[English] 日本語
Yorodumi
- PDB-6bse: Glucocorticoid receptor bound to high cooperativity monomer sequence -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6bse
TitleGlucocorticoid receptor bound to high cooperativity monomer sequence
Components
  • DNA (5'-D(P*AP*CP*CP*AP*CP*GP*TP*GP*TP*AP*CP*TP*TP*TP*TP*T)-3')
  • DNA (5'-D(P*TP*AP*AP*AP*AP*AP*GP*TP*AP*CP*AP*CP*GP*TP*GP*G)-3')
  • Glucocorticoid receptor
KeywordsGENE REGULATION / glucocorticoid receptor gene expression protein:DNA binding
Function / homology
Function and homology information


nuclear glucocorticoid receptor activity / steroid hormone binding / cellular response to glucocorticoid stimulus / cellular response to steroid hormone stimulus / steroid binding / spindle / nuclear receptor activity / chromosome / chromatin organization / sequence-specific DNA binding ...nuclear glucocorticoid receptor activity / steroid hormone binding / cellular response to glucocorticoid stimulus / cellular response to steroid hormone stimulus / steroid binding / spindle / nuclear receptor activity / chromosome / chromatin organization / sequence-specific DNA binding / nuclear speck / DNA-binding transcription factor activity / centrosome / positive regulation of transcription by RNA polymerase II / mitochondrion / zinc ion binding / nucleus / cytoplasm
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 speciesSaguinus oedipus (cotton-top tamarin)
synthetic construct (others)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsPufall, M.A.
Funding support United States, 3items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)MCB 1552862 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)K99/R00 CO149088 United States
Carver Charitable Trust01-224 United States
CitationJournal: To Be Published
Title: General and sequence-specific roles for DNA in glucocorticoid receptor DNA-binding stoichiometry
Authors: Pufall, M.A. / Zhang, L.
History
DepositionDec 2, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 5, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Oct 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
B: Glucocorticoid receptor
C: DNA (5'-D(P*TP*AP*AP*AP*AP*AP*GP*TP*AP*CP*AP*CP*GP*TP*GP*G)-3')
D: DNA (5'-D(P*AP*CP*CP*AP*CP*GP*TP*GP*TP*AP*CP*TP*TP*TP*TP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,4128
Polymers30,1514
Non-polymers2624
Water1,874104
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4570 Å2
ΔGint-23 kcal/mol
Surface area12840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.447, 95.172, 104.719
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

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


Mass: 10178.069 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saguinus oedipus (cotton-top tamarin) / Gene: NR3C1, GRL / Cell line (production host): Gold / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / Variant (production host): DE3 / References: UniProt: P79269
#2: DNA chain DNA (5'-D(P*TP*AP*AP*AP*AP*AP*GP*TP*AP*CP*AP*CP*GP*TP*GP*G)-3')


Mass: 4955.256 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (5'-D(P*AP*CP*CP*AP*CP*GP*TP*GP*TP*AP*CP*TP*TP*TP*TP*T)-3')


Mass: 4839.151 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: Zn
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 104 / 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: 3.26 Å3/Da / Density % sol: 62.27 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.08 M KCl 0.04 M Sodium cacodylate trihydrate 60% v/v (+/-)-2-Methyl-2,4-pentanediol 0.012 M Spermine tetrahydrochloride

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Oct 29, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.35→16.71 Å / Num. obs: 17036 / % possible obs: 98.68 % / Redundancy: 2 % / Biso Wilson estimate: 37.64 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.04967 / Rpim(I) all: 0.04967 / Rrim(I) all: 0.07025 / Net I/σ(I): 15.25
Reflection shellResolution: 2.35→2.434 Å / Redundancy: 2 % / Rmerge(I) obs: 0.3246 / Mean I/σ(I) obs: 2.47 / Num. unique obs: 1678 / CC1/2: 0.796 / Rpim(I) all: 0.3246 / Rrim(I) all: 0.4591 / % possible all: 99.88

