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- PDB-7lvs: The CBP TAZ1 Domain in Complex with a CITED2-HIF-1-Alpha Fusion P... -

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Basic information

Entry
Database: PDB / ID: 7lvs
TitleThe CBP TAZ1 Domain in Complex with a CITED2-HIF-1-Alpha Fusion Peptide
Components
  • Cbp/p300-interacting transactivator 2,Hypoxia-inducible factor 1-alpha
  • Histone lysine acetyltransferase CREBBP
KeywordsTRANSCRIPTION / Complex / 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 / embryonic heart tube left/right pattern formation / epithelial cell differentiation involved in mammary gland alveolus development / regulation of animal organ formation / neural fold elevation formation / adrenal cortex formation / Activation of the TFAP2 (AP-2) family of transcription factors ...cranial nerve morphogenesis / TFAP2 (AP-2) family regulates transcription of other transcription factors / embryonic process involved in female pregnancy / left/right pattern formation / embryonic heart tube left/right pattern formation / epithelial cell differentiation involved in mammary gland alveolus development / regulation of animal organ formation / neural fold elevation formation / adrenal cortex formation / Activation of the TFAP2 (AP-2) family of transcription factors / iris morphogenesis / Regulation of FOXO transcriptional activity by acetylation / TRAF6 mediated IRF7 activation / nodal signaling pathway / intestinal epithelial cell maturation / Nuclear events mediated by NFE2L2 / positive regulation of nitric oxide metabolic process / Attenuation phase / hypoxia-inducible factor-1alpha signaling pathway / LRR FLII-interacting protein 1 (LRRFIP1) activates type I IFN production / pulmonary artery morphogenesis / Regulation of gene expression by Hypoxia-inducible Factor / RUNX1 regulates transcription of genes involved in differentiation of myeloid cells / positive regulation of chemokine-mediated signaling pathway / Formation of the beta-catenin:TCF transactivating complex / NOTCH1 Intracellular Domain Regulates Transcription / RUNX3 regulates NOTCH signaling / cAMP response element binding protein binding / elastin metabolic process / embryonic camera-type eye morphogenesis / sex determination / regulation of transforming growth factor beta2 production / Notch-HLH transcription pathway / glandular epithelial cell maturation / positive regulation of male gonad development / Transcriptional and post-translational regulation of MITF-M expression and activity / hemoglobin biosynthetic process / negative regulation of mesenchymal cell apoptotic process / cardiac ventricle morphogenesis / connective tissue replacement involved in inflammatory response wound healing / determination of left/right asymmetry in lateral mesoderm / endocardial cushion development / positive regulation of peroxisome proliferator activated receptor signaling pathway / lens morphogenesis in camera-type eye / left/right axis specification / negative regulation of growth / positive regulation of hormone biosynthetic process / positive regulation of cell-cell adhesion / germ-line stem cell population maintenance / negative regulation of viral process / Cellular response to hypoxia / Regulation of lipid metabolism by PPARalpha / retina vasculature development in camera-type eye / granulocyte differentiation / mesenchymal cell apoptotic process / regulation of protein neddylation / Cytoprotection by HMOX1 / negative regulation of bone mineralization / PTK6 Expression / intracellular oxygen homeostasis / collagen metabolic process / B-1 B cell homeostasis / Estrogen-dependent gene expression / CD209 (DC-SIGN) signaling / vascular endothelial growth factor production / trophectodermal cell differentiation / peptide lactyltransferase (CoA-dependent) activity / response to fluid shear stress / outer kinetochore / peripheral nervous system development / Activation of the TFAP2 (AP-2) family of transcription factors / dopaminergic neuron differentiation / cardiac neural crest cell development involved in heart development / negative regulation of interferon-beta production / transcription regulator activator activity / N-terminal peptidyl-lysine acetylation / histone H3K18 acetyltransferase activity / histone H3K27 acetyltransferase activity / STAT3 nuclear events downstream of ALK signaling / negative regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway / negative regulation of thymocyte apoptotic process / lactate metabolic process / MRF binding / positive regulation of cytokine production involved in inflammatory response / bone morphogenesis / insulin secretion involved in cellular response to glucose stimulus / negative regulation of TOR signaling / positive regulation of vascular endothelial growth factor receptor signaling pathway / determination of left/right symmetry / response to iron ion / neural crest cell migration / Regulation of gene expression by Hypoxia-inducible Factor / face morphogenesis / embryonic hemopoiesis / regulation of glycolytic process / negative regulation of transcription by RNA polymerase I / motile cilium / DNA-binding transcription repressor activity / protein-lysine-acetyltransferase activity / cellular response to hepatocyte growth factor stimulus
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 1-alpha bHLH domain / Hypoxia-inducible factor, alpha subunit-like / Hypoxia-inducible factor-1 / PAS fold-3 / PAS fold ...CITED / CITED / Hypoxia-inducible factor-1 alpha / HIF-1 alpha, transactivation domain, C-terminal / HIF-1 alpha C terminal transactivation domain / Hypoxia-inducible factor 1-alpha bHLH domain / Hypoxia-inducible factor, alpha subunit-like / Hypoxia-inducible factor-1 / PAS fold-3 / PAS fold / 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 / : / Histone acetyltransferase p300-like, PHD domain / 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. / PAC motif / Motif C-terminal to PAS motifs (likely to contribute to PAS structural domain) / Nuclear receptor coactivator, interlocking / 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 / bromo domain / Bromodomain / Bromodomain (BrD) profile. / Bromodomain-like superfamily / Zinc finger, RING/FYVE/PHD-type
Similarity search - Domain/homology
Histone lysine acetyltransferase CREBBP / Hypoxia-inducible factor 1-alpha / Cbp/p300-interacting transactivator 2
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / AB INITIO PHASING / Resolution: 2.02 Å
AuthorsAppling, F.D. / Berlow, R.B. / Stanfield, R.L. / Dyson, H.J. / Wright, P.E.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)CA096865, CA229652 United States
CitationJournal: Structure / Year: 2021
Title: The molecular basis of allostery in a facilitated dissociation process.
Authors: Appling, F.D. / Berlow, R.B. / Stanfield, R.L. / Dyson, H.J. / Wright, P.E.
History
DepositionFeb 26, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 28, 2021Provider: repository / Type: Initial release
Revision 1.1Sep 29, 2021Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _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 / _citation.year / _citation_author.identifier_ORCID / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Dec 15, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)19,0015
Polymers18,8052
Non-polymers1963
Water64936
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4680 Å2
ΔGint-44 kcal/mol
Surface area9140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)32.061, 50.112, 41.255
Angle α, β, γ (deg.)90.000, 99.189, 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 Histone lysine acetyltransferase CREBBP / Protein-lysine acetyltransferase CREBBP


