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- PDB-7wqq: Retinoic acid receptor alpha mutant - N299H -

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Basic information

Entry
Database: PDB / ID: 7wqq
TitleRetinoic acid receptor alpha mutant - N299H
Components
  • Peptide from Nuclear receptor coactivator 1
  • Retinoic acid receptor alpha
KeywordsGENE REGULATION / Nuclear receptor / retinoic acid
Function / homology
Function and homology information


Sertoli cell fate commitment / positive regulation of binding / trachea cartilage development / ventricular cardiac muscle cell differentiation / chondroblast differentiation / embryonic camera-type eye development / glandular epithelial cell development / negative regulation of granulocyte differentiation / protein kinase B binding / cellular response to corticotropin-releasing hormone stimulus ...Sertoli cell fate commitment / positive regulation of binding / trachea cartilage development / ventricular cardiac muscle cell differentiation / chondroblast differentiation / embryonic camera-type eye development / glandular epithelial cell development / negative regulation of granulocyte differentiation / protein kinase B binding / cellular response to corticotropin-releasing hormone stimulus / growth plate cartilage development / positive regulation of T-helper 2 cell differentiation / prostate gland development / negative regulation of cartilage development / retinoic acid-responsive element binding / regulation of hematopoietic progenitor cell differentiation / positive regulation of interleukin-5 production / nuclear glucocorticoid receptor binding / positive regulation of interleukin-13 production / retinoic acid binding / response to vitamin A / labyrinthine layer morphogenesis / regulation of thyroid hormone mediated signaling pathway / positive regulation of transcription from RNA polymerase II promoter by galactose / apoptotic cell clearance / positive regulation of female receptivity / limb development / protein kinase A binding / ureteric bud development / regulation of myelination / Signaling by Retinoic Acid / DNA-binding transcription repressor activity / hypothalamus development / male mating behavior / heterocyclic compound binding / NR1H2 & NR1H3 regulate gene expression to control bile acid homeostasis / positive regulation of interleukin-4 production / face development / alpha-actinin binding / germ cell development / negative regulation of type II interferon production / negative regulation of tumor necrosis factor production / cellular response to Thyroglobulin triiodothyronine / estrous cycle / Synthesis of bile acids and bile salts / retinoic acid receptor signaling pathway / cellular response to estrogen stimulus / Endogenous sterols / Synthesis of bile acids and bile salts via 27-hydroxycholesterol / Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol / positive regulation of cell cycle / nuclear retinoid X receptor binding / cellular response to retinoic acid / response to retinoic acid / histone acetyltransferase activity / regulation of cellular response to insulin stimulus / Recycling of bile acids and salts / histone acetyltransferase / cellular response to hormone stimulus / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / positive regulation of adipose tissue development / peroxisome proliferator activated receptor signaling pathway / RORA activates gene expression / lactation / positive regulation of neuron differentiation / Regulation of lipid metabolism by PPARalpha / hormone-mediated signaling pathway / cerebellum development / mRNA regulatory element binding translation repressor activity / BMAL1:CLOCK,NPAS2 activates circadian gene expression / SUMOylation of transcription cofactors / Activation of gene expression by SREBF (SREBP) / nuclear receptor coactivator activity / negative regulation of miRNA transcription / liver development / response to progesterone / response to cytokine / neural tube closure / female pregnancy / nuclear estrogen receptor binding / hippocampus development / nuclear receptor binding / RNA polymerase II transcription regulatory region sequence-specific DNA binding / Heme signaling / SUMOylation of intracellular receptors / regulation of synaptic plasticity / mRNA transcription by RNA polymerase II / Transcriptional activation of mitochondrial biogenesis / multicellular organism growth / PPARA activates gene expression / Cytoprotection by HMOX1 / chromatin DNA binding / cerebral cortex development / mRNA 5'-UTR binding / transcription coactivator binding / histone deacetylase binding / Transcriptional regulation of white adipocyte differentiation / Activation of anterior HOX genes in hindbrain development during early embryogenesis / Nuclear Receptor transcription pathway / Transcriptional regulation of granulopoiesis
Similarity search - Function
: / : / Retinoic acid receptor / Nuclear receptor coactivator 1 / 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 ...: / : / Retinoic acid receptor / Nuclear receptor coactivator 1 / 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. / PAS fold / PAS fold / PAS domain / PAS repeat profile. / PAS domain / PAS domain superfamily / Nuclear hormone receptor / Nuclear hormones receptors DNA-binding region signature. / Zinc finger, nuclear hormone receptor-type / Zinc finger, C4 type (two domains) / Nuclear hormone receptors DNA-binding domain profile. / c4 zinc finger in nuclear hormone receptors / Nuclear hormone receptor, ligand-binding domain / Nuclear hormone receptor-like domain superfamily / Ligand-binding domain of nuclear hormone receptor / Nuclear receptor (NR) ligand-binding (LBD) domain profile. / Ligand binding domain of hormone receptors / Zinc finger, NHR/GATA-type
Similarity search - Domain/homology
Chem-5Z6 / Retinoic acid receptor alpha / Nuclear receptor coactivator 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsHuang, X.X. / Ng, L.M. / Teh, B.T.
Funding support Singapore, 1items
OrganizationGrant numberCountry
Other governmentOFIRG16may055 Singapore
CitationJournal: To Be Published
Title: Effects of breast fibroepithelial tumor associated retinoic acid receptor alpha ligand binding domain mutations on receptor function and retinoid signaling
Authors: Huang, X.X. / Ng, L.M. / Teh, B.T.
History
DepositionJan 25, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 25, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: 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

