[English] 日本語
Yorodumi
- PDB-3m9e: Thyroid hormone beta DNA binding domain homodimer with inverted p... -

+
Open data


ID or keywords:

Loading...

-
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


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 / Nuclear Receptor transcription pathway / thyroid hormone receptor signaling pathway / positive regulation of thyroid hormone receptor signaling pathway ...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 / Nuclear Receptor transcription pathway / thyroid hormone receptor signaling pathway / positive regulation of thyroid hormone receptor signaling pathway / positive regulation of ossification / cellular response to thyroid hormone stimulus / regulation of cholesterol metabolic process / regulation of heart contraction / type I pneumocyte differentiation / thyroid hormone binding / regulation of lipid metabolic process / embryonic organ development / retinoic acid receptor signaling pathway / animal organ morphogenesis / sensory perception of sound / mRNA transcription by RNA polymerase II / chromatin DNA binding / transcription coactivator binding / RNA polymerase II transcription regulator complex / nuclear receptor activity / sequence-specific double-stranded DNA binding / double-stranded DNA binding / cell differentiation / RNA polymerase II cis-regulatory region sequence-specific DNA binding / negative regulation of DNA-templated transcription / chromatin binding / positive regulation of cell population proliferation / regulation of transcription by RNA polymerase II / negative regulation of transcription by RNA polymerase II / enzyme binding / 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 ...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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

-
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

-
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

-
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)

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more