[English] 日本語
Yorodumi
- PDB-1ga5: CRYSTAL STRUCTURE OF THE ORPHAN NUCLEAR RECEPTOR REV-ERB(ALPHA) D... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1ga5
TitleCRYSTAL STRUCTURE OF THE ORPHAN NUCLEAR RECEPTOR REV-ERB(ALPHA) DNA-BINDING DOMAIN BOUND TO ITS COGNATE RESPONSE ELEMENT
Components
  • 5'-D(*CP*AP*AP*CP*TP*AP*GP*GP*TP*CP*AP*CP*TP*AP*GP*GP*TP*CP*AP*G)-3'
  • 5'-D(*CP*TP*GP*AP*CP*CP*TP*AP*GP*TP*GP*AP*CP*CP*TP*AP*GP*TP*(5IT)P*G)-3'
  • ORPHAN NUCLEAR RECEPTOR NR1D1
KeywordsTRANSCRIPTION/DNA / ORPHAN RECEPTOR / NUCLEAR RECEPTOR / DNA-BINDING / REVERB / REV-ERB / TRANSCRIPTION-DNA COMPLEX
Function / homology
Function and homology information


regulation of circadian sleep/wake cycle / positive regulation of bile acid biosynthetic process / : / circadian temperature homeostasis / regulation of type B pancreatic cell proliferation / negative regulation of astrocyte activation / negative regulation of microglial cell activation / negative regulation of toll-like receptor 4 signaling pathway / negative regulation of neuroinflammatory response / response to leptin ...regulation of circadian sleep/wake cycle / positive regulation of bile acid biosynthetic process / : / circadian temperature homeostasis / regulation of type B pancreatic cell proliferation / negative regulation of astrocyte activation / negative regulation of microglial cell activation / negative regulation of toll-like receptor 4 signaling pathway / negative regulation of neuroinflammatory response / response to leptin / regulation of insulin secretion involved in cellular response to glucose stimulus / glycogen biosynthetic process / regulation of fat cell differentiation / negative regulation of cold-induced thermogenesis / nuclear steroid receptor activity / E-box binding / intracellular glucose homeostasis / regulation of lipid metabolic process / cellular response to interleukin-1 / proteasomal protein catabolic process / intracellular receptor signaling pathway / negative regulation of canonical NF-kappaB signal transduction / hormone-mediated signaling pathway / cholesterol homeostasis / transcription corepressor binding / RNA polymerase II transcription regulatory region sequence-specific DNA binding / circadian regulation of gene expression / Heme signaling / Transcriptional activation of mitochondrial biogenesis / PPARA activates gene expression / regulation of circadian rhythm / protein destabilization / Nuclear Receptor transcription pathway / DNA-binding transcription repressor activity, RNA polymerase II-specific / negative regulation of inflammatory response / nuclear receptor activity / sequence-specific double-stranded DNA binding / : / cellular response to tumor necrosis factor / cellular response to lipopolysaccharide / dendritic spine / cell differentiation / DNA-binding transcription factor activity, RNA polymerase II-specific / transcription cis-regulatory region binding / nuclear body / RNA polymerase II cis-regulatory region sequence-specific DNA binding / negative regulation of DNA-templated transcription / heme binding / dendrite / chromatin / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / zinc ion binding / nucleoplasm / nucleus / cytoplasm
Similarity search - Function
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 ...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) / Nuclear receptor subfamily 1 group D member 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsSierk, M.L. / Zhao, Q. / Rastinejad, F.
Citation
Journal: Biochemistry / Year: 2001
Title: DNA Deformability as a Recognition Feature in the RevErb Response Element
Authors: Sierk, M.L. / Zhao, Q. / Rastinejad, F.
#1: Journal: Mol.Cell / Year: 1998
Title: Structural Elements of an Orphan Nuclear Receptor-DNA Complex
Authors: Zhao, Q. / Khorasanizadeh, S. / Miyoshi, Y. / Lazar, M. / Rastinejad, F.
History
DepositionNov 29, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 16, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Advisory / Refinement description / Category: pdbx_validate_polymer_linkage / software / Item: _software.classification / _software.name
Revision 1.4Aug 9, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / 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 / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
C: 5'-D(*CP*AP*AP*CP*TP*AP*GP*GP*TP*CP*AP*CP*TP*AP*GP*GP*TP*CP*AP*G)-3'
D: 5'-D(*CP*TP*GP*AP*CP*CP*TP*AP*GP*TP*GP*AP*CP*CP*TP*AP*GP*TP*(5IT)P*G)-3'
G: 5'-D(*CP*AP*AP*CP*TP*AP*GP*GP*TP*CP*AP*CP*TP*AP*GP*GP*TP*CP*AP*G)-3'
H: 5'-D(*CP*TP*GP*AP*CP*CP*TP*AP*GP*TP*GP*AP*CP*CP*TP*AP*GP*TP*(5IT)P*G)-3'
A: ORPHAN NUCLEAR RECEPTOR NR1D1
B: ORPHAN NUCLEAR RECEPTOR NR1D1
E: ORPHAN NUCLEAR RECEPTOR NR1D1
F: ORPHAN NUCLEAR RECEPTOR NR1D1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,89116
Polymers68,3688
Non-polymers5238
Water5,026279
1
C: 5'-D(*CP*AP*AP*CP*TP*AP*GP*GP*TP*CP*AP*CP*TP*AP*GP*GP*TP*CP*AP*G)-3'
D: 5'-D(*CP*TP*GP*AP*CP*CP*TP*AP*GP*TP*GP*AP*CP*CP*TP*AP*GP*TP*(5IT)P*G)-3'
A: ORPHAN NUCLEAR RECEPTOR NR1D1
B: ORPHAN NUCLEAR RECEPTOR NR1D1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,4458
Polymers34,1844
Non-polymers2624
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
G: 5'-D(*CP*AP*AP*CP*TP*AP*GP*GP*TP*CP*AP*CP*TP*AP*GP*GP*TP*CP*AP*G)-3'
H: 5'-D(*CP*TP*GP*AP*CP*CP*TP*AP*GP*TP*GP*AP*CP*CP*TP*AP*GP*TP*(5IT)P*G)-3'
E: ORPHAN NUCLEAR RECEPTOR NR1D1
F: ORPHAN NUCLEAR RECEPTOR NR1D1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,4458
Polymers34,1844
Non-polymers2624
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)44.920, 52.020, 78.880
Angle α, β, γ (deg.)85.84, 76.61, 74.48
Int Tables number1
Space group name H-MP1