Downloads & links

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Assembly

Deposited unit
A: Retinoic acid receptor alpha
C: Peptide from Nuclear receptor coactivator 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,1073
Polymers31,7432
Non-polymers3641
Water2,558142
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1040 Å2
ΔGint-9 kcal/mol
Surface area11070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.915, 64.979, 49.205
Angle α, β, γ (deg.)90.000, 105.230, 90.000
Int Tables number5
Space group name H-MC121
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Components on special symmetry positions
IDModelComponents
11A-657-

HOH

21A-674-

HOH

31A-710-

HOH

41A-713-

HOH

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Components

#1: Protein Retinoic acid receptor alpha / / RAR-alpha / Nuclear receptor subfamily 1 group B member 1


Mass: 30150.787 Da / Num. of mol.: 1 / Mutation: N299H
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RARA, NR1B1 / Production host: Escherichia coli (E. coli) / References: UniProt: P10276
#2: Protein/peptide Peptide from Nuclear receptor coactivator 1 /


Mass: 1591.880 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q15788, histone acetyltransferase
#3: Chemical ChemComp-5Z6 / 4-[(E)-3-(3,5-ditert-butylphenyl)-3-oxidanylidene-prop-1-enyl]benzoic acid


Mass: 364.477 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H28O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 142 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.16 Å3/Da / Density % sol: 43.07 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: 0.05M Bis-Tris Propane pH 5.0, 0.05M Citric acid, 18% PEG 3350

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Data collection

DiffractionMean temperature: 293 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: TPS 05A / Wavelength: 1 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Apr 14, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.88→50 Å / Num. obs: 20866 / % possible obs: 95.6 % / Redundancy: 2.8 % / Biso Wilson estimate: 25.2 Å2 / Rmerge(I) obs: 0.076 / Rpim(I) all: 0.052 / Rrim(I) all: 0.092 / Χ2: 0.657 / Net I/σ(I): 6.1 / Num. measured all: 59454
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.88-1.951.60.68314800.5520.6010.9130.36369.1
1.95-2.0320.50220870.6250.4110.6520.43294.9
2.03-2.122.60.39721520.7810.2960.4980.4699.4
2.12-2.2330.29921600.8840.2030.3630.459100
2.23-2.373.20.25121540.9270.1630.30.56299.9
2.37-2.553.30.18621830.9560.1190.2210.60499.9
2.55-2.813.30.12621720.9770.0810.150.68399.4
2.81-3.213.20.07221630.9920.0480.0870.69898.8
3.21-4.0530.04121570.9970.0290.0510.88197.6
4.05-502.90.0321580.9980.0210.0371.06496.9

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Processing

Software
NameVersionClassification
PHENIX1.20_4459refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3KMR

