[English] 日本語
Yorodumi
- PDB-7yxo: Crystal structure of WT AncGR2-LBD bound to dexamethasone and SHP... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7yxo
TitleCrystal structure of WT AncGR2-LBD bound to dexamethasone and SHP coregulator fragment
Components
  • Ancestral Glucocorticoid Receptor2
  • SHP NR Box 1 Peptide
KeywordsNUCLEAR PROTEIN / Nuclear Receptor / Transcription Factor / Dexamethasone
Function / homology
Function and homology information


transcription regulator inhibitor activity / peroxisome proliferator activated receptor binding / nuclear thyroid hormone receptor binding / bile acid and bile salt transport / estrogen response element binding / animal organ regeneration / response to glucose / nuclear retinoid X receptor binding / nuclear receptor-mediated steroid hormone signaling pathway / Notch signaling pathway ...transcription regulator inhibitor activity / peroxisome proliferator activated receptor binding / nuclear thyroid hormone receptor binding / bile acid and bile salt transport / estrogen response element binding / animal organ regeneration / response to glucose / nuclear retinoid X receptor binding / nuclear receptor-mediated steroid hormone signaling pathway / Notch signaling pathway / cholesterol metabolic process / circadian regulation of gene expression / positive regulation of insulin secretion / negative regulation of DNA-binding transcription factor activity / response to organic cyclic compound / Nuclear Receptor transcription pathway / circadian rhythm / nuclear receptor activity / transcription corepressor activity / response to ethanol / protein domain specific binding / negative regulation of gene expression / intracellular membrane-bounded organelle / negative regulation of DNA-templated transcription / positive regulation of gene expression / protein-containing complex binding / chromatin / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / protein homodimerization activity / nucleoplasm / nucleus / cytoplasm
Similarity search - Function
Nuclear receptor subfamily 0 group B member 1/2 / : / Nuclear hormone receptor / 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
Similarity search - Domain/homology
DEXAMETHASONE / Ancestral Glucocorticoid Receptor2 / Nuclear receptor subfamily 0 group B member 2
Similarity search - Component
Biological speciesunidentified (others)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.99 Å
AuthorsJimenez-Panizo, A. / Estebanez-Perpina, E. / Fuentes-Prior, P.
Funding support Spain, 4items
OrganizationGrant numberCountry
Other governmentBFU-Retos2017-86906-R Spain
Other governmentSAF2017-71878-REDT Spain
Other governmentSAF2015-71878-REDT Spain
Other governmentRTI2018-101500-B-I00 Spain
CitationJournal: Nucleic Acids Res. / Year: 2022
Title: The multivalency of the glucocorticoid receptor ligand-binding domain explains its manifold physiological activities.
Authors: Jimenez-Panizo, A. / Alegre-Marti, A. / Tettey, T.T. / Fettweis, G. / Abella, M. / Anton, R. / Johnson, T.A. / Kim, S. / Schiltz, R.L. / Nunez-Barrios, I. / Font-Diaz, J. / Caelles, C. / ...Authors: Jimenez-Panizo, A. / Alegre-Marti, A. / Tettey, T.T. / Fettweis, G. / Abella, M. / Anton, R. / Johnson, T.A. / Kim, S. / Schiltz, R.L. / Nunez-Barrios, I. / Font-Diaz, J. / Caelles, C. / Valledor, A.F. / Perez, P. / Rojas, A.M. / Fernandez-Recio, J. / Presman, D.M. / Hager, G.L. / Fuentes-Prior, P. / Estebanez-Perpina, E.
History
DepositionFeb 16, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 7, 2022Provider: repository / Type: Initial release
Revision 1.1Dec 14, 2022Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jan 18, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._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
A: Ancestral Glucocorticoid Receptor2
B: SHP NR Box 1 Peptide
C: Ancestral Glucocorticoid Receptor2
D: SHP NR Box 1 Peptide
E: Ancestral Glucocorticoid Receptor2
F: SHP NR Box 1 Peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,25714
Polymers89,5616
Non-polymers2,6958
Water1448
1
A: Ancestral Glucocorticoid Receptor2
B: SHP NR Box 1 Peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,9575
Polymers29,8542
Non-polymers1,1033
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2040 Å2
ΔGint-22 kcal/mol
Surface area12080 Å2
MethodPISA
2
C: Ancestral Glucocorticoid Receptor2
D: SHP NR Box 1 Peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,0536
Polymers29,8542
Non-polymers1,1994
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2490 Å2
ΔGint-33 kcal/mol
Surface area12460 Å2
MethodPISA
3
E: Ancestral Glucocorticoid Receptor2
F: SHP NR Box 1 Peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,2463
Polymers29,8542
Non-polymers3921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1720 Å2
ΔGint-13 kcal/mol
Surface area11990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)180.200, 180.200, 169.180
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number98
Space group name H-MI4122
Components on special symmetry positions
IDModelComponents
11A-1003-

