[English] 日本語
Yorodumi
- PDB-7prw: The glucocorticoid receptor in complex with velsecorat, a PGC1a c... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7prw
TitleThe glucocorticoid receptor in complex with velsecorat, a PGC1a coactivator fragment and sgk 23bp
Components
  • DNA (5'-D(*GP*TP*AP*CP*AP*GP*AP*AP*CP*AP*TP*TP*TP*TP*GP*TP*CP*CP*GP*TP*CP*GP*A)-3')
  • DNA (5'-D(*TP*CP*GP*AP*CP*GP*GP*AP*CP*AP*AP*AP*AP*TP*GP*TP*TP*CP*TP*GP*TP*AP*C)-3')
  • Glucocorticoid receptor
  • Peroxisome proliferator-activated receptor gamma coactivator 1-alphaPeroxisome proliferator-activated receptor gamma
KeywordsSIGNALING PROTEIN / nuclear receptor / ligand-activated transcription factor / multi-domain / complex / agonist
Function / homology
Function and homology information


positive regulation of mitochondrial DNA metabolic process / positive regulation of muscle tissue development / Regulation of NPAS4 gene transcription / regulation of glucocorticoid biosynthetic process / nuclear glucocorticoid receptor activity / positive regulation of cellular respiration / positive regulation of fatty acid oxidation / steroid hormone binding / PTK6 Expression / neuroinflammatory response ...positive regulation of mitochondrial DNA metabolic process / positive regulation of muscle tissue development / Regulation of NPAS4 gene transcription / regulation of glucocorticoid biosynthetic process / nuclear glucocorticoid receptor activity / positive regulation of cellular respiration / positive regulation of fatty acid oxidation / steroid hormone binding / PTK6 Expression / neuroinflammatory response / glucocorticoid metabolic process / : / microglia differentiation / mammary gland duct morphogenesis / maternal behavior / : / astrocyte differentiation / lncRNA binding / cellular response to glucocorticoid stimulus / response to muscle activity / cellular respiration / Activation of PPARGC1A (PGC-1alpha) by phosphorylation / motor behavior / temperature homeostasis / regulation of gluconeogenesis / adrenal gland development / cellular response to steroid hormone stimulus / positive regulation of ATP biosynthetic process / response to starvation / intracellular glucose homeostasis / fatty acid oxidation / response to dietary excess / estrogen response element binding / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / adipose tissue development / energy homeostasis / brown fat cell differentiation / intracellular steroid hormone receptor signaling pathway / core promoter sequence-specific DNA binding / positive regulation of gluconeogenesis / digestion / cellular response to transforming growth factor beta stimulus / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / respiratory electron transport chain / TBP-class protein binding / steroid binding / mitochondrion organization / cellular response to dexamethasone stimulus / RNA splicing / SUMOylation of transcription cofactors / nuclear receptor coactivator activity / synaptic transmission, glutamatergic / chromosome segregation / gluconeogenesis / transcription initiation at RNA polymerase II promoter / nuclear receptor binding / negative regulation of smooth muscle cell proliferation / transcription coregulator activity / RNA polymerase II transcription regulatory region sequence-specific DNA binding / Hsp90 protein binding / circadian regulation of gene expression / Heme signaling / SUMOylation of intracellular receptors / Transcriptional activation of mitochondrial biogenesis / regulation of circadian rhythm / PPARA activates gene expression / chromatin DNA binding / PML body / mRNA processing / DNA-binding transcription repressor activity, RNA polymerase II-specific / positive regulation of DNA-binding transcription factor activity / positive regulation of miRNA transcription / Transcriptional regulation of white adipocyte differentiation / Nuclear Receptor transcription pathway / spindle / Regulation of RUNX2 expression and activity / nuclear receptor activity / positive regulation of neuron apoptotic process / sequence-specific double-stranded DNA binding / Circadian Clock / positive regulation of cold-induced thermogenesis / chromatin organization / cellular response to oxidative stress / gene expression / DNA-binding transcription activator activity, RNA polymerase II-specific / protein-containing complex assembly / neuron apoptotic process / DNA-binding transcription factor binding / RNA polymerase II-specific DNA-binding transcription factor binding / negative regulation of neuron apoptotic process / Potential therapeutics for SARS / sequence-specific DNA binding / transcription coactivator activity / protein stabilization / DNA-binding transcription factor activity, RNA polymerase II-specific / mitochondrial matrix / nuclear speck / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / cell division
Similarity search - Function
PGC-1alpha, RNA recognition motif / PGC-1 / Glucocorticoid receptor / Glucocorticoid receptor / RNA recognition motif / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain / RNA-binding domain superfamily / Nuclear hormone receptor ...PGC-1alpha, RNA recognition motif / PGC-1 / Glucocorticoid receptor / Glucocorticoid receptor / RNA recognition motif / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain / RNA-binding 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 / Nucleotide-binding alpha-beta plait domain superfamily
Similarity search - Domain/homology
Velsecorat / DNA / DNA (> 10) / Glucocorticoid receptor / Peroxisome proliferator-activated receptor gamma coactivator 1-alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.502 Å
AuthorsPostel, S. / Edman, K. / Wissler, L.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2023
Title: Quaternary glucocorticoid receptor structure highlights allosteric interdomain communication.
Authors: Postel, S. / Wissler, L. / Johansson, C.A. / Gunnarsson, A. / Gordon, E. / Collins, B. / Castaldo, M. / Kohler, C. / Oling, D. / Johansson, P. / Froderberg Roth, L. / Beinsteiner, B. / ...Authors: Postel, S. / Wissler, L. / Johansson, C.A. / Gunnarsson, A. / Gordon, E. / Collins, B. / Castaldo, M. / Kohler, C. / Oling, D. / Johansson, P. / Froderberg Roth, L. / Beinsteiner, B. / Dainty, I. / Delaney, S. / Klaholz, B.P. / Billas, I.M.L. / Edman, K.
History
DepositionSep 22, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 8, 2023Provider: repository / Type: Initial release
Revision 1.1Feb 15, 2023Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title ..._citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Mar 29, 2023Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Glucocorticoid receptor
B: Glucocorticoid receptor
C: DNA (5'-D(*TP*CP*GP*AP*CP*GP*GP*AP*CP*AP*AP*AP*AP*TP*GP*TP*TP*CP*TP*GP*TP*AP*C)-3')
D: DNA (5'-D(*GP*TP*AP*CP*AP*GP*AP*AP*CP*AP*TP*TP*TP*TP*GP*TP*CP*CP*GP*TP*CP*GP*A)-3')
F: Peroxisome proliferator-activated receptor gamma coactivator 1-alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,25217
Polymers105,4055
Non-polymers1,84712
Water1,15364
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10880 Å2
ΔGint-12 kcal/mol
Surface area35810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.21, 122.724, 130.449
Angle α, β, γ (deg.)90, 90, 90
Int Tables number19
Space group name H-MP212121

