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- PDB-7qgs: Crystal structure of p300 CH1 domain in complex with CITIF (a CIT... -

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Basic information

Entry
Database: PDB / ID: 7qgs
TitleCrystal structure of p300 CH1 domain in complex with CITIF (a CITED2-HIF-1alpha hybrid)
Components
  • Cbp/p300-interacting transactivator 2,Hypoxia-inducible factor 1-alpha
  • Histone acetyltransferase
KeywordsPROTEIN BINDING / hypoxia / transcription factor / intrinsically disordered protein
Function / homology
Function and homology information


cranial nerve morphogenesis / TFAP2 (AP-2) family regulates transcription of other transcription factors / embryonic process involved in female pregnancy / left/right pattern formation / pulmonary artery morphogenesis / epithelial cell differentiation involved in mammary gland alveolus development / embryonic heart tube left/right pattern formation / neural fold elevation formation / regulation of animal organ formation / adrenal cortex formation ...cranial nerve morphogenesis / TFAP2 (AP-2) family regulates transcription of other transcription factors / embryonic process involved in female pregnancy / left/right pattern formation / pulmonary artery morphogenesis / epithelial cell differentiation involved in mammary gland alveolus development / embryonic heart tube left/right pattern formation / neural fold elevation formation / regulation of animal organ formation / adrenal cortex formation / iris morphogenesis / nodal signaling pathway / positive regulation of chemokine-mediated signaling pathway / hypoxia-inducible factor-1alpha signaling pathway / embryonic camera-type eye morphogenesis / elastin metabolic process / glandular epithelial cell maturation / sex determination / regulation of transforming growth factor beta2 production / positive regulation of male gonad development / connective tissue replacement involved in inflammatory response wound healing / endocardial cushion development / determination of left/right asymmetry in lateral mesoderm / cardiac ventricle morphogenesis / negative regulation of mesenchymal cell apoptotic process / positive regulation of peroxisome proliferator activated receptor signaling pathway / hemoglobin biosynthetic process / granulocyte differentiation / lens morphogenesis in camera-type eye / retina vasculature development in camera-type eye / left/right axis specification / positive regulation of hormone biosynthetic process / mesenchymal cell apoptotic process / collagen metabolic process / positive regulation of mitophagy / positive regulation of cell-cell adhesion / Cellular response to hypoxia / negative regulation of cardiac muscle cell proliferation / intestinal epithelial cell maturation / negative regulation of growth / regulation of protein neddylation / negative regulation of bone mineralization / PTK6 Expression / lactate metabolic process / intracellular oxygen homeostasis / response to fluid shear stress / trophectodermal cell differentiation / B-1 B cell homeostasis / vascular endothelial growth factor production / peripheral nervous system development / negative regulation of TOR signaling / negative regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway / cardiac neural crest cell development involved in heart development / transcription regulator activator activity / dopaminergic neuron differentiation / STAT3 nuclear events downstream of ALK signaling / Activation of the TFAP2 (AP-2) family of transcription factors / positive regulation of cytokine production involved in inflammatory response / motile cilium / negative regulation of thymocyte apoptotic process / positive regulation of vascular endothelial growth factor receptor signaling pathway / bone morphogenesis / positive regulation of signaling receptor activity / insulin secretion involved in cellular response to glucose stimulus / response to iron ion / response to muscle activity / determination of left/right symmetry / neural crest cell migration / embryonic hemopoiesis / Regulation of gene expression by Hypoxia-inducible Factor / regulation of glycolytic process / histone acetyltransferase binding / muscle cell cellular homeostasis / erythrocyte development / FOXO-mediated transcription of cell death genes / PTK6 promotes HIF1A stabilization / regulation of aerobic respiration / digestive tract morphogenesis / DNA-binding transcription repressor activity / DNA-binding transcription activator activity / positive regulation of neuroblast proliferation / ventricular septum morphogenesis / axonal transport of mitochondrion / positive regulation of epithelial cell migration / LBD domain binding / heart looping / bone mineralization / TOR signaling / E-box binding / outflow tract morphogenesis / positive regulation of transforming growth factor beta receptor signaling pathway / SMAD binding / skeletal muscle cell differentiation / positive regulation of insulin secretion involved in cellular response to glucose stimulus / intracellular glucose homeostasis / uterus development / decidualization / neuroblast proliferation / positive regulation of vascular endothelial growth factor production / epithelial to mesenchymal transition
Similarity search - Function
CITED / CITED / Hypoxia-inducible factor-1 alpha / HIF-1 alpha, transactivation domain, C-terminal / HIF-1 alpha C terminal transactivation domain / Hypoxia-inducible factor, alpha subunit-like / Hypoxia-inducible factor-1 / PAS fold-3 / PAS fold / Zinc finger, TAZ-type ...CITED / CITED / Hypoxia-inducible factor-1 alpha / HIF-1 alpha, transactivation domain, C-terminal / HIF-1 alpha C terminal transactivation domain / Hypoxia-inducible factor, alpha subunit-like / Hypoxia-inducible factor-1 / PAS fold-3 / PAS fold / 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 / PAC motif / Motif C-terminal to PAS motifs (likely to contribute to PAS structural domain) / 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. / PAS fold / PAS fold / 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
Similarity search - Domain/homology
Hypoxia-inducible factor 1-alpha / Histone acetyltransferase / Cbp/p300-interacting transactivator 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsHegedus, Z. / Wilson, A.J. / Edwards, T.A.
Funding support United Kingdom, 6items
OrganizationGrant numberCountry
Engineering and Physical Sciences Research CouncilEP/N013573/1 United Kingdom
Engineering and Physical Sciences Research CouncilEP/KO39292/1 United Kingdom
Engineering and Physical Sciences Research CouncilBB/L01386X/1 United Kingdom
H2020 Marie Curie Actions of the European CommissionMSCA-IF-2016-749012 United Kingdom
Hungarian National Research, Development and Innovation OfficeNKFIH PD 135324 United Kingdom
Royal Society191087 United Kingdom
CitationJournal: Rsc Chem Biol / Year: 2022
Title: Understanding p300-transcription factor interactions using sequence variation and hybridization.
Authors: Hobor, F. / Hegedus, Z. / Ibarra, A.A. / Petrovicz, V.L. / Bartlett, G.J. / Sessions, R.B. / Wilson, A.J. / Edwards, T.A.
History
DepositionDec 10, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 11, 2022Provider: repository / Type: Initial release
Revision 1.1Jun 15, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: Cbp/p300-interacting transactivator 2,Hypoxia-inducible factor 1-alpha
A: Histone acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,4915
Polymers17,2952
Non-polymers1963
Water73941
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)30.505, 48.599, 39.825
Angle α, β, γ (deg.)90.000, 103.867, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein Cbp/p300-interacting transactivator 2,Hypoxia-inducible factor 1-alpha / MSG-related protein 1 / MRG-1 / P35srj / HIF-1-alpha / HIF1-alpha / ARNT-interacting protein / ...MSG-related protein 1 / MRG-1 / P35srj / HIF-1-alpha / HIF1-alpha / ARNT-interacting protein / Basic-helix-loop-helix-PAS protein MOP1 / Class E basic helix-loop-helix protein 78 / bHLHe78 / Member of PAS protein 1 / PAS domain-containing protein 8


