[English] 日本語
Yorodumi
- PDB-1nhz: Crystal Structure of the Antagonist Form of Glucocorticoid Receptor -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1nhz
TitleCrystal Structure of the Antagonist Form of Glucocorticoid Receptor
ComponentsGLUCOCORTICOID RECEPTOR
KeywordsHormone receptor / PROTEIN-LIGAND COMPLEX / ANTI PARALLEL ALPHA HELIX SANDWICH
Function / homology
Function and homology information


Regulation of NPAS4 gene transcription / regulation of glucocorticoid biosynthetic process / nuclear glucocorticoid receptor activity / steroid hormone binding / glucocorticoid metabolic process / response to cortisol / PTK6 Expression / neuroinflammatory response / mammary gland duct morphogenesis / microglia differentiation ...Regulation of NPAS4 gene transcription / regulation of glucocorticoid biosynthetic process / nuclear glucocorticoid receptor activity / steroid hormone binding / glucocorticoid metabolic process / response to cortisol / PTK6 Expression / neuroinflammatory response / mammary gland duct morphogenesis / microglia differentiation / maternal behavior / astrocyte differentiation / adrenal gland development / regulation of gluconeogenesis / cellular response to glucocorticoid stimulus / cellular response to steroid hormone stimulus / motor behavior / estrogen response element binding / cellular response to dexamethasone stimulus / nuclear receptor-mediated steroid hormone signaling pathway / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / cellular response to transforming growth factor beta stimulus / core promoter sequence-specific DNA binding / steroid binding / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / TBP-class protein binding / RNA polymerase II transcription regulatory region sequence-specific DNA binding / synaptic transmission, glutamatergic / chromosome segregation / SUMOylation of intracellular receptors / promoter-specific chromatin binding / Hsp90 protein binding / Nuclear Receptor transcription pathway / response to wounding / positive regulation of miRNA transcription / DNA-binding transcription repressor activity, RNA polymerase II-specific / spindle / nuclear receptor activity / sequence-specific double-stranded DNA binding / Regulation of RUNX2 expression and activity / : / positive regulation of neuron apoptotic process / chromatin organization / DNA-binding transcription activator activity, RNA polymerase II-specific / gene expression / Potential therapeutics for SARS / DNA-binding transcription factor activity, RNA polymerase II-specific / nuclear speck / RNA polymerase II cis-regulatory region sequence-specific DNA binding / mitochondrial matrix / DNA-binding transcription factor activity / cell division / negative regulation of DNA-templated transcription / apoptotic process / synapse / centrosome / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / protein kinase binding / chromatin / negative regulation of transcription by RNA polymerase II / signal transduction / positive regulation of transcription by RNA polymerase II / protein-containing complex / RNA binding / zinc ion binding / nucleoplasm / identical protein binding / nucleus / membrane / cytosol / cytoplasm
Similarity search - Function
Glucocorticoid receptor / Glucocorticoid 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. ...Glucocorticoid receptor / Glucocorticoid 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
Chem-486 / HEXANE-1,6-DIOL / Glucocorticoid receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsKauppi, B. / Jakob, C. / Farnegardh, M. / Yang, J. / Ahola, H. / Alarcon, M. / Calles, K. / Engstrom, O. / Harlan, J. / Muchmore, S. ...Kauppi, B. / Jakob, C. / Farnegardh, M. / Yang, J. / Ahola, H. / Alarcon, M. / Calles, K. / Engstrom, O. / Harlan, J. / Muchmore, S. / Ramqvist, A.-K. / Thorell, S. / Ohman, L. / Greer, J. / Gustafsson, J.-A. / Carlstedt-Duke, J. / Carlquist, M.
CitationJournal: J.Biol.Chem. / Year: 2003
Title: The Three-dimensional Structures of Antagonistic and Agonistic Forms of the Glucocorticoid Receptor Ligand-binding Domain: RU-486 INDUCES A TRANSCONFORMATION THAT LEADS TO ACTIVE ANTAGONISM.
Authors: Kauppi, B. / Jakob, C. / Farnegardh, M. / Yang, J. / Ahola, H. / Alarcon, M. / Calles, K. / Engstrom, O. / Harlan, J. / Muchmore, S. / Ramqvist, A.-K. / Thorell, S. / Ohman, L. / Greer, J. / ...Authors: Kauppi, B. / Jakob, C. / Farnegardh, M. / Yang, J. / Ahola, H. / Alarcon, M. / Calles, K. / Engstrom, O. / Harlan, J. / Muchmore, S. / Ramqvist, A.-K. / Thorell, S. / Ohman, L. / Greer, J. / Gustafsson, J.-A. / Carlstedt-Duke, J. / Carlquist, M.
History
DepositionDec 20, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 6, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Sep 2, 2020Group: Database references / Derived calculations / Structure summary
Category: chem_comp / struct_keywords ...chem_comp / struct_keywords / struct_ref_seq_dif / struct_site
Item: _chem_comp.pdbx_synonyms / _struct_keywords.text ..._chem_comp.pdbx_synonyms / _struct_keywords.text / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 27, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.5Feb 14, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: GLUCOCORTICOID RECEPTOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,9395
Polymers32,1551
Non-polymers7844
Water2,306128
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: GLUCOCORTICOID RECEPTOR
hetero molecules

