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- PDB-3kmr: Crystal structure of RARalpha ligand binding domain in complex wi... -

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Basic information

Entry
Database: PDB / ID: 3kmr
TitleCrystal structure of RARalpha ligand binding domain in complex with an agonist ligand (Am580) and a coactivator fragment
Components
  • Nuclear receptor coactivator 1
  • Retinoic acid receptor alpha
KeywordsTRANSCRIPTION / nuclear receptor transcription factor ligand binding domain / DNA-binding / Metal-binding / Nucleus / Phosphoprotein / Proto-oncogene / Receptor / Transcription regulation / Zinc-finger / Activator / Acyltransferase / Isopeptide bond / Transferase
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 / protein kinase B binding / negative regulation of granulocyte differentiation / growth plate cartilage development / glandular epithelial cell development ...Sertoli cell fate commitment / positive regulation of binding / trachea cartilage development / ventricular cardiac muscle cell differentiation / chondroblast differentiation / embryonic camera-type eye development / protein kinase B binding / negative regulation of granulocyte differentiation / growth plate cartilage development / glandular epithelial cell 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-13 production / positive regulation of interleukin-5 production / outflow tract septum morphogenesis / retinoic acid binding / labyrinthine layer morphogenesis / positive regulation of transcription from RNA polymerase II promoter by galactose / regulation of thyroid hormone receptor signaling pathway / TGFBR3 expression / positive regulation of female receptivity / response to vitamin A / limb development / apoptotic cell clearance / regulation of myelination / Signaling by Retinoic Acid / ureteric bud development / DNA-binding transcription repressor activity / NR1H2 & NR1H3 regulate gene expression to control bile acid homeostasis / protein kinase A binding / hypothalamus development / male mating behavior / heterocyclic compound binding / positive regulation of interleukin-4 production / alpha-actinin binding / face development / germ cell development / negative regulation of type II interferon production / cellular response to Thyroglobulin triiodothyronine / Synthesis of bile acids and bile salts / negative regulation of tumor necrosis factor production / cellular response to estrogen stimulus / Synthesis of bile acids and bile salts via 27-hydroxycholesterol / Endogenous sterols / Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol / nuclear retinoid X receptor binding / response to retinoic acid / progesterone receptor signaling pathway / Transcriptional regulation of brown and beige adipocyte differentiation by EBF2 / retinoic acid receptor signaling pathway / cellular response to hormone stimulus / histone H4K16 acetyltransferase activity / histone H3K56 acetyltransferase activity / histone H3K23 acetyltransferase activity / histone H2AK5 acetyltransferase activity / histone H2AK9 acetyltransferase activity / histone H2BK5 acetyltransferase activity / histone H2BK12 acetyltransferase activity / histone H3K4 acetyltransferase activity / histone H3K27 acetyltransferase activity / histone H3K36 acetyltransferase activity / histone H3K122 acetyltransferase activity / histone H3K18 acetyltransferase activity / histone H3K9 acetyltransferase activity / histone H3K14 acetyltransferase activity / histone H4K5 acetyltransferase activity / histone H4K8 acetyltransferase activity / histone H4K12 acetyltransferase activity / Recycling of bile acids and salts / histone acetyltransferase / estrous cycle / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / cellular response to retinoic acid / estrogen receptor signaling pathway / positive regulation of cell cycle / positive regulation of adipose tissue development / : / lactation / Regulation of lipid metabolism by PPARalpha / peroxisome proliferator activated receptor signaling pathway / regulation of cellular response to insulin stimulus / response to cytokine / positive regulation of neuron differentiation / cerebellum development / BMAL1:CLOCK,NPAS2 activates circadian expression / mRNA regulatory element binding translation repressor activity / negative regulation of miRNA transcription / SUMOylation of transcription cofactors / Activation of gene expression by SREBF (SREBP) / liver development / hippocampus development / response to progesterone / nuclear receptor binding / RNA polymerase II transcription regulatory region sequence-specific DNA binding / nuclear estrogen receptor binding / female pregnancy / neural tube closure
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 / Nuclear receptor coactivators bHLH domain / PAS 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 / Retinoid X Receptor / Retinoid X Receptor / PAS domain superfamily / Nuclear hormone receptor / Nuclear hormones receptors DNA-binding region signature. / Zinc finger, nuclear hormone receptor-type / Double treble clef zinc finger, C4 type / 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 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-EQN / Retinoic acid receptor alpha / Nuclear receptor coactivator 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsBourguet, W. / Teyssier, C.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2010
Title: A unique secondary-structure switch controls constitutive gene repression by retinoic acid receptor.
Authors: le Maire, A. / Teyssier, C. / Erb, C. / Grimaldi, M. / Alvarez, S. / de Lera, A.R. / Balaguer, P. / Gronemeyer, H. / Royer, C.A. / Germain, P. / Bourguet, W.
History
DepositionNov 11, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 2, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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: Nuclear receptor coactivator 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,9113
Polymers31,5592
Non-polymers3511
Water2,180121
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area990 Å2
ΔGint-9 kcal/mol
Surface area11270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.307, 61.218, 49.444
Angle α, β, γ (deg.)90.00, 105.38, 90.00
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 29967.590 Da / Num. of mol.: 1 / Fragment: ligand binding domain (UNP RESIDUE 176-421)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NR1B1, RARA / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P10276
#2: Protein/peptide Nuclear receptor coactivator 1 / NCoA-1 / Steroid receptor coactivator 1 / SRC-1 / RIP160 / Protein Hin-2 / Renal carcinoma antigen NY-REN-52


