[English] 日本語
Yorodumi
- PDB-4whf: Crystal Structure of TR3 LBD in complex with 1-(3,4,5-trihydroxyp... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4whf
TitleCrystal Structure of TR3 LBD in complex with 1-(3,4,5-trihydroxyphenyl)decan-1-one
ComponentsNuclear receptor subfamily 4 group A member 1
KeywordsTRANSCRIPTION / LBD
Function / homology
Function and homology information


neurotransmitter secretion involved in regulation of skeletal muscle contraction / regulation of type B pancreatic cell proliferation / non-canonical inflammasome complex assembly / detection of lipopolysaccharide / cellular response to corticotropin-releasing hormone stimulus / AKT phosphorylates targets in the nucleus / endothelial cell chemotaxis / nuclear glucocorticoid receptor binding / cellular response to fibroblast growth factor stimulus / cell migration involved in sprouting angiogenesis ...neurotransmitter secretion involved in regulation of skeletal muscle contraction / regulation of type B pancreatic cell proliferation / non-canonical inflammasome complex assembly / detection of lipopolysaccharide / cellular response to corticotropin-releasing hormone stimulus / AKT phosphorylates targets in the nucleus / endothelial cell chemotaxis / nuclear glucocorticoid receptor binding / cellular response to fibroblast growth factor stimulus / cell migration involved in sprouting angiogenesis / fat cell differentiation / skeletal muscle cell differentiation / Constitutive Signaling by AKT1 E17K in Cancer / negative regulation of cell cycle / cellular response to vascular endothelial growth factor stimulus / response to electrical stimulus / positive regulation of endothelial cell proliferation / response to amphetamine / lipopolysaccharide binding / Nuclear Receptor transcription pathway / nuclear receptor activity / sequence-specific double-stranded DNA binding / presynapse / DNA-binding transcription activator activity, RNA polymerase II-specific / nuclear membrane / transcription regulator complex / transcription by RNA polymerase II / DNA-binding transcription factor activity, RNA polymerase II-specific / inflammatory response / positive regulation of apoptotic process / protein heterodimerization activity / RNA polymerase II cis-regulatory region sequence-specific DNA binding / apoptotic process / chromatin / regulation of transcription by RNA polymerase II / signal transduction / positive regulation of transcription by RNA polymerase II / mitochondrion / DNA binding / zinc ion binding / nucleoplasm / identical protein binding / nucleus / cytosol
Similarity search - Function
Orphan nuclear receptor, HMR type / Orphan nuclear receptor / Retinoid X Receptor / Retinoid X 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 ...Orphan nuclear receptor, HMR type / Orphan nuclear receptor / Retinoid X Receptor / Retinoid X 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 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
1-(3,4,5-trihydroxyphenyl)decan-1-one / Nuclear receptor subfamily 4immunitygroup A member 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.27 Å
AuthorsLi, F.W. / Cai, Q.X. / Li, A.Z. / Tian, X.Y. / Wang, W.J. / Wang, Y. / Hou, P.P. / Wu, Q. / Lin, T.W.
CitationJournal: Chem.Biol. / Year: 2015
Title: Induction of Autophagic Death in Cancer Cells by Agonizing TR3 and Attenuating Akt2 Activity
Authors: Wang, W.J. / Wang, Y. / Hou, P.P. / Li, F.W. / Zhou, B. / Chen, H.Z. / Bian, X.L. / Cai, Q.X. / Xing, Y.Z. / He, J.P. / Zhang, H. / Huang, P.Q. / Lin, T. / Wu, Q.
History
DepositionSep 22, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 9, 2015Provider: repository / Type: Initial release
Revision 1.1Oct 14, 2015Group: Derived calculations
Revision 1.2Mar 20, 2024Group: 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_struct_oper_list / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
B: Nuclear receptor subfamily 4 group A member 1
A: Nuclear receptor subfamily 4 group A member 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,2318
Polymers57,4912
Non-polymers7416
Water3,423190
1
B: Nuclear receptor subfamily 4 group A member 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,8372
Polymers28,7451
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Nuclear receptor subfamily 4 group A member 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,3946
Polymers28,7451
Non-polymers6495
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)74.378, 76.440, 128.664
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11B
21A

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: ALA / Beg label comp-ID: ALA / End auth comp-ID: PHE / End label comp-ID: PHE / Refine code: _ / Auth seq-ID: 31 - 267 / Label seq-ID: 13 - 249

Dom-IDAuth asym-IDLabel asym-ID
1BA
2AB
DetailsThe biological unit is a monomer. There are 2 biological units in the asymmetric unit (chains A and chains B).

