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

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Basic information

Entry
Database: PDB / ID: 3kmz
TitleCrystal structure of RARalpha ligand binding domain in complex with the inverse agonist BMS493 and a corepressor fragment
Components
  • Nuclear receptor corepressor 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 / Chromatin regulator / Repressor
Function / homology
Function and homology information


Sertoli cell fate commitment / positive regulation of binding / NR1D1 (REV-ERBA) represses gene expression / trachea cartilage development / ventricular cardiac muscle cell differentiation / chondroblast differentiation / embryonic camera-type eye development / glandular epithelial cell development / Loss of MECP2 binding ability to the NCoR/SMRT complex / protein kinase B binding ...Sertoli cell fate commitment / positive regulation of binding / NR1D1 (REV-ERBA) represses gene expression / trachea cartilage development / ventricular cardiac muscle cell differentiation / chondroblast differentiation / embryonic camera-type eye development / glandular epithelial cell development / Loss of MECP2 binding ability to the NCoR/SMRT complex / protein kinase B binding / growth plate cartilage development / regulation of hematopoietic progenitor cell differentiation / negative regulation of granulocyte differentiation / positive regulation of T-helper 2 cell differentiation / prostate gland development / negative regulation of cartilage development / negative regulation of androgen receptor signaling pathway / retinoic acid-responsive element binding / positive regulation of interleukin-5 production / negative regulation of JNK cascade / retinoic acid binding / response to vitamin A / negative regulation of glycolytic process / apoptotic cell clearance / limb development / nuclear thyroid hormone receptor binding / ureteric bud development / protein kinase A binding / regulation of myelination / Signaling by Retinoic Acid / DNA-binding transcription repressor activity / positive regulation of interleukin-13 production / heterocyclic compound binding / NR1H2 & NR1H3 regulate gene expression to control bile acid homeostasis / negative regulation of fatty acid metabolic process / Notch-HLH transcription pathway / face development / alpha-actinin binding / germ cell development / locomotor rhythm / histone deacetylase complex / negative regulation of type II interferon production / Regulation of MECP2 expression and activity / negative regulation of tumor necrosis factor production / positive regulation of interleukin-4 production / spindle assembly / retinoic acid receptor signaling pathway / cellular response to estrogen stimulus / positive regulation of cell cycle / response to retinoic acid / cellular response to retinoic acid / Nuclear signaling by ERBB4 / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / transcription repressor complex / positive regulation of neuron differentiation / Regulation of lipid metabolism by PPARalpha / hormone-mediated signaling pathway / mRNA regulatory element binding translation repressor activity / negative regulation of miRNA transcription / liver development / female pregnancy / response to cytokine / neural tube closure / HDACs deacetylate histones / nuclear receptor binding / hippocampus development / Downregulation of SMAD2/3:SMAD4 transcriptional activity / RNA polymerase II transcription regulatory region sequence-specific DNA binding / regulation of synaptic plasticity / multicellular organism growth / Heme signaling / SUMOylation of intracellular receptors / mRNA transcription by RNA polymerase II / Transcriptional activation of mitochondrial biogenesis / mRNA 5'-UTR binding / transcription coactivator binding / PPARA activates gene expression / Cytoprotection by HMOX1 / NOTCH1 Intracellular Domain Regulates Transcription / chromatin DNA binding / mitotic spindle / Constitutive Signaling by NOTCH1 PEST Domain Mutants / Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants / Transcriptional regulation of white adipocyte differentiation / Activation of anterior HOX genes in hindbrain development during early embryogenesis / HCMV Early Events / Nuclear Receptor transcription pathway / Transcriptional regulation of granulopoiesis / histone deacetylase binding / RNA polymerase II transcription regulator complex / transcription corepressor activity / nuclear receptor activity / Circadian Clock / sequence-specific double-stranded DNA binding / actin cytoskeleton / response to estradiol / chromatin organization / response to ethanol / regulation of apoptotic process / cellular response to lipopolysaccharide
Similarity search - Function
: / : / N-CoR, GPS2-interacting domain / G-protein pathway suppressor 2-interacting domain / Retinoic acid receptor / SANT domain profile. / SANT domain / Myb domain / Myb-like DNA-binding domain / SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains ...: / : / N-CoR, GPS2-interacting domain / G-protein pathway suppressor 2-interacting domain / Retinoic acid receptor / SANT domain profile. / SANT domain / Myb domain / Myb-like DNA-binding domain / SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains / SANT/Myb domain / Retinoid X Receptor / Retinoid X Receptor / Homeobox-like 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 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-EQO / Nuclear receptor corepressor 1 / Retinoic acid receptor alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsBourguet, W. / le Maire, A.
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_conn / 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_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 22, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: Retinoic acid receptor alpha
C: Nuclear receptor corepressor 1
A: Retinoic acid receptor alpha
D: Nuclear receptor corepressor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,06615
Polymers64,4284
Non-polymers1,63811
Water5,368298
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7410 Å2
ΔGint-50 kcal/mol
Surface area21560 Å2
MethodPISA
2
B: Retinoic acid receptor alpha
C: Nuclear receptor corepressor 1
hetero molecules