Mass: 1591.880 Da / Num. of mol.: 1 / Fragment: NR interaction motif 2 (UNP RESIDUE 686-698) / Source method: obtained synthetically / Details: synthetic / References: UniProt: Q15788, histone acetyltransferase
#3: Chemical ChemComp-EQN / 4-{[(5,5,8,8-tetramethyl-5,6,7,8-tetrahydronaphthalen-2-yl)carbonyl]amino}benzoic acid


Mass: 351.439 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H25NO3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 121 / 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: 2.19 Å3/Da / Density % sol: 39.75 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 15% (w/v) PEG 6000, 5% (w/v) glycerol, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.9395 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 14, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9395 Å / Relative weight: 1
ReflectionResolution: 1.8→35 Å / Num. all: 22172 / Num. obs: 22172 / Redundancy: 2.6 % / Biso Wilson estimate: 25.51 Å2 / Rmerge(I) obs: 0.03 / Rsym value: 0.043 / Net I/σ(I): 16.2
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.226 / Mean I/σ(I) obs: 3.6 / Num. unique all: 2665 / Rsym value: 0.319

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
MOLREPphasing
REFMAC5.4.0062refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1DKF

1dkf


Resolution: 1.8→32.02 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.927 / SU B: 6.423 / SU ML: 0.093 / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / ESU R: 0.147 / ESU R Free: 0.138 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23716 720 3.2 %RANDOM
Rwork0.19744 ---
obs0.19875 21452 93.78 %-
all-22172 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.809 Å2
Baniso -1Baniso -2Baniso -3
1--0.43 Å20 Å2-0.84 Å2
2--0.19 Å20 Å2
3----0.21 Å2
Refinement stepCycle: LAST / Resolution: 1.8→32.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1937 0 26 121 2084
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0222000
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.72.0142707
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.4695244
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.71224.45883
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.8315384
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.5191514
X-RAY DIFFRACTIONr_chiral_restr0.0730.2318
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0211451
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.491.51225
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.9821994
X-RAY DIFFRACTIONr_scbond_it1.753775
X-RAY DIFFRACTIONr_scangle_it2.7714.5712
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.294 40 -
Rwork0.274 1205 -
obs--71.18 %
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)
12.9204-1.20561.19431.1517-0.43192.2730.00760.2930.0291-0.0271-0.08490.0439-0.20140.17840.0773-0.11740.02850.0157-0.02730.0028-0.1778-8.279-0.212-13.845
28.87081.4022-1.886924.5453-3.250312.23240.1747-0.4924-0.14380.8383-0.14241.00250.0664-0.2588-0.0323-0.0620.05270.11290.07990.047-0.0381-23.807-4.43-1.372
38.03488.713410.993112.24249.974424.92410.18630.1062-0.2429-0.11560.00460.17170.09050.1369-0.1908-0.10210.06420.01330.0012-0.0396-0.0488-8.152-8.617-13.124
41.8425-0.48920.75870.6144-0.3931.45320.02490.1219-0.1372-0.0359-0.05530.0805-0.13130.13240.0304-0.06650.01040.01040.0127-0.0006-0.0934-6.854-4.281-11.705
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A182 - 415
2X-RAY DIFFRACTION2C629 - 639
3X-RAY DIFFRACTION3B1
4X-RAY DIFFRACTION4D1 - 85

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