-
Components

#1: DNA chain 5'-D(*CP*AP*AP*CP*TP*AP*GP*GP*TP*CP*AP*CP*TP*AP*GP*GP*TP*CP*AP*G)-3'


Mass: 6142.993 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Synthesized optimal DR2 target
#2: DNA chain 5'-D(*CP*TP*GP*AP*CP*CP*TP*AP*GP*TP*GP*AP*CP*CP*TP*AP*GP*TP*(5IT)P*G)-3'


Mass: 6236.835 Da / Num. of mol.: 2 / Source method: obtained synthetically
Details: Synthesized optimal DR2 target complementary strand with 5-iodo-thymidine
#3: Protein
ORPHAN NUCLEAR RECEPTOR NR1D1 / REV-ERB(ALPHA)


Mass: 10902.009 Da / Num. of mol.: 4 / Fragment: DNA-BINDING DOMAIN PLUS C-TERMINAL EXTENSION
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NR1D1 OR THRAL OR EAR1 OR HREV / Plasmid: PGEX / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P20393
#4: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 279 / 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: 2.49 Å3/Da / Density % sol: 50.64 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 25% PEG8000, 5mM MgCl2, 400 mM NaCl, Tris, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 290K
Components of the solutions
IDNameCrystal-IDSol-ID
1PEG800011
2MgCl211
3NaCl11
4Tris11
Crystal grow
*PLUS
Temperature: 17 ℃ / Details: Zhao, Q., (1998) Mol. Cell, 1, 849.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
10.6 mMDNA1drop
21.2 mMprotein1drop
320-25 %PEG80001reservoir
45 mM1reservoirMgCl2
5400 mM1reservoirNaCl
6Tris1reservoirpH7.5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.9054 Å
DetectorType: MARRESEARCH / Detector: AREA DETECTOR / Date: Dec 15, 1997 / Details: segmented mirror
RadiationMonochromator: single crystal germanium triangular monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9054 Å / Relative weight: 1
ReflectionResolution: 2.35→19.6 Å / Num. all: 25370 / Num. obs: 25370 / % possible obs: 75 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.8 % / Biso Wilson estimate: 49.8 Å2 / Rmerge(I) obs: 0.083 / Net I/σ(I): 6.8
Reflection shellResolution: 2.35→2.43 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.393 / Mean I/σ(I) obs: 2.5 / % possible all: 0.49
Reflection
*PLUS
% possible obs: 87.3 %
Reflection shell
*PLUS
% possible obs: 82.8 % / Num. unique obs: 2476 / Rmerge(I) obs: 0.323 / Mean I/σ(I) obs: 2.9

-
Processing

Software
NameVersionClassification
AMoREphasing
CNS0.9refinement
MAR345data collection
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1A6Y, residues 132-198 from chain A & B, plus DNA

1a6y


Resolution: 2.4→19.6 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 818521.39 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
Details: NCS restraints used until final round of refinement
RfactorNum. reflection% reflectionSelection details
Rfree0.299 1940 9.9 %RANDOM
Rwork0.253 ---
all0.2357 19630 --
obs0.2357 19630 75 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 42.65 Å2 / ksol: 0.27 e/Å3
Displacement parametersBiso mean: 49 Å2
Baniso -1Baniso -2Baniso -3
1-30.65 Å27.4 Å2-2.34 Å2
2---17.89 Å2-4.41 Å2
3----12.77 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.51 Å0.41 Å
Luzzati d res low-5 Å
Luzzati sigma a0.62 Å0.58 Å
Refinement stepCycle: LAST / Resolution: 2.4→19.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2363 1628 8 279 4278
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d20.3
X-RAY DIFFRACTIONc_improper_angle_d1.03
X-RAY DIFFRACTIONc_mcbond_it2.921.5
X-RAY DIFFRACTIONc_mcangle_it4.632
X-RAY DIFFRACTIONc_scbond_it5.332
X-RAY DIFFRACTIONc_scangle_it7.712.5
Refine LS restraints NCSNCS model details: CONSTR
LS refinement shellResolution: 2.4→2.49 Å / Rfactor Rfree error: 0.026 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.4156 165 9 %
Rwork0.3895 2640 -
obs--63 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2DNA-RNA_REP_1.0.PARAMDNA-RNA_1.0.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION4ZINC.PARAMZINC.TOP
Software
*PLUS
Name: CNS / Version: 0.9 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.4 Å / σ(F): 0 / % reflection Rfree: 9.9 % / Rfactor obs: 0.253
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 49 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg20.3
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.03
X-RAY DIFFRACTIONc_mcbond_it1.5
X-RAY DIFFRACTIONc_scbond_it2
X-RAY DIFFRACTIONc_mcangle_it2
X-RAY DIFFRACTIONc_scangle_it2.5
LS refinement shell
*PLUS
% reflection Rfree: 9 %

+
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