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- PDB-1bsx: STRUCTURE AND SPECIFICITY OF NUCLEAR RECEPTOR-COACTIVATOR INTERACTIONS -

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Basic information

Entry
Database: PDB / ID: 1bsx
TitleSTRUCTURE AND SPECIFICITY OF NUCLEAR RECEPTOR-COACTIVATOR INTERACTIONS
Components
  • PROTEIN (GRIP1)
  • PROTEIN (THYROID HORMONE RECEPTOR BETA)
KeywordsHORMONE/GROWTH FACTOR / NUCLEAR RECEPTORS / COACTIVATORS / GRIP1 / SPECIFICITY INTERACTION SITE / HORMONE-GROWTH FACTOR COMPLEX
Function / homology
Function and homology information


retinal cone cell apoptotic process / negative regulation of female receptivity / female courtship behavior / thyroid hormone binding / retinal cone cell development / thyroid hormone receptor signaling pathway / positive regulation of thyroid hormone receptor signaling pathway / cellular response to thyroid hormone stimulus / regulation of heart contraction / type I pneumocyte differentiation ...retinal cone cell apoptotic process / negative regulation of female receptivity / female courtship behavior / thyroid hormone binding / retinal cone cell development / thyroid hormone receptor signaling pathway / positive regulation of thyroid hormone receptor signaling pathway / cellular response to thyroid hormone stimulus / regulation of heart contraction / type I pneumocyte differentiation / retinoic acid receptor signaling pathway / SUMOylation of intracellular receptors / mRNA transcription by RNA polymerase II / sensory perception of sound / chromatin DNA binding / Nuclear Receptor transcription pathway / transcription coactivator binding / RNA polymerase II transcription regulator complex / nuclear receptor activity / sequence-specific double-stranded DNA binding / DNA-binding transcription factor activity, RNA polymerase II-specific / cell differentiation / nuclear body / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / DNA-templated transcription / chromatin / enzyme binding / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / DNA binding / zinc ion binding / nucleoplasm / nucleus
Similarity search - Function
Thyroid hormone receptor / : / Retinoid X Receptor / Retinoid X Receptor / 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 ...Thyroid hormone receptor / : / Retinoid X Receptor / Retinoid X Receptor / 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
3,5,3'TRIIODOTHYRONINE / Thyroid hormone receptor beta
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3.7 Å
AuthorsWagner, R.L. / Darimont, B.D. / Apriletti, J.W. / Stallcup, M.R. / Kushner, P.J. / Baxter, J.D. / Fletterick, R.J. / Yamamoto, K.R.
CitationJournal: Genes Dev. / Year: 1998
Title: Structure and specificity of nuclear receptor-coactivator interactions.
Authors: Darimont, B.D. / Wagner, R.L. / Apriletti, J.W. / Stallcup, M.R. / Kushner, P.J. / Baxter, J.D. / Fletterick, R.J. / Yamamoto, K.R.
History
DepositionAug 31, 1998Deposition site: BNL / Processing site: RCSB
Revision 1.0Aug 26, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 30, 2018Group: Data collection / Derived calculations / Experimental preparation
Category: exptl_crystal / pdbx_struct_assembly ...exptl_crystal / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop
Item: _exptl_crystal.density_Matthews
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 2.1Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PROTEIN (THYROID HORMONE RECEPTOR BETA)
X: PROTEIN (GRIP1)
B: PROTEIN (THYROID HORMONE RECEPTOR BETA)
Y: PROTEIN (GRIP1)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,1396
Polymers61,8374
Non-polymers1,3022
Water00
1
A: PROTEIN (THYROID HORMONE RECEPTOR BETA)
X: PROTEIN (GRIP1)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,5703
Polymers30,9192
Non-polymers6511
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1740 Å2
ΔGint-11 kcal/mol
Surface area11910 Å2
MethodPISA
2
B: PROTEIN (THYROID HORMONE RECEPTOR BETA)
Y: PROTEIN (GRIP1)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,5703
Polymers30,9192
Non-polymers6511
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1740 Å2
ΔGint-11 kcal/mol
Surface area11910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.200, 95.200, 137.600
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.52697, 0.84909, -0.03674), (-0.41049, 0.29214, 0.8638), (0.74418, -0.44012, 0.50249)
Vector: -68.69247, 48.3266, -6.73853)

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Components

#1: Protein PROTEIN (THYROID HORMONE RECEPTOR BETA)


Mass: 29410.996 Da / Num. of mol.: 2 / Fragment: LIGAND BINDING DOMAIN
Source method: isolated from a genetically manipulated source
Details: HIS-TAGGED (THE FOLLOWING RESIDUES WERE NOT SEEN IN THE ELECTRON DENSITY: MGSSHHHHHHSSGLVPRGSHM)
Source: (gene. exp.) Homo sapiens (human) / Plasmid: PET28 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21DE3 / References: UniProt: P10828
#2: Protein/peptide PROTEIN (GRIP1) / MTIF2


Mass: 1507.738 Da / Num. of mol.: 2 / Fragment: NR-BOX2 FROM NUCLEAR RECEPTOR INTERACTION DOMAIN / Source method: obtained synthetically
#3: Chemical ChemComp-T3 / 3,5,3'TRIIODOTHYRONINE / T3 / THYROID HORMONE / LIOTHYRONINE


Mass: 650.973 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H12I3NO4

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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: 2.91 Å3/Da / Density % sol: 52 %
Crystal growpH: 4.9 / Details: pH 4.9
Crystal
*PLUS
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
215 %PEG40001drop
3200 mMsodium citrate1drop
410 %PEG40001reservoir
5100 mMammonium acetate1reservoir
650 mMsodium citrate1reservoir
1peptide1drop

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Data collection

DiffractionMean temperature: 105 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Nov 15, 1997
RadiationMonochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 3.6→25 Å / Num. obs: 8490 / % possible obs: 96.3 % / Observed criterion σ(I): -3 / Redundancy: 4 % / Rmerge(I) obs: 0.077 / Rsym value: 0.077 / Net I/σ(I): 12
Reflection shellResolution: 3.6→3.66 Å / Rmerge(I) obs: 0.261 / Mean I/σ(I) obs: 3.7 / Rsym value: 0.261 / % possible all: 96.3
Reflection
*PLUS
Num. measured all: 35565
Reflection shell
*PLUS
% possible obs: 96.3 % / Num. unique obs: 411

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Processing

Software
NameClassification
AMoREphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: HUMAN THYROID HORMONE RECEPTOR BETA

Resolution: 3.7→100 Å / Data cutoff high rms absF: 10000 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.299 775 10 %RANDOM
Rwork0.249 ---
obs0.249 7851 96.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 36 Å2 / ksol: 0.27 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.717 Å2-2.278 Å20 Å2
2---0.717 Å20 Å2
3---1.434 Å2
Refinement stepCycle: LAST / Resolution: 3.7→100 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3994 0 46 0 4040
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
Refine LS restraints NCSNCS model details: STRICT
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2TIT.PARTIT.TOP
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
Highest resolution: 3.7 Å / Num. reflection all: 7851 / Num. reflection obs: 7614 / σ(F): 2 / % reflection Rfree: 10 % / Rfactor all: 0.254
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0098
X-RAY DIFFRACTIONc_angle_deg1.6

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