3kmr


Resolution: 1.9→32.52 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 0.09 / Phase error: 21.38 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2056 1838 9.53 %
Rwork0.166 17450 -
obs0.1699 19288 90.17 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 132.3 Å2 / Biso mean: 38.6659 Å2 / Biso min: 14.57 Å2
Refinement stepCycle: final / Resolution: 1.9→32.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1882 0 54 142 2078
Biso mean--25.8 39.76 -
Num. residues----237
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9-1.950.342810.303880388455
1.95-2.010.31381110.25381105121675
2.01-2.070.25211390.21251273141286
2.07-2.150.24821380.18351335147390
2.15-2.230.20921490.16981385153494
2.23-2.340.2081470.15131396154394
2.34-2.460.18781490.14871420156996
2.46-2.610.19461550.15381444159997
2.61-2.810.21031520.16471433158598
2.81-3.10.25671530.16021458161198
3.1-3.540.21111520.16891455160798
3.54-4.460.16021540.14361459161397
4.47-32.520.18971580.16631484164297
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.60361.30240.35092.1786-1.23322.4868-0.1607-0.41310.71761.07160.1027-0.3078-0.5532-0.16240.12470.41480.0691-0.04160.3608-0.07790.354529.789916.257520.652
22.27470.28071.05071.0030.08062.8024-0.05510.0278-0.17810.11340.22320.02630.26190.2398-0.23340.20980.01470.01510.26-0.00640.198939.4092-8.944814.2089
32.695-2.4059-1.29368.6032.94643.4656-0.079-0.1305-0.19160.6344-0.06390.08820.2361-0.19490.15180.2083-0.01150.01340.2410.05220.196226.9761-6.183516.2385
43.8461-0.5454-0.22171.48870.2531.9081-0.032-0.03940.13680.01080.03120.2615-0.1482-0.1770.00550.19820.02580.01410.18150.02310.172421.44864.668412.2111
52.60680.2973-0.13242.6415-0.44191.9524-0.00250.04660.06130.03660.0236-0.0012-0.08090.1559-0.02210.14720.00080.01310.2008-0.01930.14339.379-4.93635.7823
67.28580.32942.17983.16930.31012.19410.18540.1679-0.15330.0053-0.0432-0.12750.1440.1851-0.13580.20960.0541-0.01270.1950.03190.224123.875310.50658.8078
74.70550.97051.00434.49580.09812.8538-0.23610.4150.5808-0.20640.1454-0.4419-0.39950.17830.04390.3808-0.008-0.03450.20640.01820.397129.005120.21798.5251
82.20191.87930.422.48840.93971.2786-0.13190.25360.1279-0.32840.2574-0.0033-0.1465-0.0286-0.11670.21940.01110.00360.27670.02420.246227.66481.71780.4306
91.47230.4551-0.04235.27662.74124.87770.038-0.2492-0.487-0.1065-0.28110.26270.5027-0.08660.18820.2697-0.02040.03430.30480.10130.400819.554-12.398210.3742
109.58844.24362.85443.42593.82516.8010.1857-0.87790.11480.2644-0.71031.37940.4104-0.39770.53780.30830.02250.07720.47080.09930.589212.7984-2.23420.0852
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 181 through 198 )A181 - 198
2X-RAY DIFFRACTION2chain 'A' and (resid 199 through 221 )A199 - 221
3X-RAY DIFFRACTION3chain 'A' and (resid 222 through 245 )A222 - 245
4X-RAY DIFFRACTION4chain 'A' and (resid 246 through 276 )A246 - 276
5X-RAY DIFFRACTION5chain 'A' and (resid 277 through 319 )A277 - 319
6X-RAY DIFFRACTION6chain 'A' and (resid 320 through 344 )A320 - 344
7X-RAY DIFFRACTION7chain 'A' and (resid 345 through 372 )A345 - 372
8X-RAY DIFFRACTION8chain 'A' and (resid 373 through 400 )A373 - 400
9X-RAY DIFFRACTION9chain 'A' and (resid 401 through 414 )A401 - 414
10X-RAY DIFFRACTION10chain 'C' and (resid 632 through 640 )C632 - 640

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