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- PDB-5y7w: Crystal structure of the Nco-A1 PAS-B domain with YL-2 -

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Basic information

Entry
Database: PDB / ID: 5y7w
TitleCrystal structure of the Nco-A1 PAS-B domain with YL-2
Components
  • Nuclear receptor coactivator 1
  • YL-2 peptide
KeywordsTRANSCRIPTION/INIHIBITOR / inflammatory allergic diseases and cancers / Nuclear receptor coactivator 1 / stapled peptide / TRANSCRIPTION-INIHIBITOR complex
Function / homology
Function and homology information


NR1H2 & NR1H3 regulate gene expression to control bile acid homeostasis / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / SUMOylation of transcription cofactors / Recycling of bile acids and salts / Synthesis of bile acids and bile salts / Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol / Synthesis of bile acids and bile salts via 27-hydroxycholesterol / Endogenous sterols / HATs acetylate histones / Regulation of lipid metabolism by PPARalpha ...NR1H2 & NR1H3 regulate gene expression to control bile acid homeostasis / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / SUMOylation of transcription cofactors / Recycling of bile acids and salts / Synthesis of bile acids and bile salts / Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol / Synthesis of bile acids and bile salts via 27-hydroxycholesterol / Endogenous sterols / HATs acetylate histones / Regulation of lipid metabolism by PPARalpha / Cytoprotection by HMOX1 / Estrogen-dependent gene expression / nuclear retinoic acid receptor binding / labyrinthine layer morphogenesis / regulation of thyroid hormone mediated signaling pathway / positive regulation of transcription from RNA polymerase II promoter by galactose / positive regulation of female receptivity / hypothalamus development / male mating behavior / cellular response to Thyroglobulin triiodothyronine / estrous cycle / nuclear retinoid X receptor binding / response to retinoic acid / histone acetyltransferase activity / regulation of cellular response to insulin stimulus / histone acetyltransferase / cellular response to hormone stimulus / positive regulation of adipose tissue development / peroxisome proliferator activated receptor signaling pathway / lactation / positive regulation of neuron differentiation / cerebellum development / nuclear receptor coactivator activity / response to progesterone / nuclear estrogen receptor binding / hippocampus development / nuclear receptor binding / RNA polymerase II transcription regulatory region sequence-specific DNA binding / mRNA transcription by RNA polymerase II / cerebral cortex development / RNA polymerase II transcription regulator complex / male gonad development / response to estradiol / transcription regulator complex / transcription coactivator activity / protein dimerization activity / positive regulation of apoptotic process / chromatin binding / chromatin / protein-containing complex binding / positive regulation of DNA-templated transcription / positive regulation of transcription by RNA polymerase II / protein-containing complex / DNA binding / nucleoplasm / nucleus / plasma membrane / cytosol
Similarity search - Function
Nuclear receptor coactivator 1 / PAS domain / Nuclear receptor coactivator, DUF1518 / Nuclear receptor coactivator, Ncoa-type, interlocking / Nuclear receptor coactivator, Ncoa-type, interlocking domain superfamily / Nuclear receptor coactivator, DUF1518 / Nuclear receptor coactivator / DUF1518 / Nuclear receptor coactivator, receptor-binding domain / Nuclear receptor coactivator ...Nuclear receptor coactivator 1 / PAS domain / Nuclear receptor coactivator, DUF1518 / Nuclear receptor coactivator, Ncoa-type, interlocking / Nuclear receptor coactivator, Ncoa-type, interlocking domain superfamily / Nuclear receptor coactivator, DUF1518 / Nuclear receptor coactivator / DUF1518 / Nuclear receptor coactivator, receptor-binding domain / Nuclear receptor coactivator / Steroid receptor coactivator / Unstructured region on nuclear receptor coactivator protein / PAS domain / Nuclear receptor coactivator, interlocking / 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. / Beta-Lactamase / PAS fold / PAS fold / PAS domain / PAS repeat profile. / PAS domain / PAS domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Nuclear receptor coactivator 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.25 Å
AuthorsLee, Y.J. / Yoon, H.S. / Lee, J.H. / Bae, J.H. / Song, J.Y. / Lim, H.S.
Funding support Korea, Republic Of, 2items
OrganizationGrant numberCountry
National Research Foundation (Korea)NRF-2017R1A2B3004941 Korea, Republic Of
National Research Foundation (Korea)NRF-2017M3A9G4052952 Korea, Republic Of
CitationJournal: J. Am. Chem. Soc. / Year: 2017
Title: Targeted Inhibition of the NCOA1/STAT6 Protein-Protein Interaction
Authors: Lee, Y. / Yoon, H. / Hwang, S.M. / Shin, M.K. / Lee, J.H. / Oh, M. / Im, S.H. / Song, J. / Lim, H.S.
History
DepositionAug 18, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 15, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.d_res_high

