[English] 日本語
Yorodumi
- PDB-7qgs: Crystal structure of p300 CH1 domain in complex with CITIF (a CIT... -

+
Open data


ID or keywords:

Loading...

-
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


embryonic process involved in female pregnancy / cranial nerve morphogenesis / TFAP2 (AP-2) family regulates transcription of other transcription factors / 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 ...embryonic process involved in female pregnancy / cranial nerve morphogenesis / TFAP2 (AP-2) family regulates transcription of other transcription factors / 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 / hypoxia-inducible factor-1alpha signaling pathway / embryonic camera-type eye morphogenesis / glandular epithelial cell maturation / positive regulation of chemokine-mediated signaling pathway / elastin metabolic process / sex determination / regulation of transforming growth factor beta2 production / positive regulation of male gonad development / endocardial cushion development / connective tissue replacement involved in inflammatory response wound healing / hemoglobin biosynthetic process / negative regulation of mesenchymal cell apoptotic process / determination of left/right asymmetry in lateral mesoderm / cardiac ventricle morphogenesis / positive regulation of peroxisome proliferator activated receptor signaling pathway / granulocyte differentiation / lens morphogenesis in camera-type eye / positive regulation of hormone biosynthetic process / left/right axis specification / retina vasculature development in camera-type eye / intestinal epithelial cell maturation / Cellular response to hypoxia / negative regulation of growth / negative regulation of cardiac muscle cell proliferation / positive regulation of cell-cell adhesion / mesenchymal cell apoptotic process / positive regulation of mitophagy / regulation of protein neddylation / PTK6 Expression / negative regulation of bone mineralization / intracellular oxygen homeostasis / collagen metabolic process / trophectodermal cell differentiation / B-1 B cell homeostasis / response to fluid shear stress / vascular endothelial growth factor production / peripheral nervous system development / dopaminergic neuron differentiation / Activation of the TFAP2 (AP-2) family of transcription factors / cardiac neural crest cell development involved in heart development / transcription regulator activator activity / negative regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway / lactate metabolic process / STAT3 nuclear events downstream of ALK signaling / positive regulation of cytokine production involved in inflammatory response / negative regulation of thymocyte apoptotic process / motile cilium / positive regulation of vascular endothelial growth factor receptor signaling pathway / negative regulation of TOR signaling / bone morphogenesis / positive regulation of signaling receptor activity / insulin secretion involved in cellular response to glucose stimulus / determination of left/right symmetry / response to iron ion / response to muscle activity / neural crest cell migration / regulation of glycolytic process / Regulation of gene expression by Hypoxia-inducible Factor / embryonic hemopoiesis / FOXO-mediated transcription of cell death genes / DNA-binding transcription activator activity / DNA-binding transcription repressor activity / PTK6 promotes HIF1A stabilization / digestive tract morphogenesis / regulation of aerobic respiration / histone acetyltransferase binding / ventricular septum morphogenesis / muscle cell cellular homeostasis / positive regulation of neuroblast proliferation / positive regulation of epithelial cell migration / LBD domain binding / axonal transport of mitochondrion / bone mineralization / positive regulation of transforming growth factor beta receptor signaling pathway / heart looping / E-box binding / intracellular glucose homeostasis / skeletal muscle cell differentiation / SMAD binding / outflow tract morphogenesis / uterus development / positive regulation of insulin secretion involved in cellular response to glucose stimulus / decidualization / cellular response to interleukin-1 / positive regulation of vascular endothelial growth factor production / neuroblast proliferation / negative regulation of reactive oxygen species metabolic process / positive regulation of blood vessel endothelial cell migration
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 domain / Myc-type, basic helix-loop-helix (bHLH) domain / Myc-type, basic helix-loop-helix (bHLH) domain profile. / Helix-loop-helix DNA-binding domain superfamily / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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


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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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%

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more