B: Retinoic acid receptor alpha
C: Nuclear receptor corepressor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,97414
Polymers64,4284
Non-polymers1,54610
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_454-x-1,y,-z-11
Buried area7820 Å2
ΔGint-52 kcal/mol
Surface area21130 Å2
MethodPISA
3
A: Retinoic acid receptor alpha
D: Nuclear receptor corepressor 1
hetero molecules

A: Retinoic acid receptor alpha
D: Nuclear receptor corepressor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,15816
Polymers64,4284
Non-polymers1,73012
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-x-1,y,-z1
Buried area7920 Å2
ΔGint-51 kcal/mol
Surface area21080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.831, 105.625, 53.382
Angle α, β, γ (deg.)90.00, 89.92, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11B
21A
12C
22D
/ NCS ensembles :
ID
1
2

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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.: 2 / Fragment: ligand binding domain
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 corepressor 1 / N-CoR1 / N-CoR


Mass: 2246.609 Da / Num. of mol.: 2 / Fragment: NR1 / Source method: obtained synthetically / Details: synthetic / References: UniProt: O75376
#3: Chemical ChemComp-EQO / 4-{(E)-2-[5,5-dimethyl-8-(phenylethynyl)-5,6-dihydronaphthalen-2-yl]ethenyl}benzoic acid


Mass: 404.500 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C29H24O2
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 298 / 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: 2.46 Å3/Da / Density % sol: 49.99 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 18% PEG 3350 (w/v), 0.15M NH4Cl, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 4, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 2.1→43.4 Å / Num. all: 32768 / Num. obs: 32768 / Redundancy: 2.8 % / Rmerge(I) obs: 0.064 / Rsym value: 0.079 / Net I/σ(I): 13.2
Reflection shellResolution: 2.1→2.21 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.341 / Mean I/σ(I) obs: 3 / Rsym value: 0.422

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Processing

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

1dkf


Resolution: 2.1→43.4 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.933 / SU B: 9.837 / SU ML: 0.12 / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / ESU R: 0.205 / ESU R Free: 0.184 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22973 1666 5.1 %RANDOM
Rwork0.17205 ---
obs0.17497 31093 96.59 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.592 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20.01 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.1→43.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3798 0 116 298 4212
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0224026
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2162.0175441
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg11.865.08498
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.31424.419172
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.81515752
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.6451530
X-RAY DIFFRACTIONr_chiral_restr0.0720.2635
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0212928
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_it0.5261.52425
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.03723956
X-RAY DIFFRACTIONr_scbond_it1.56931601
X-RAY DIFFRACTIONr_scangle_it2.5734.51476
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1B1740medium positional0.180.5
2C156medium positional0.170.5
1B1740medium thermal0.272
2C156medium thermal0.282
LS refinement shellResolution: 2.1→2.155 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.246 124 -
Rwork0.211 2319 -
obs--98.51 %
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)
10.7596-0.02870.22790.87380.30831.06440.062-0.02-0.12-0.01330.00590.01790.03810.0232-0.0679-0.05940.0329-0.0194-0.04530.0003-0.0003-39.9021.219-20.005
20.7990.0056-0.24820.89960.26931.03170.06610.01670.12350.0194-0.0030.0157-0.03280.0165-0.0631-0.0632-0.03320.0277-0.04370.00120.0009-39.88249.597-6.686
34.8826-5.5187-3.59696.34063.99482.69840.19950.11880.3001-0.53510.0748-0.1814-0.33310.2414-0.27430.0142-0.01370.0290.0076-0.0389-0.0341-33.05114.684-29.904
43.71214.77363.90986.84875.094.21670.09280.0193-0.31680.46160.2138-0.2630.26710.2924-0.3066-0.0030.0006-0.0275-0.0027-0.0327-0.0417-33.08636.0833.156
510.18796.24141.00724.13242.34789.8029-0.09420.90110.65430.0662-0.1708-0.0025-0.2176-0.06840.2651-0.0240.0514-0.01550.00370.0184-0.0169-38.51510.375-17.965
611.0316-5.4396-0.59063.13312.15217.7113-0.5406-0.6981-1.0704-0.7486-0.0206-0.13040.384-0.05670.5611-0.0194-0.05380.00920.02070.03460.0119-38.49240.414-8.741
70.06820.01690.02890.58510.07610.14620.0302-0.00270.0177-0.0109-0.03060.03160.00630.06560.0005-0.0534-0.00220.00710.00680.0037-0.0311-38.10526.347-12.702
80.9754-0.45040.03272.08830.50210.14340.0765-0.03640.0945-0.01110.2731-0.45290.0115-0.1293-0.3496-0.0567-0.0191-0.04190.0674-0.0115-0.1372-42.54729.148-10.849
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1B182 - 401
2X-RAY DIFFRACTION2A182 - 401
3X-RAY DIFFRACTION3C2047 - 2065
4X-RAY DIFFRACTION4D2047 - 2065
5X-RAY DIFFRACTION5X1
6X-RAY DIFFRACTION6X2
7X-RAY DIFFRACTION7F1 - 298
8X-RAY DIFFRACTION8G1 - 9

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