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- PDB-3m9e: Thyroid hormone beta DNA binding domain homodimer with inverted p... -

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Basic information

Entry
Database: PDB / ID: 3m9e
TitleThyroid hormone beta DNA binding domain homodimer with inverted palindrome TRE
Components
  • DNA (5'-D(*AP*TP*TP*GP*AP*CP*CP*TP*CP*AP*GP*CP*TP*GP*AP*GP*GP*TP*CP*AP*AP*T)-3')
  • Thyroid hormone receptor beta
KeywordsTRANSCRIPTION/DNA / PROTEIN-DNA COMPLEX / DNA-binding / Metal-binding / Nucleus / Receptor / Transcription / Transcription regulation / Zinc-finger / TRANSCRIPTION-DNA complex
Function / homology
Function and homology information


negative regulation of eye photoreceptor cell development / regulation of triglyceride metabolic process / retinal cone cell apoptotic process / negative regulation of female receptivity / female courtship behavior / retinal cone cell development / SUMOylation of intracellular receptors / positive regulation of chondrocyte differentiation / thyroid hormone receptor signaling pathway / Nuclear Receptor transcription pathway ...negative regulation of eye photoreceptor cell development / regulation of triglyceride metabolic process / retinal cone cell apoptotic process / negative regulation of female receptivity / female courtship behavior / retinal cone cell development / SUMOylation of intracellular receptors / positive regulation of chondrocyte differentiation / thyroid hormone receptor signaling pathway / Nuclear Receptor transcription pathway / positive regulation of ossification / regulation of cholesterol metabolic process / regulation of heart contraction / type I pneumocyte differentiation / thyroid hormone binding / transcription factor binding / regulation of lipid metabolic process / embryonic organ development / hormone-mediated signaling pathway / animal organ morphogenesis / sensory perception of sound / RNA polymerase II transcription regulatory region sequence-specific DNA binding / chromatin DNA binding / RNA polymerase II transcription regulator complex / nuclear receptor activity / signaling receptor activity / double-stranded DNA binding / cell differentiation / negative regulation of DNA-templated transcription / host cell nucleus / positive regulation of cell population proliferation / regulation of transcription by RNA polymerase II / enzyme binding / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / zinc ion binding / identical protein binding / nucleus
Similarity search - Function
Erythroid Transcription Factor GATA-1, subunit A / Erythroid Transcription Factor GATA-1; Chain A / Thyroid hormone receptor / 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 ...Erythroid Transcription Factor GATA-1, subunit A / Erythroid Transcription Factor GATA-1; Chain A / Thyroid hormone receptor / 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 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
DNA / DNA (> 10) / Thyroid hormone receptor beta
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.406 Å
AuthorsChen, Y.
CitationJournal: Mol.Endocrinol. / Year: 2010
Title: Structure of a thyroid hormone receptor DNA-binding domain homodimer bound to an inverted palindrome DNA response element.
Authors: Chen, Y. / Young, M.A.
History
DepositionMar 22, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 18, 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 / pdbx_struct_conn_angle / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _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: Thyroid hormone receptor beta
B: Thyroid hormone receptor beta
C: DNA (5'-D(*AP*TP*TP*GP*AP*CP*CP*TP*CP*AP*GP*CP*TP*GP*AP*GP*GP*TP*CP*AP*AP*T)-3')
D: DNA (5'-D(*AP*TP*TP*GP*AP*CP*CP*TP*CP*AP*GP*CP*TP*GP*AP*GP*GP*TP*CP*AP*AP*T)-3')
E: Thyroid hormone receptor beta
F: Thyroid hormone receptor beta
G: DNA (5'-D(*AP*TP*TP*GP*AP*CP*CP*TP*CP*AP*GP*CP*TP*GP*AP*GP*GP*TP*CP*AP*AP*T)-3')
H: DNA (5'-D(*AP*TP*TP*GP*AP*CP*CP*TP*CP*AP*GP*CP*TP*GP*AP*GP*GP*TP*CP*AP*AP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,86216
Polymers76,3398
Non-polymers5238
Water4,179232
1
A: Thyroid hormone receptor beta
B: Thyroid hormone receptor beta
C: DNA (5'-D(*AP*TP*TP*GP*AP*CP*CP*TP*CP*AP*GP*CP*TP*GP*AP*GP*GP*TP*CP*AP*AP*T)-3')
D: DNA (5'-D(*AP*TP*TP*GP*AP*CP*CP*TP*CP*AP*GP*CP*TP*GP*AP*GP*GP*TP*CP*AP*AP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,4318
Polymers38,1704
Non-polymers2624
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6500 Å2
ΔGint-44 kcal/mol
Surface area17810 Å2
MethodPISA
2
E: Thyroid hormone receptor beta
F: Thyroid hormone receptor beta
G: DNA (5'-D(*AP*TP*TP*GP*AP*CP*CP*TP*CP*AP*GP*CP*TP*GP*AP*GP*GP*TP*CP*AP*AP*T)-3')
H: DNA (5'-D(*AP*TP*TP*GP*AP*CP*CP*TP*CP*AP*GP*CP*TP*GP*AP*GP*GP*TP*CP*AP*AP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,4318
Polymers38,1704
Non-polymers2624
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5630 Å2
ΔGint-37 kcal/mol
Surface area18570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.738, 83.468, 75.743
Angle α, β, γ (deg.)90.00, 98.28, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Thyroid hormone receptor beta / c-erbA-beta / c-erbA-2 / Nuclear receptor subfamily 1 group A member 2