-
Components

-
DNA chain , 2 types, 2 molecules CD

#2: DNA chain DNA (5'-D(*TP*CP*GP*AP*CP*GP*GP*AP*CP*AP*AP*AP*AP*TP*GP*TP*TP*CP*TP*GP*TP*AP*C)-3')


Mass: 7064.585 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: DNA chain DNA (5'-D(*GP*TP*AP*CP*AP*GP*AP*AP*CP*AP*TP*TP*TP*TP*GP*TP*CP*CP*GP*TP*CP*GP*A)-3')


Mass: 7055.571 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)

-
Protein / Protein/peptide , 2 types, 3 molecules ABF

#1: Protein Glucocorticoid receptor / / GR / Nuclear receptor subfamily 3 group C member 1


Mass: 44511.457 Da / Num. of mol.: 2 / Mutation: S404A, N517D, V571M, F602S, C638D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NR3C1, GRL / Cell line (production host): Sf21 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P04150
#4: Protein/peptide Peroxisome proliferator-activated receptor gamma coactivator 1-alpha / Peroxisome proliferator-activated receptor gamma / PGC-1-alpha / PPAR-gamma coactivator 1-alpha / PPARGC-1-alpha / Ligand effect modulator 6 / PGC1a ...PGC-1-alpha / PPAR-gamma coactivator 1-alpha / PPARGC-1-alpha / Ligand effect modulator 6 / PGC1a coactivator fragment


Mass: 2261.611 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q9UBK2

-
Non-polymers , 4 types, 76 molecules

#5: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#6: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#7: Chemical ChemComp-82H / Velsecorat / 3-[5-[(1R,2S)-2-(2,2-difluoropropanoylamino)-1-(2,3-dihydro-1,4-benzodioxin-6-yl)propoxy]indazol-1-yl]-N-[(3R)-oxolan-3-yl]benzamide / 3-[5-[(1R,2S)-2-[2,2-bis(fluoranyl)propanoylamino]-1-(2,3-dihydro-1,4-benzodioxin-6-yl)propoxy]indazol-1-yl]-N-[(3R)-oxolan-3-yl]benzamide