-
Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3G99

3g99


Resolution: 2.35→16.75 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.37 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2294 789 4.67 %
Rwork0.1922 --
obs0.194 16883 99.07 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.35→16.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1106 653 4 104 1867
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0121858
X-RAY DIFFRACTIONf_angle_d1.2932628
X-RAY DIFFRACTIONf_dihedral_angle_d19.7141006
X-RAY DIFFRACTIONf_chiral_restr0.06289
X-RAY DIFFRACTIONf_plane_restr0.007227
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.35-2.49680.30341220.24862658X-RAY DIFFRACTION100
2.4968-2.68890.27831320.23422645X-RAY DIFFRACTION100
2.6889-2.95810.23831170.23122690X-RAY DIFFRACTION100
2.9581-3.38310.25711310.20852687X-RAY DIFFRACTION99
3.3831-4.25080.27431340.19982583X-RAY DIFFRACTION95
4.2508-16.75050.15711530.14022831X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / 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)
16.02814.14464.96839.94326.55355.4856-0.11610.40450.5242-0.75820.05680.8199-0.646-1.15030.45680.04170.02050.02720.72480.19170.2678-19.079829.4266-13.1642
29.3485-0.42694.96466.01580.52937.656-0.11670.92480.6543-0.39670.2239-0.1462-0.6546-0.0013-0.16680.35850.01120.06560.36720.05830.2255-7.37533.7799-12.0884
30.3407-0.8747-0.89912.2432.30312.3647-0.4362-2.52431.56160.9541-1.4892-3.5798-0.78010.36861.67330.8028-0.3647-0.2811.28430.22441.08031.178233.38530.5407
47.55170.10280.64996.3789-0.6846.47470.07770.19130.37750.08910.00460.0734-0.067-0.09210.01480.28440.08280.06070.4350.00820.1917-13.206126.5752.0062
53.9222-1.7711-1.64272.60991.5226.4997-0.0435-0.6913-0.06560.0461-0.39870.41120.1115-0.72130.47280.14380.0104-0.00290.3346-0.00980.2309-6.817625.5929-5.2534
66.50494.5643-3.80573.4732-3.22343.36260.26771.21830.3587-0.0248-0.2795-1.6007-1.63660.0123-0.11340.4614-0.0710.15340.47120.08160.3999-1.297829.5372-15.835
71.3108-0.96581.92142.5345-1.95452.97690.0865-1.09530.40921.41220.3235-0.6332-0.05580.9478-0.29910.6447-0.0781-0.08280.5996-0.09150.3886-6.709735.369925.8442
83.8585-0.1444-2.0338.28821.20185.60150.09760.69350.5302-0.3198-0.73851.3088-1.0322-1.14030.54690.6550.19740.03430.5665-0.24660.594-17.91139.986917.6832
98.12741.0233-0.21142.2983.73748.497-0.1256-0.1755-0.41990.02930.09360.41630.2249-0.5205-0.01780.2606-0.0154-0.00460.32680.03010.2104-16.039825.033210.1172
106.7262-2.34550.18836.55932.83832.82920.0498-0.85570.24740.1191-0.2436-0.2032-0.43850.06430.1460.2962-0.0817-0.03270.3461-0.07320.2544-11.736430.670115.3513
119.1209-2.38640.94860.6428-0.4632.692-0.4271-1.97840.3861.17840.52050.5215-0.3832-0.4899-0.06731.2825-0.09040.34790.8097-0.17420.4236-19.436836.440628.5481
122.2444-1.97172.87564.3304-5.85838.1350.67630.2459-0.1601-0.71310.69781.6189-0.78690.2064-1.29520.88130.0389-0.02830.88210.16230.565-13.727141.6895-29.1669
132.91952.4518-1.43162.431-2.32446.79291.0840.43320.2620.9073-0.374-0.0298-0.22840.0392-1.00960.6478-0.0057-0.03560.58630.08820.5248-5.856845.6448-14.0189
147.51344.975-2.91154.0389-0.13345.47470.8796-0.72190.5731.5802-0.39871.0186-2.428-0.9053-0.41321.07160.13430.13240.5524-0.05440.5106-13.837246.21333.8596
152.2505-0.65762.66453.3499-3.4987.07250.68510.6048-0.532-0.14460.3080.1162-0.95750.0501-0.65591.2418-0.13050.05470.3899-0.07980.5179-7.334943.367114.1605
162.13570.4115-1.78028.70895.40587.66680.77540.3360.995-0.93240.2733-1.042-1.6442-0.9637-0.77831.3724-0.0035-0.08930.6291-0.08240.6611-6.78551.24419.4527
173.37771.109-2.082.5674-3.08047.1738-0.10930.60120.5929-0.0660.68030.2037-0.8572-0.9266-0.65050.7035-0.02230.09680.35330.10570.4612-9.927844.4768-13.9855
184.0838-3.67913.46193.4919-4.13318.73060.96210.0037-1.74660.68263.7284-1.6623-0.37822.2338-4.59890.8060.1718-0.08491.1861-0.16480.928-5.349538.2059-31.8496
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 417 through 429 )
2X-RAY DIFFRACTION2chain 'A' and (resid 430 through 450 )
3X-RAY DIFFRACTION3chain 'A' and (resid 451 through 455 )
4X-RAY DIFFRACTION4chain 'A' and (resid 456 through 473 )
5X-RAY DIFFRACTION5chain 'A' and (resid 474 through 484 )
6X-RAY DIFFRACTION6chain 'A' and (resid 485 through 489 )
7X-RAY DIFFRACTION7chain 'B' and (resid 419 through 438 )
8X-RAY DIFFRACTION8chain 'B' and (resid 439 through 454 )
9X-RAY DIFFRACTION9chain 'B' and (resid 455 through 464 )
10X-RAY DIFFRACTION10chain 'B' and (resid 465 through 483 )
11X-RAY DIFFRACTION11chain 'B' and (resid 484 through 490 )
12X-RAY DIFFRACTION12chain 'C' and (resid 1 through 5 )
13X-RAY DIFFRACTION13chain 'C' and (resid 6 through 10 )
14X-RAY DIFFRACTION14chain 'C' and (resid 11 through 15 )
15X-RAY DIFFRACTION15chain 'C' and (resid 16 through 16 )
16X-RAY DIFFRACTION16chain 'D' and (resid 1 through 5 )
17X-RAY DIFFRACTION17chain 'D' and (resid 6 through 15 )
18X-RAY DIFFRACTION18chain 'D' and (resid 16 through 16 )

+
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