cells / muscle organ development / 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 / TRAF6 mediated IRF7 activation / platelet formation / histone acetyltransferase binding / megakaryocyte development / peptide-lysine-N-acetyltransferase activity / nuclear androgen receptor binding / NFE2L2 regulating anti-oxidant/detoxification enzymes / regulation of tubulin deacetylation / macrophage derived foam cell differentiation / FOXO-mediated transcription of cell death genes / NFE2L2 regulating tumorigenic genes / internal protein amino acid acetylation / STAT family protein binding / acyltransferase activity / Myogenesis / protein acetylation / positive regulation of cardiac muscle hypertrophy / fat cell differentiation / Formation of paraxial mesoderm / RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known / positive regulation of transforming growth factor beta receptor signaling pathway / SMAD binding / ERK/MAPK targets / PI5P Regulates TP53 Acetylation / Zygotic genome activation (ZGA) / acetyltransferase activity / stimulatory C-type lectin receptor signaling pathway / cellular response to nutrient levels / RUNX3 regulates p14-ARF / NF-kappaB binding / histone acetyltransferase complex / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / Attenuation phase / negative regulation of protein-containing complex assembly / canonical NF-kappaB signal transduction / negative regulation of gluconeogenesis / somitogenesis / pre-mRNA intronic binding / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / regulation of cellular response to heat / skeletal muscle tissue development / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / histone acetyltransferase activity / histone acetyltransferase / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups
Similarity search - Function
SRF-like / Transcription factor, MADS-box / CREB-binding Protein; Chain A / TAZ domain / Holliday junction regulator protein family C-terminal / Holliday junction regulator protein family C-terminal repeat / MADS MEF2-like / Transcription factor, MADS-box / Transcription factor, MADS-box superfamily / SRF-type transcription factor (DNA-binding and dimerisation domain) ...SRF-like / Transcription factor, MADS-box / CREB-binding Protein; Chain A / TAZ domain / Holliday junction regulator protein family C-terminal / Holliday junction regulator protein family C-terminal repeat / MADS MEF2-like / Transcription factor, MADS-box / Transcription factor, MADS-box superfamily / SRF-type transcription factor (DNA-binding and dimerisation domain) / MADS-box domain signature. / MADS-box domain profile. / MADS / 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 / Up-down Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
DNA / DNA (> 10) / Myocyte-specific enhancer factor 2A / Histone acetyltransferase p300
Similarity search - Component
Biological speciesHomo sapiens (human)
Synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1921 Å
AuthorsHe, J. / Ye, J. / Riquelme, C. / Liu, J.O.
CitationJournal: Nucleic Acids Res. / Year: 2011
Title: Structure of p300 bound to MEF2 on DNA reveals a mechanism of enhanceosome assembly.
Authors: He, J. / Ye, J. / Cai, Y. / Riquelme, C. / Liu, J.O. / Liu, X. / Han, A. / Chen, L.
History
DepositionOct 8, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 10, 2011Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.2Jul 17, 2019Group: Data collection / Refinement description / Source and taxonomy
Category: pdbx_entity_src_syn / software
Item: _pdbx_entity_src_syn.ncbi_taxonomy_id / _pdbx_entity_src_syn.organism_scientific ..._pdbx_entity_src_syn.ncbi_taxonomy_id / _pdbx_entity_src_syn.organism_scientific / _software.classification / _software.contact_author / _software.contact_author_email / _software.location / _software.name / _software.type / _software.version
Revision 1.3Sep 6, 2023Group: 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 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Myocyte-specific enhancer factor 2A
B: Myocyte-specific enhancer factor 2A
C: Myocyte-specific enhancer factor 2A
D: Myocyte-specific enhancer factor 2A
I: Myocyte-specific enhancer factor 2A
J: Myocyte-specific enhancer factor 2A
E: DNA (5'-D(*A*AP*AP*CP*TP*AP*TP*TP*TP*AP*TP*AP*AP*GP*A)-3')
F: DNA (5'-D(*TP*TP*CP*TP*TP*AP*TP*AP*AP*AP*TP*AP*GP*TP*T)-3')
G: DNA (5'-D(*A*AP*AP*CP*TP*AP*TP*TP*TP*AP*TP*AP*AP*GP*A)-3')
H: DNA (5'-D(*TP*TP*CP*TP*TP*AP*TP*AP*AP*AP*TP*AP*GP*TP*T)-3')
K: DNA (5'-D(*A*AP*AP*CP*TP*AP*TP*TP*TP*AP*TP*AP*AP*GP*A)-3')
L: DNA (5'-D(*TP*TP*CP*TP*TP*AP*TP*AP*AP*AP*TP*AP*GP*TP*T)-3')
P: Histone acetyltransferase p300
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,44316
Polymers104,24713
Non-polymers1963
Water4,720262
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)74.846, 90.926, 144.802
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 2 types, 7 molecules ABCDIJP

#1: Protein
Myocyte-specific enhancer factor 2A / Serum response factor-like protein 1


Mass: 10628.313 Da / Num. of mol.: 6 / Fragment: N terminal domain (UNP residues 2-91)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MEF2, MEF2A / Plasmid: pET30b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q02078
#4: Protein Histone acetyltransferase p300 / p300 HAT / E1A-associated protein p300