Mass: 606.616 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C32H32F2N4O6 / Feature type: SUBJECT OF INVESTIGATION
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 64 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.99 Å3/Da / Density % sol: 63.25 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 8.6 % PEG3350, 0.3 M 1,6-hexanediol, 0.1 M guanidine hydrochloride, 2 % 2,2,2-trifluoroethanol, 0.1 M BIS-TRIS propane pH 6.5

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.9655 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Mar 7, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9655 Å / Relative weight: 1
ReflectionResolution: 2.502→89.385 Å / Num. obs: 23070 / % possible obs: 93.4 % / Redundancy: 6.3 % / CC1/2: 0.999 / Rmerge(I) obs: 0.082 / Rpim(I) all: 0.036 / Rrim(I) all: 0.09 / Net I/σ(I): 12.6
Reflection shellResolution: 2.502→2.872 Å / Rmerge(I) obs: 0.792 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 1154 / CC1/2: 0.744 / Rpim(I) all: 0.373 / Rrim(I) all: 0.878

-
Processing

Software
NameVersionClassification
BUSTER2.11.8refinement
autoPROC1.1.7data processing
autoPROC1.1.7data scaling
MOLREPphasing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3G9O, 4P6W

3g9o

4p6w


Resolution: 2.502→89.39 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.885 / Cross valid method: THROUGHOUT / SU Rfree Blow DPI: 0.428
RfactorNum. reflection% reflectionSelection details
Rfree0.2632 1160 -RANDOM
Rwork0.2018 ---
obs0.2048 23070 51.1 %-
Displacement parametersBiso mean: 88.15 Å2
Baniso -1Baniso -2Baniso -3
1-8.6505 Å20 Å20 Å2
2---6.9762 Å20 Å2
3----1.6743 Å2
Refine analyzeLuzzati coordinate error obs: 0.37 Å
Refinement stepCycle: LAST / Resolution: 2.502→89.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5299 939 116 64 6418
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0086585HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.939079HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2199SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes970HARMONIC5
X-RAY DIFFRACTIONt_it6585HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion835SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact4779SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion2.49
X-RAY DIFFRACTIONt_other_torsion21.47
LS refinement shellResolution: 2.502→2.72 Å
RfactorNum. reflection% reflection
Rfree0.3854 30 -
Rwork0.2917 --
obs--4.69 %
Refinement TLS params.

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)
110.67544.3161.624112.0646-0.722.3736-0.8516-0.37180.3901-0.37180.40860.66060.39010.66060.443-0.2031-0.1638-0.1240.13980.0190.3302-0.576710.1868-15.191
29.8389-5.11262.624612.7484-1.17952.94360.21041.12460.58111.12460.69260.31350.58110.3135-0.9030.13660.1386-0.2296-0.08290.2960.209-1.7589-13.5096-7.2503
32.94790.5994-0.54174.1326-0.85862.6897-0.07292.4857-0.21692.4857-0.44761.0135-0.21691.01350.5205-0.47620.0941-0.4844-0.99350.08780.041210.93911.4901-1.405
43.77-2.67290.231620.7753-4.98653.6666-0.01992.0522-0.20362.0522-0.47410.7578-0.20360.75780.494-0.50250.1524-0.6223-0.98680.0848-0.10611.70630.4783-2.0961
54.1816-0.0586-0.89918.06971.72126.7559-0.26434.00810.95614.0081-0.0084-0.65380.9561-0.65380.27271.5292-0.02540.30510.69720.0357-0.623-28.4256-1.829817.6901
63.74631.1312-1.12677.5045-0.31847.3765-0.5346-4.41151.2625-4.41150.2116-1.60041.2625-1.60040.32292.371-0.2301-0.23020.6747-0.1247-0.5114-31.7172-1.3526-15.19
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|415-488 }A415 - 488
2X-RAY DIFFRACTION2{ B|418-488 }B418 - 488
3X-RAY DIFFRACTION3{ C|* }C1 - 23
4X-RAY DIFFRACTION4{ D|* }D1 - 23
5X-RAY DIFFRACTION5{ A|526-777 }A526 - 777
6X-RAY DIFFRACTION6{ B|526-777 }B526 - 777

+
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