Mass: 12333.387 Da / Num. of mol.: 4 / Fragment: DNA binding domain (UNP residues 104 to 206)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Erba2, Nr1a2, ROD, Thrb / Plasmid: ppSUMO / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(Rossetta2) / References: UniProt: P18113
#2: DNA chain
DNA (5'-D(*AP*TP*TP*GP*AP*CP*CP*TP*CP*AP*GP*CP*TP*GP*AP*GP*GP*TP*CP*AP*AP*T)-3')


Mass: 6751.379 Da / Num. of mol.: 4 / Source method: obtained synthetically / Details: The sequence is idealized
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 232 / 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: 2

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Sample preparation

CrystalDensity Matthews: 3.02 Å3/Da / Density % sol: 59.29 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 20% PEG 3350, 0.2M ammonium sulfate, 0.05M Bis-Tris, 5mM MgCl2, 2uM ZnCl2, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.979 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 2, 2009
RadiationMonochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.4→42.2 Å / Num. all: 35442 / Num. obs: 34766 / % possible obs: 98.1 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 6.7 % / Net I/σ(I): 27.1
Reflection shellResolution: 2.4→2.49 Å / % possible all: 92.1

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHENIXmodel building
PHENIX(phenix.refine: 1.6_289)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2NLL

2nll


Resolution: 2.406→42.182 Å / SU ML: 0.32 / σ(F): 1.33 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2308 1767 5.08 %RANDOM
Rwork0.1794 ---
all0.1902 35442 --
obs0.1819 34766 98.09 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 49.332 Å2 / ksol: 0.356 e/Å3
Refinement stepCycle: LAST / Resolution: 2.406→42.182 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3265 1788 8 232 5293
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.015363
X-RAY DIFFRACTIONf_angle_d1.3087560
X-RAY DIFFRACTIONf_dihedral_angle_d24.6762182
X-RAY DIFFRACTIONf_chiral_restr0.068816
X-RAY DIFFRACTIONf_plane_restr0.004655
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.406-2.4710.31381220.28112346X-RAY DIFFRACTION91
2.471-2.54380.29821400.2582469X-RAY DIFFRACTION96
2.5438-2.62580.28311290.24182499X-RAY DIFFRACTION97
2.6258-2.71970.30781470.22362511X-RAY DIFFRACTION98
2.7197-2.82860.28191480.23242525X-RAY DIFFRACTION99
2.8286-2.95730.29691340.21922530X-RAY DIFFRACTION99
2.9573-3.11310.25631340.2232572X-RAY DIFFRACTION99
3.1131-3.30810.29861370.19192549X-RAY DIFFRACTION98
3.3081-3.56340.20451730.17472500X-RAY DIFFRACTION99
3.5634-3.92180.20251300.15372600X-RAY DIFFRACTION100
3.9218-4.48870.18541240.14282612X-RAY DIFFRACTION100
4.4887-5.65310.18621280.14262617X-RAY DIFFRACTION100
5.6531-42.18840.18131210.14172669X-RAY DIFFRACTION100
Refinement TLS params.