Mass: 6402.204 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q99967, UniProt: Q16665
#2: Protein Histone acetyltransferase /


Mass: 10892.716 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EP300 / Production host: Escherichia coli (E. coli) / References: UniProt: Q7Z6C1, histone acetyltransferase
#3: Chemical ChemComp-ZN / ZINC ION


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


Mass: 18.015 Da / Num. of mol.: 41 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 1.66 Å3/Da / Density % sol: 25.78 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 0.1 M HEPES pH 6.5, PEG 6K 35%

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 1.28367 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Feb 17, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.28367 Å / Relative weight: 1
ReflectionResolution: 2→38.66 Å / Num. obs: 7708 / % possible obs: 99.7 % / Redundancy: 6.6 % / Biso Wilson estimate: 48.17 Å2 / CC1/2: 0.991 / Rmerge(I) obs: 0.109 / Rpim(I) all: 0.047 / Rrim(I) all: 0.119 / Net I/σ(I): 7.5
Reflection shellResolution: 2→2.03 Å / Redundancy: 6 % / Rmerge(I) obs: 0.744 / Mean I/σ(I) obs: 2.9 / Num. unique obs: 355 / CC1/2: 0.87 / Rpim(I) all: 0.325 / Rrim(I) all: 0.814 / % possible all: 96.5

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
Aimlessdata scaling
xia2data reduction
PHASERphasing
Cootmodel building
DIALSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7LVS

7lvs


Resolution: 2→38.66 Å / SU ML: 0.0979 / Cross valid method: FREE R-VALUE / σ(F): 1.4 / Phase error: 36.1924
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.245 398 5.18 %
Rwork0.2208 7279 -
obs0.2221 7677 99.26 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 79.04 Å2
Refinement stepCycle: LAST / Resolution: 2→38.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1166 0 3 41 1210
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01591181
X-RAY DIFFRACTIONf_angle_d1.54511591
X-RAY DIFFRACTIONf_chiral_restr0.0706180
X-RAY DIFFRACTIONf_plane_restr0.009212
X-RAY DIFFRACTIONf_dihedral_angle_d16.264159
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.290.30011270.30472381X-RAY DIFFRACTION98.39
2.29-2.880.33981300.29962426X-RAY DIFFRACTION99.65
2.88-38.660.21611410.19222472X-RAY DIFFRACTION99.77

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