Mass: 11281.177 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Crebbp, Cbp / Production host: Escherichia coli (E. coli)
References: UniProt: P45481, histone acetyltransferase, Transferases; Acyltransferases; Transferring groups other than aminoacyl groups
#2: 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: 7523.444 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CITED2, MRG1, HIF1A, BHLHE78, MOP1, PASD8 / Production host: Escherichia coli (E. coli) / References: UniProt: Q99967, UniProt: Q16665
#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.: 36 / 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: 1.74 Å3/Da / Density % sol: 29.3 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1 M HEPES pH 6.87, 28% PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.3 / Wavelength: 0.97648 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 7, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97648 Å / Relative weight: 1
ReflectionResolution: 2→40.73 Å / Num. obs: 8465 / % possible obs: 100 % / Redundancy: 7.1 % / CC1/2: 0.878 / Net I/σ(I): 17.9
Reflection shellResolution: 2.0193→2.1458 Å / Num. unique obs: 562 / CC1/2: 0.91

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
HKL-2000data scaling
Arcimboldophasing
RefinementMethod to determine structure: AB INITIO PHASING / Resolution: 2.02→40.73 Å / SU ML: 0.3266 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 32.6525
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2406 882 10.47 %
Rwork0.2107 7543 -
obs0.2137 8425 98.24 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 59.75 Å2
Refinement stepCycle: LAST / Resolution: 2.02→40.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1214 0 3 36 1253
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0031231
X-RAY DIFFRACTIONf_angle_d0.64471662
X-RAY DIFFRACTIONf_chiral_restr0.0368191
X-RAY DIFFRACTIONf_plane_restr0.0028220
X-RAY DIFFRACTIONf_dihedral_angle_d17.4033774
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.02-2.150.39071330.39491150X-RAY DIFFRACTION90.42
2.15-2.310.45391380.38991272X-RAY DIFFRACTION99.02
2.31-2.540.27961680.24741242X-RAY DIFFRACTION99.93
2.54-2.910.25261520.22761282X-RAY DIFFRACTION100
2.91-3.670.26491450.19421276X-RAY DIFFRACTION100
3.67-40.730.17551460.16621321X-RAY DIFFRACTION100

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