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- PDB-1ga5: CRYSTAL STRUCTURE OF THE ORPHAN NUCLEAR RECEPTOR REV-ERB(ALPHA) D... -

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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 / NR1D1 (REV-ERBA) represses gene expression / circadian temperature homeostasis / regulation of type B pancreatic cell proliferation / negative regulation of astrocyte activation / negative regulation of microglial cell activation / negative regulation of neuroinflammatory response / negative regulation of toll-like receptor 4 signaling pathway / response to leptin ...regulation of circadian sleep/wake cycle / positive regulation of bile acid biosynthetic process / NR1D1 (REV-ERBA) represses gene expression / circadian temperature homeostasis / regulation of type B pancreatic cell proliferation / negative regulation of astrocyte activation / negative regulation of microglial cell activation / negative regulation of neuroinflammatory response / negative regulation of toll-like receptor 4 signaling pathway / 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 / negative regulation of canonical NF-kappaB signal transduction / hormone-mediated signaling pathway / transcription corepressor binding / cholesterol homeostasis / RNA polymerase II transcription regulatory region sequence-specific DNA binding / protein destabilization / circadian regulation of gene expression / Heme signaling / regulation of circadian rhythm / Transcriptional activation of mitochondrial biogenesis / PPARA activates gene expression / DNA-binding transcription repressor activity, RNA polymerase II-specific / negative regulation of inflammatory response / Nuclear Receptor transcription pathway / nuclear receptor activity / sequence-specific double-stranded DNA binding / Circadian Clock / cellular response to tumor necrosis factor / cellular response to lipopolysaccharide / dendritic spine / cell differentiation / nuclear body / transcription cis-regulatory region binding / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / negative regulation of DNA-templated transcription / dendrite / heme binding / 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 / 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 ...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 / 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 / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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

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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

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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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

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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

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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 %

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