SO4

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21C
12A
22E
13C
23E

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: PRO / Beg label comp-ID: PRO / Refine code: _

Dom-IDEns-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11HISHISAA530 - 7752 - 247
21HISHISCC530 - 7752 - 247
12LEULEUAA530 - 7732 - 245
22LEULEUEE530 - 7732 - 245
13LEULEUCC530 - 7732 - 245
23LEULEUEE530 - 7732 - 245

NCS ensembles :
ID
1
2
3

-
Components

-
Protein / Protein/peptide , 2 types, 6 molecules ACEBDF

#1: Protein Ancestral Glucocorticoid Receptor2


Mass: 28649.363 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) unidentified (others) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1X8XLE9
#2: Protein/peptide SHP NR Box 1 Peptide / Orphan nuclear receptor SHP / Small heterodimer partner / Nuclear receptor subfamily 0 group B member 2


Mass: 1204.440 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q15466

-
Non-polymers , 4 types, 16 molecules

#3: Chemical ChemComp-DEX / DEXAMETHASONE / 9A-FLUORO-16BETA-METHYLPREDNISOLONE


Mass: 392.461 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C22H29FO5 / Feature type: SUBJECT OF INVESTIGATION / Comment: medication, antibiotic*YM
#4: Chemical ChemComp-CPS / 3-[(3-CHOLAMIDOPROPYL)DIMETHYLAMMONIO]-1-PROPANESULFONATE / CHAPS


Mass: 614.877 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C32H58N2O7S / Comment: detergent*YM
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 8 / 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: 3.87 Å3/Da / Density % sol: 68.19 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 0.1 M Tris-HCl, pH 8.0, 0.2 M sodium chloride, 2.0 M ammonium sulfate

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 7, 2017
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.748
11L, -K, H20.124
11-H, L, K30.128
ReflectionResolution: 2.99→90.1 Å / Num. obs: 23704 / % possible obs: 100 % / Redundancy: 9.4 % / Biso Wilson estimate: 73.5 Å2 / CC1/2: 0.982 / Rpim(I) all: 0.149 / Rrim(I) all: 0.307 / Net I/σ(I): 6.6
Reflection shellResolution: 2.99→3.18 Å / Redundancy: 9.5 % / Mean I/σ(I) obs: 2.2 / Num. unique obs: 4229 / CC1/2: 0.386 / Rpim(I) all: 0.815 / % possible all: 100

-
Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5UFS

5ufs


Resolution: 2.99→90.1 Å / Cor.coef. Fo:Fc: 0.87 / Cor.coef. Fo:Fc free: 0.825 / SU B: 20.234 / SU ML: 0.378 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.1 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2801 1194 5 %RANDOM
Rwork0.2417 ---
obs0.2437 22492 83.51 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 177.94 Å2 / Biso mean: 67.754 Å2 / Biso min: 0.5 Å2
Baniso -1Baniso -2Baniso -3
1--15 Å2-0 Å2-0 Å2
2---15 Å2-0 Å2
3---29.99 Å2
Refinement stepCycle: final / Resolution: 2.99→90.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5918 0 183 8 6109
Biso mean--55.4 33.47 -
Num. residues----732
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0126233
X-RAY DIFFRACTIONr_angle_refined_deg1.5551.6248454
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.5655719
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.05122.456285
X-RAY DIFFRACTIONr_dihedral_angle_3_deg22.057151135
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.5881530
X-RAY DIFFRACTIONr_chiral_restr0.1230.2803
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.024399
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A73960.17
12C73960.17
21A69460.19
22E69460.19
31C69320.19
32E69320.19
LS refinement shellResolution: 2.992→3.07 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20

+
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