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Nuclear receptor coactivator 1
B: Nuclear receptor coactivator 1
C: YL-2 peptide
D: YL-2 peptide


Theoretical massNumber of molelcules
Total (without water)32,6744
Polymers32,6744
Non-polymers00
Water2,108117
1
A: Nuclear receptor coactivator 1
C: YL-2 peptide


Theoretical massNumber of molelcules
Total (without water)16,3372
Polymers16,3372
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1190 Å2
ΔGint-9 kcal/mol
Surface area8270 Å2
MethodPISA
2
B: Nuclear receptor coactivator 1
D: YL-2 peptide


Theoretical massNumber of molelcules
Total (without water)16,3372
Polymers16,3372
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1240 Å2
ΔGint-8 kcal/mol
Surface area7240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.501, 62.501, 137.177
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

#1: Protein Nuclear receptor coactivator 1 / / NCoA-1 / Nuclear receptor coactivator protein 1 / mNRC-1 / Steroid receptor coactivator 1 / SRC-1


Mass: 14500.489 Da / Num. of mol.: 2 / Fragment: UNP residues 257-367
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Ncoa1, Src1 / Production host: Escherichia coli (E. coli) / References: UniProt: P70365, histone acetyltransferase
#2: Protein/peptide YL-2 peptide


Mass: 1836.261 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 117 / 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: 47.92 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 0.1M HEPES (pH7.5), 10% v/v isopropanol, 20% w/v polyethylene glycol 4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.9794 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jul 11, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2.25→50 Å / Num. obs: 14389 / % possible obs: 99.88 % / Redundancy: 20.7 % / Biso Wilson estimate: 19.37 Å2 / Rmerge(I) obs: 0.128 / Rpim(I) all: 0.029 / Rrim(I) all: 0.131 / Χ2: 1.003 / Net I/σ(I): 31.1
Reflection shellResolution: 2.25→2.29 Å / Redundancy: 21.2 % / Mean I/σ(I) obs: 8 / Num. unique obs: 1431 / Χ2: 0.918 / % possible all: 99.51

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
HKL-2000data scaling
PHASERmodel building
PDB_EXTRACT3.22data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1OJ5

1oj5


Resolution: 2.25→34.919 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 23.6 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2036 736 5.12 %
Rwork0.1642 --
obs0.1662 14382 99.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.25→34.919 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2039 0 0 117 2156
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072121
X-RAY DIFFRACTIONf_angle_d0.9152878
X-RAY DIFFRACTIONf_dihedral_angle_d10.4051654
X-RAY DIFFRACTIONf_chiral_restr0.045318
X-RAY DIFFRACTIONf_plane_restr0.005365
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.249-2.42260.29111440.21892711X-RAY DIFFRACTION100
2.4226-2.66630.27351370.18442730X-RAY DIFFRACTION100
2.6663-3.0520.21741680.17732704X-RAY DIFFRACTION100
3.052-3.84440.19361490.14782736X-RAY DIFFRACTION100
3.8444-34.92340.15861380.14842765X-RAY DIFFRACTION100

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