[English] 日本語
Yorodumi
- PDB-2r40: Crystal structure of 20E bound EcR/USP -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2r40
TitleCrystal structure of 20E bound EcR/USP
Components
  • Ecdysone Receptor
  • Ultraspiracle
KeywordsGENE REGULATION / nuclear receptor ligand-binding domain / anti-parallel alpha-helical sandwich / ecdysone receptor / EcR
Function / homology
Function and homology information


ecdysone binding / ecdysone receptor signaling pathway / nuclear steroid receptor activity / nuclear receptor activity / cell differentiation / RNA polymerase II cis-regulatory region sequence-specific DNA binding / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / DNA binding / zinc ion binding / nucleus
Similarity search - Function
Ecdysteroid receptor / Ecdysone receptor, ligand-binding domain / Retinoid X receptor/HNF4 / : / : / Retinoid X Receptor / Retinoid X Receptor / Nuclear hormone receptor / Nuclear hormones receptors DNA-binding region signature. / Zinc finger, nuclear hormone receptor-type ...Ecdysteroid receptor / Ecdysone receptor, ligand-binding domain / Retinoid X receptor/HNF4 / : / : / Retinoid X Receptor / Retinoid X Receptor / 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 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-20E / Chem-EPH / CITRATE ANION / Ecdysone receptor / Gene regulation protein
Similarity search - Component
Biological speciesHeliothis virescens (tobacco budworm)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.402 Å
AuthorsMoras, D. / Billas, I.M.L. / Browning, C.
CitationJournal: J.Biol.Chem. / Year: 2007
Title: Critical Role of Desolvation in the Binding of 20-Hydroxyecdysone to the Ecdysone Receptor
Authors: Browning, C. / Martin, E. / Loch, C. / Wurtz, J.M. / Moras, D. / Stote, R.H. / Dejaegere, A.P. / Billas, I.M.L.
History
DepositionAug 30, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 2, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 999 SEQUENCE THE SEQUENCE OF CHAIN D IN THIS STRUCTURE IS CORRECT BASED ON THE DIRECT SEQUENCING

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
D: Ecdysone Receptor
A: Ultraspiracle
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,8897
Polymers60,3212
Non-polymers1,5685
Water1,53185
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: Ecdysone Receptor
A: Ultraspiracle
hetero molecules

D: Ecdysone Receptor
A: Ultraspiracle
hetero molecules


Theoretical massNumber of molelcules
Total (without water)123,77714
Polymers120,6414
Non-polymers3,13610
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_554x-y,-y,-z-1/31
Buried area6630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.001, 58.001, 303.592
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121

-
Components

-
Protein , 2 types, 2 molecules DA

#1: Protein Ecdysone Receptor / Ecdysteroid receptor / 20-hydroxy-ecdysone receptor / 20E receptor / EcRH / HvEcR


Mass: 30368.961 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Heliothis virescens (tobacco budworm) / Gene: EcR / Plasmid: pET32b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O18473
#2: Protein Ultraspiracle / Gene regulation protein


Mass: 29951.760 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Heliothis virescens (tobacco budworm) / Plasmid: pACYC11b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q7SIF6

-
Non-polymers , 6 types, 90 molecules

#3: Chemical ChemComp-FLC / CITRATE ANION


Mass: 189.100 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H5O7
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-20E / (2beta,3beta,5beta,22R)-2,3,14,20,22,25-hexahydroxycholest-7-en-6-one / 2-beta,3-beta,14,20,22,25-Hexahydroxy-5-beta-cholet-7-en-6- one


Mass: 480.634 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H44O7 / Comment: hormone*YM
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#7: Chemical ChemComp-EPH / L-ALPHA-PHOSPHATIDYL-BETA-OLEOYL-GAMMA-PALMITOYL-PHOSPHATIDYLETHANOLAMINE


Mass: 709.933 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C39H68NO8P / Comment: phospholipid*YM
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 85 / 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: 2.44 Å3/Da / Density % sol: 49.67 %
Crystal growTemperature: 297 K / Method: vapor diffusion, hanging drop / Details: VAPOR DIFFUSION, HANGING DROP, temperature 297K

-
Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.9 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.402→33.73 Å / Num. all: 24092

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.2.0019refinement
PDB_EXTRACT3data extraction
ADSCQuantumdata collection
AMoREphasing
RefinementResolution: 2.402→33.73 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.893 / SU B: 16.621 / SU ML: 0.204 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.468 / ESU R Free: 0.302 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.282 2391 9.9 %RANDOM
Rwork0.224 ---
all0.23 24087 --
obs0.23 24087 99.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 53.164 Å2
Baniso -1Baniso -2Baniso -3
1-0.12 Å20.06 Å20 Å2
2--0.12 Å20 Å2
3----0.18 Å2
Refinement stepCycle: LAST / Resolution: 2.402→33.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3781 0 107 85 3973
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0223985
X-RAY DIFFRACTIONr_angle_refined_deg1.2892.0065390
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.7955473
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.17423.486175
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.70415722
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.4151534
X-RAY DIFFRACTIONr_chiral_restr0.0870.2616
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022906
X-RAY DIFFRACTIONr_nbd_refined0.2060.21937
X-RAY DIFFRACTIONr_nbtor_refined0.2990.22759
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.140.2111
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2910.242
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0570.22
X-RAY DIFFRACTIONr_mcbond_it0.5651.52461
X-RAY DIFFRACTIONr_mcangle_it0.93723853
X-RAY DIFFRACTIONr_scbond_it1.32131719
X-RAY DIFFRACTIONr_scangle_it2.0664.51537
LS refinement shellResolution: 2.402→2.464 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.315 164 -
Rwork0.247 1521 -
all-1685 -
obs--98.14 %
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)
11.5853-0.28050.32894.2343-2.21954.7428-0.03360.1507-0.0832-0.27470.03610.07960.2763-0.1911-0.0025-0.01510.02640.016-0.2695-0.0093-0.243222.5393-12.31-36.9447
22.12570.5790.02153.08690.76494.320.1786-0.1198-0.05790.2553-0.1915-0.28530.1360.24090.0129-0.03860.0059-0.0741-0.29560.1124-0.138731.8657-11.7995-11.0578
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A206 - 455
2X-RAY DIFFRACTION2D287 - 529

+
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