-
Components

#1: Protein Nuclear receptor subfamily 4 group A member 1 / Early response protein NAK1 / Nuclear hormone receptor NUR/77 / Nur77 / Orphan nuclear receptor HMR ...Early response protein NAK1 / Nuclear hormone receptor NUR/77 / Nur77 / Orphan nuclear receptor HMR / Orphan nuclear receptor TR3 / ST-59 / Testicular receptor 3


Mass: 28745.305 Da / Num. of mol.: 2 / Fragment: ligand binding domain, UNP residues 351-598
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NR4A1, GFRP1, HMR, NAK1 / Plasmid: pET22b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P22736
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-3MX / 1-(3,4,5-trihydroxyphenyl)decan-1-one


Mass: 280.359 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H24O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 190 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 3.18 Å3/Da / Density % sol: 61.33 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 4.2 / Details: PEG4000, Sodium citrate, Glycerol

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 22, 2014 / Details: mirrors
RadiationMonochromator: Ni FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.27→50 Å / Num. obs: 29178 / % possible obs: 84.8 % / Redundancy: 2.7 % / Rmerge(I) obs: 0.093 / Rpim(I) all: 0.062 / Rrim(I) all: 0.112 / Χ2: 1.644 / Net I/av σ(I): 14.323 / Net I/σ(I): 10.2 / Num. measured all: 78624
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.3-2.342.60.4914830.7280.3310.5961.36288.2
2.34-2.382.60.44114970.7610.2950.5351.38488.6
2.38-2.432.60.39915100.790.270.4851.45389.2
2.43-2.482.70.35215070.8480.2320.4251.43389
2.48-2.532.60.32115090.8760.210.3861.54489.4
2.53-2.592.60.28615050.8820.1910.3461.56187.9
2.59-2.662.70.2615020.9050.1720.3141.58189.1
2.66-2.732.70.22515030.930.1450.271.66889
2.73-2.812.70.18914880.9480.1240.2281.68587.4
2.81-2.92.70.17215060.9530.1130.2071.71387.9
2.9-32.70.15114980.9650.0990.1821.82286.8
3-3.122.80.14914490.9670.0970.181.88885
3.12-3.262.80.11614640.9760.0760.1391.85285.3
3.26-3.442.70.09514380.9850.0630.1151.99784.2
3.44-3.652.70.07914160.9870.0530.0961.80382.5
3.65-3.932.60.07213930.9890.0480.0871.95780.1
3.93-4.332.70.06213990.9910.0420.0751.77280.2
4.33-4.952.60.05413560.990.0390.0671.64277.4
4.95-6.242.80.05414180.9860.0370.0671.4880
6.24-502.80.04613370.9920.0310.0561.24471

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
HKL-2000data reduction
Cootmodel building
PDB_EXTRACT3.15data extraction
Blu-Icedata collection
PHASERphasing
HKLdata reduction
HKLdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.27→34.02 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.891 / SU B: 6.776 / SU ML: 0.166 / Cross valid method: THROUGHOUT / ESU R: 0.297 / ESU R Free: 0.244 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26786 1422 4.9 %RANDOM
Rwork0.21684 ---
obs0.21932 27719 83.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 40.416 Å2
Baniso -1Baniso -2Baniso -3
1-1.27 Å20 Å2-0 Å2
2---0.22 Å20 Å2
3----1.05 Å2
Refinement stepCycle: LAST / Resolution: 2.27→34.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3616 0 50 190 3856
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0193735
X-RAY DIFFRACTIONr_bond_other_d0.0070.023723
X-RAY DIFFRACTIONr_angle_refined_deg1.7982.015045
X-RAY DIFFRACTIONr_angle_other_deg1.43938572
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2685455
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.52723.247154
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.97915653
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.8391528
X-RAY DIFFRACTIONr_chiral_restr0.1150.2585
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0214066
X-RAY DIFFRACTIONr_gen_planes_other0.0070.02812
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_it3.2683.8121835
X-RAY DIFFRACTIONr_mcbond_other3.2643.811834
X-RAY DIFFRACTIONr_mcangle_it4.7245.6832285
X-RAY DIFFRACTIONr_mcangle_other4.7235.6852286
X-RAY DIFFRACTIONr_scbond_it4.0364.1871900
X-RAY DIFFRACTIONr_scbond_other4.0354.1871901
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.0576.1352761
X-RAY DIFFRACTIONr_long_range_B_refined9.05336.08416377
X-RAY DIFFRACTIONr_long_range_B_other9.05336.08416378
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 12791 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.2 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1B
2A
LS refinement shellResolution: 2.268→2.327 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.316 83 -
Rwork0.271 1806 -
obs--75.05 %

+
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://pdbjlvh1.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