A: GLUCOCORTICOID RECEPTOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,87810
Polymers64,3102
Non-polymers1,5688
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area7050 Å2
ΔGint-4 kcal/mol
Surface area23400 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)74.859, 109.764, 39.261
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-95-

HOH

-
Components

#1: Protein GLUCOCORTICOID RECEPTOR / GR


Mass: 32155.072 Da / Num. of mol.: 1
Fragment: residue 500-777, hinge and steroid binding domains
Mutation: N517D, F602S, C638D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): Sf9 / References: UniProt: P04150
#2: Chemical ChemComp-486 / 11-(4-DIMETHYLAMINO-PHENYL)-17-HYDROXY-13-METHYL-17-PROP-1-YNYL-1,2,6,7,8,11,12,13,14,15,16,17-DODEC AHYDRO-CYCLOPENTA[A]PHENANTHREN-3-ONE / RU-486 / MIFEPRISTONE


Mass: 429.594 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C29H35NO2
#3: Chemical ChemComp-HEZ / HEXANE-1,6-DIOL


Mass: 118.174 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H14O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 128 / 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: 2.7 Å3/Da / Density % sol: 54.04 %
Crystal growTemperature: 288 K / Method: vapor diffusion, hanging drop / pH: 8.2
Details: PEG 8000, 1, 6-hexanediol, NaSCN, Tris-HCl, pH 8.2, VAPOR DIFFUSION, HANGING DROP, temperature 288K
Crystal grow
*PLUS
Temperature: 12 ℃ / pH: 8.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
115 %PEG80001reservoir
2900 mM1,6-hexanediol1reservoir
3600 mM1reservoirNaSCN
4100 mMTris-HCl1reservoirpH8.2
510 mMTris-HCl1droppH8.5
62.5 mMdithiothreitol1drop
750000 nMRU-4861drop
85-12 mg/mlprotein1drop

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.97 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 26, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 2.3→39.26 Å / Num. all: 14833 / Num. obs: 14815 / % possible obs: 99.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Biso Wilson estimate: 35 Å2 / Rmerge(I) obs: 0.045 / Rsym value: 0.035 / Net I/σ(I): 8.8
Reflection shellResolution: 2.3→2.42 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.141 / Mean I/σ(I) obs: 6.1 / Num. unique all: 2064 / Rsym value: 0.121 / % possible all: 99.1
Reflection
*PLUS
Highest resolution: 2.3 Å / Lowest resolution: 40 Å / % possible obs: 98.1 % / Rmerge(I) obs: 0.106
Reflection shell
*PLUS
% possible obs: 98 % / Rmerge(I) obs: 0.348 / Mean I/σ(I) obs: 2.1

-
Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
REFMAC5.1.19refinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→62.02 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.881 / SU B: 6.11 / SU ML: 0.156 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.299 / ESU R Free: 0.253 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27585 743 5 %RANDOM
Rwork0.2044 ---
all0.20787 14815 --
obs0.20787 14072 98.67 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 16.433 Å2
Baniso -1Baniso -2Baniso -3
1-0.05 Å20 Å20 Å2
2--2.84 Å20 Å2
3----2.89 Å2
Refinement stepCycle: LAST / Resolution: 2.3→62.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1952 0 56 128 2136
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0222050
X-RAY DIFFRACTIONr_bond_other_d0.0030.021903
X-RAY DIFFRACTIONr_angle_refined_deg1.7971.9922767
X-RAY DIFFRACTIONr_angle_other_deg2.36334441
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0835237
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_chiral_restr0.110.2309
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022174
X-RAY DIFFRACTIONr_gen_planes_other0.0130.02412
X-RAY DIFFRACTIONr_nbd_refined0.230.2487
X-RAY DIFFRACTIONr_nbd_other0.2320.22221
X-RAY DIFFRACTIONr_nbtor_other0.1050.21230
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1870.2103
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2680.212
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2340.262
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2690.215
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it0.7971.51193
X-RAY DIFFRACTIONr_mcangle_it1.53821931
X-RAY DIFFRACTIONr_scbond_it2.5013857
X-RAY DIFFRACTIONr_scangle_it4.044.5836
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.251 64
Rwork0.196 1002
Refinement
*PLUS
Highest resolution: 2.3 Å / Lowest resolution: 40 Å / Rfactor Rfree: 0.263 / Rfactor Rwork: 0.228
Solvent computation
*PLUS
Displacement parameters
*PLUS
LS refinement shell
*PLUS
Highest resolution: 2.3 Å / Lowest resolution: 2.36 Å

+
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