Mass: 12957.544 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EP300, P300 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q09472, histone acetyltransferase

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DNA chain , 2 types, 6 molecules EGKFHL

#2: DNA chain DNA (5'-D(*A*AP*AP*CP*TP*AP*TP*TP*TP*AP*TP*AP*AP*GP*A)-3')


Mass: 4600.049 Da / Num. of mol.: 3 / Fragment: CH3 domain (UNP Residues 1721-1837) / Mutation: C4A / Source method: obtained synthetically / Details: chemical synthesis / Source: (synth.) Synthetic construct (others)
#3: DNA chain DNA (5'-D(*TP*TP*CP*TP*TP*AP*TP*AP*AP*AP*TP*AP*GP*TP*T)-3')


Mass: 4573.006 Da / Num. of mol.: 3 / Source method: obtained synthetically / Details: chemical synthesis / Source: (synth.) Synthetic construct (others)

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Non-polymers , 2 types, 265 molecules

#5: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 262 / 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: 47.95 %
Crystal growTemperature: 288 K / Method: vapor diffusion, hanging drop / pH: 6.8
Details: 16% PEG 1000, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 288K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 10, 2006
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.09→30 Å / Num. all: 65790 / Num. obs: 59524 / % possible obs: 99.9 % / Redundancy: 7 % / Rmerge(I) obs: 0.087 / Rsym value: 0.061 / Net I/σ(I): 27.3
Reflection shellResolution: 2.09→2.16 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.709 / Mean I/σ(I) obs: 1.95 / Rsym value: 0.66 / % possible all: 100

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Processing

Software
NameVersionClassificationNB
PHENIX1.6.1_357refinement
CNSrefinement
PDB_EXTRACT3.1data extraction
ADSCQuantumdata collection
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1EGW

1egw


Resolution: 2.1921→29.666 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.31 / σ(F): 0.04 / Phase error: 27.11 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2724 4968 10.09 %
Rwork0.2194 --
obs0.2247 49213 95.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 28.369 Å2 / ksol: 0.343 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--1.2443 Å2-0 Å20 Å2
2---0.0768 Å2-0 Å2
3---1.4876 Å2
Refinement stepCycle: LAST / Resolution: 2.1921→29.666 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5296 1785 3 262 7346
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0087362
X-RAY DIFFRACTIONf_angle_d1.32410236
X-RAY DIFFRACTIONf_dihedral_angle_d21.6072990
X-RAY DIFFRACTIONf_chiral_restr0.081147
X-RAY DIFFRACTIONf_plane_restr0.004998
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1921-2.2170.35771270.25071161X-RAY DIFFRACTION76
2.217-2.24310.35541460.28811155X-RAY DIFFRACTION78
2.2431-2.27040.38221430.30871294X-RAY DIFFRACTION83
2.2704-2.29910.29021500.2391334X-RAY DIFFRACTION89
2.2991-2.32940.2841790.22311413X-RAY DIFFRACTION94
2.3294-2.36130.31741580.21791435X-RAY DIFFRACTION94
2.3613-2.3950.3051650.21791455X-RAY DIFFRACTION95
2.395-2.43070.31081470.22091461X-RAY DIFFRACTION95
2.4307-2.46870.28721570.22071470X-RAY DIFFRACTION96
2.4687-2.50910.27291680.21661465X-RAY DIFFRACTION96
2.5091-2.55240.26451530.2281505X-RAY DIFFRACTION98
2.5524-2.59880.33211590.23491472X-RAY DIFFRACTION97
2.5988-2.64870.29081470.22571485X-RAY DIFFRACTION97
2.6487-2.70280.28451510.23251512X-RAY DIFFRACTION97
2.7028-2.76150.34591750.23781503X-RAY DIFFRACTION99
2.7615-2.82570.29491700.25661481X-RAY DIFFRACTION98
2.8257-2.89630.2971570.26611531X-RAY DIFFRACTION98
2.8963-2.97450.32021890.25231484X-RAY DIFFRACTION98
2.9745-3.0620.3151770.25551502X-RAY DIFFRACTION98
3.062-3.16070.30991830.25961509X-RAY DIFFRACTION99
3.1607-3.27350.3081740.23771536X-RAY DIFFRACTION99
3.2735-3.40440.25461850.22271517X-RAY DIFFRACTION99
3.4044-3.55910.24961820.20731529X-RAY DIFFRACTION100
3.5591-3.74640.27231810.18951511X-RAY DIFFRACTION99
3.7464-3.98060.23861760.19521554X-RAY DIFFRACTION99
3.9806-4.28710.21881680.181561X-RAY DIFFRACTION100
4.2871-4.7170.21031770.16431553X-RAY DIFFRACTION100
4.717-5.3960.20311660.17511595X-RAY DIFFRACTION100
5.396-6.7850.26781830.1941592X-RAY DIFFRACTION100
6.785-29.66850.16371750.15821670X-RAY DIFFRACTION99
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.param
X-RAY DIFFRACTION2CNS_TOPPAR:dna-rna_rep.param
X-RAY DIFFRACTION3CNS_TOPPAR:ion.param
X-RAY DIFFRACTION4CNS_TOPPAR:water_rep.param

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