Refine-ID: X-RAY DIFFRACTION

IDMethodL11 (°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)
1refined2.2781-0.46640.28260.4519-1.04651.34050.164-0.3048-0.4288-0.04990.29770.32040.0678-0.1882-0.39730.259-0.0451-0.0770.33030.16420.483231.6659.358248.1412
23.9923-1.22621.65050.4766-0.92863.1980.403-0.0033-0.1652-0.17191.00591.0818-0.1829-0.9419-0.74970.23380.09140.15750.4490.36810.6311
34.87350.29651.10340.91891.43342.3328-0.90620.0360.13320.20350.07031.46751.43130.87140.66471.46640.1370.16621.24670.60291.6403
44.06590.28750.14821.5483-0.15710.0429-0.1142-0.07810.339-0.09020.20290.02670.0483-0.079-0.01750.1819-0.0099-0.02880.1659-0.02530.0829
54.6268-2.8711-1.09732.88822.32263.00590.4227-0.61491.5662-0.3447-0.2106-1.5322-0.71720.2497-0.35230.3537-0.04340.07890.223-0.26130.78
64.88013.656-0.22715.94840.89020.387-0.02220.38150.15881.1042-0.8683-0.0047-0.07830.00580.78281.2983-0.26020.23831.23180.26671.7796
74.78461.3459-0.63592.5771-0.39291.0364-0.15231.21342.4643-0.02710.53420.1207-0.0906-0.1253-0.40310.2801-0.08410.03690.49970.32620.9042
84.6046-0.8291-0.21363.1381-1.1520.3682-0.4095-0.10590.85730.54940.72060.2964-0.3434-0.2902-0.32630.24470.06780.04610.32080.12980.5186
94.8514-0.43641.06134.1407-0.51250.7735-0.26650.25191.40870.27070.4291-0.1909-0.1527-0.3892-0.13050.20280.09670.04530.36530.18580.4931
108.87811.00740.90140.35180.3434-0.0178-0.79520.92282.1644-0.34710.62540.0576-0.0913-0.37490.06530.2514-0.10920.0350.4170.28530.8494
112.0088-0.8571-0.05471.37620.68391.68740.0112-0.2439-0.32750.05420.2820.25230.08150.2641-0.21590.2192-0.03350.02130.3532-0.04180.2681
123.6048-0.8503-0.32721.8950.13461.5360.24610.71170.1468-0.11330.1270.00580.2150.1044-0.24240.3016-0.0195-0.0350.3852-0.16460.2187
135.92132.322-0.0643.7411-1.98391.36810.4471-0.1618-1.0965-0.9886-0.7947-0.2986-0.0307-0.14250.1870.90770.4187-0.37480.794-0.41120.9696
145.34480.7441-0.63690.8125-0.44310.78820.1340.21280.41690.0753-0.01580.38650.0211-0.0267-0.11960.22930.02170.0460.2392-0.01920.4465
152.2488-0.23560.05943.1854-2.89642.6958-0.4330.37290.077-1.08-1.2641-1.9465-0.4036-0.01271.63330.6534-0.04190.04790.32610.12430.8281
167.1953-0.84421.32870.1433-0.38352.2691-0.0552-0.6832-0.5334-0.0761-0.56760.31890.10090.02210.25491.1636-0.24810.16440.6125-0.02391.2489
170.54210.23860.22654.7506-1.24520.9619-0.26320.8615-1.0118-0.06110.47320.12840.11540.0447-0.18740.2929-0.06860.02950.4657-0.12370.5973
185.8878-2.83370.07891.88790.59211.0348-0.26870.1666-1.4010.60460.64770.58370.45660.3585-0.28730.37150.0711-0.01580.381-0.14620.8532
194.5338-3.09261.31245.4150.80961.84650.01460.5756-1.80740.32280.34130.71940.20560.43-0.41850.20320.0757-0.02390.3529-0.15350.4945
205.115-0.3924-0.41681.082-0.21090.1971-0.67450.37-0.9302-0.53530.44040.2771-0.0077-0.18270.16160.2652-0.1376-0.00930.4323-0.18450.5414
Refinement TLS groupSelection details: chain H and resid 12:22)

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