[English] 日本語
Yorodumi
- PDB-5va0: Glucocorticoid Receptor DNA Binding Domain in complex with AP-1 r... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5va0
TitleGlucocorticoid Receptor DNA Binding Domain in complex with AP-1 response element from VCAM-1 Promoter
Components
  • DNA (5'-D(*CP*GP*GP*CP*TP*GP*AP*CP*TP*CP*AP*TP*CP*AP*AP*G)-3')
  • DNA (5'-D(*CP*TP*TP*GP*AP*TP*GP*AP*GP*TP*CP*AP*GP*CP*CP*G)-3')
  • Glucocorticoid receptor
Keywordstranscription/dna / Nuclear Receptor / Transcription Factor / DNA Binding / Development / Protein-DNA complex / transcription-dna complex
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 / Regulation of RUNX2 expression and activity / sequence-specific double-stranded DNA binding / : / 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 / cytoplasm / cytosol
Similarity search - Function
Glucocorticoid receptor / Glucocorticoid receptor / Erythroid Transcription Factor GATA-1, subunit A / Erythroid Transcription Factor GATA-1; Chain A / : / 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 / Erythroid Transcription Factor GATA-1, subunit A / Erythroid Transcription Factor GATA-1; Chain A / : / 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 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
DNA / DNA (> 10) / Glucocorticoid receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.295 Å
AuthorsWeikum, E.R. / Ortlund, E.A.
CitationJournal: Nucleic Acids Res. / Year: 2017
Title: Tethering not required: the glucocorticoid receptor binds directly to activator protein-1 recognition motifs to repress inflammatory genes.
Authors: Weikum, E.R. / de Vera, I.M.S. / Nwachukwu, J.C. / Hudson, W.H. / Nettles, K.W. / Kojetin, D.J. / Ortlund, E.A.
History
DepositionMar 24, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 9, 2017Provider: repository / Type: Initial release
Revision 1.1Aug 16, 2017Group: Database references / Refinement description / Category: citation / citation_author / software
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed ..._citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Sep 13, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Glucocorticoid receptor
C: DNA (5'-D(*CP*GP*GP*CP*TP*GP*AP*CP*TP*CP*AP*TP*CP*AP*AP*G)-3')
D: DNA (5'-D(*CP*TP*TP*GP*AP*TP*GP*AP*GP*TP*CP*AP*GP*CP*CP*G)-3')
B: Glucocorticoid receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,1548
Polymers25,8924
Non-polymers2624
Water75742
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, In addition, NMR titration experiments.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3250 Å2
ΔGint-25 kcal/mol
Surface area13550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.442, 96.280, 105.223
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

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


Mass: 8047.488 Da / Num. of mol.: 2 / Fragment: unp residues 84-155
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NR3C1, GRL / Production host: Escherichia coli (E. coli) / References: UniProt: P04150
#2: DNA chain DNA (5'-D(*CP*GP*GP*CP*TP*GP*AP*CP*TP*CP*AP*TP*CP*AP*AP*G)-3')


Mass: 4883.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: DNA chain DNA (5'-D(*CP*TP*TP*GP*AP*TP*GP*AP*GP*TP*CP*AP*GP*CP*CP*G)-3')


Mass: 4914.190 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#4: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 42 / 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: 3.86 Å3/Da / Density % sol: 68.12 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 0.05 M Na Cacodylate (pH 7), 5 mM MgCl2, 1 mM Spermine, and 2 % t-Butanol

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jan 13, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.28→50 Å / Num. obs: 18797 / % possible obs: 96.7 % / Redundancy: 6.9 % / Biso Wilson estimate: 41.19 Å2 / Rmerge(I) obs: 0.133 / Rpim(I) all: 0.056 / Rrim(I) all: 0.145 / Χ2: 1.398 / Net I/σ(I): 7.3 / Num. measured all: 130117
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.28-2.366.70.80717230.7170.3380.8770.80190.1
2.36-2.467.30.53718840.9340.2140.5790.844100
2.46-2.577.30.42419080.9520.1680.4570.949100
2.57-2.77.30.37619090.9570.150.4051.359100
2.7-2.877.30.24719230.9820.0980.2661.255100
2.87-3.097.30.17819230.9870.070.1921.391100
3.09-3.417.20.09119310.9990.0370.0991.74100
3.41-3.95.30.12617670.9920.0590.142.02889.8
3.9-4.916.90.07917270.9950.0320.0851.93987.3
4.91-506.60.13221020.9830.0560.1441.88599.6

-
Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
HKL-2000data scaling
PDB_EXTRACT3.22data extraction
PHENIX1.9_1692phasing
HKL-2000data reduction
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4HN5

4hn5


Resolution: 2.295→34.483 Å / SU ML: 0.3 / Cross valid method: NONE / σ(F): 1.35 / Phase error: 24.59 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2314 1231 7.02 %
Rwork0.1974 16302 -
obs0.1999 17533 94.13 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 93.18 Å2 / Biso mean: 42.9987 Å2 / Biso min: 22.97 Å2
Refinement stepCycle: final / Resolution: 2.295→34.483 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1092 650 4 42 1788
Biso mean--32.56 39.1 -
Num. residues----174
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081834
X-RAY DIFFRACTIONf_angle_d0.9722595
X-RAY DIFFRACTIONf_chiral_restr0.049284
X-RAY DIFFRACTIONf_plane_restr0.005223
X-RAY DIFFRACTIONf_dihedral_angle_d18.335993
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.2946-2.38650.31091380.25821841197998
2.3865-2.4950.26071430.244318962039100
2.495-2.62650.32621430.239319002043100
2.6265-2.7910.25421430.225218842027100
2.791-3.00640.26861430.238319022045100
3.0064-3.30870.2421440.21431906205099
3.3087-3.7870.3033920.23441197128963
3.787-4.76920.17741290.16141715184488
4.7692-34.48650.18261560.154920612217100

+
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