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

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Basic information

Entry
Database: PDB / ID: 1hlz
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*TP*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 / response to leptin / negative regulation of neuroinflammatory response / negative regulation of toll-like receptor 4 signaling pathway ...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 / response to leptin / negative regulation of neuroinflammatory response / negative regulation of toll-like receptor 4 signaling pathway / regulation of insulin secretion involved in cellular response to glucose stimulus / glycogen biosynthetic process / negative regulation of cold-induced thermogenesis / regulation of fat cell differentiation / nuclear steroid receptor activity / E-box binding / intracellular glucose homeostasis / regulation of lipid metabolic process / proteasomal protein catabolic process / cellular response to interleukin-1 / 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 / circadian regulation of gene expression / Heme signaling / protein destabilization / Transcriptional activation of mitochondrial biogenesis / regulation of circadian rhythm / 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 / Nuclear hormone receptor-like domain superfamily ...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: 2.8 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
DepositionDec 4, 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 1.3Aug 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 / 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 / _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.pdbx_dist_value / _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*TP*G)-3'
A: ORPHAN NUCLEAR RECEPTOR NR1D1
B: ORPHAN NUCLEAR RECEPTOR NR1D1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,3348
Polymers34,0724
Non-polymers2624
Water1629
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)35.867, 39.603, 58.565
Angle α, β, γ (deg.)84.13, 72.09, 70.20
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.: 1 / 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*TP*G)-3'


Mass: 6124.965 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: Synthesized optimal DR2 target complementary strand
#3: Protein ORPHAN NUCLEAR RECEPTOR NR1D1 / REV-ERB(ALPHA)


Mass: 10902.009 Da / Num. of mol.: 2 / Fragment: DNA-BINDING DOMAIN PLUS C-TERMINAL EXTENSION
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / 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.: 4 / Source method: obtained synthetically / Formula: Zn
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 9 / 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: 2.16 Å3/Da / Density % sol: 42.93 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 25% PEG8000, 5 mM MgCl2, 400 mM NaCl, Tris buffer, 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: NSLS / Beamline: X4A / Wavelength: 0.92016 Å
DetectorType: FUJI / Detector: IMAGE PLATE / Date: Apr 5, 1997
Details: Double crystal monochromator with sagittally focussed second crystal. Two spherical mirrors.
RadiationMonochromator: Double crystal monochromator with sagittally focussed second crystal
Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92016 Å / Relative weight: 1
ReflectionResolution: 2.7→18.62 Å / Num. all: 7671 / Num. obs: 7671 / % possible obs: 97 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.1 % / Biso Wilson estimate: 58.3 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 9
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 2.1 / Num. unique all: 7691 / % possible all: 92.7
Reflection
*PLUS
Num. obs: 6854 / % possible obs: 96.6 % / Rmerge(I) obs: 0.078
Reflection shell
*PLUS
% possible obs: 93.3 % / Num. unique obs: 732 / Rmerge(I) obs: 0.258 / Mean I/σ(I) obs: 3.18

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Processing

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

1a6y


Resolution: 2.8→18.6 Å / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
Details: Conjugate-gradient minimization against a maximum-likelihood structure factor target. NCS restraints between upstream and downstream monomers and DNA half-sites used throughout refinement. ...Details: Conjugate-gradient minimization against a maximum-likelihood structure factor target. NCS restraints between upstream and downstream monomers and DNA half-sites used throughout refinement. Harmonic restraints used throughout refinement.
RfactorNum. reflection% reflectionSelection details
Rfree0.3103 732 -Random
Rwork0.2599 ---
all0.2599 6854 --
obs0.2599 6854 96.9 %-
Displacement parametersBiso mean: 60.81 Å2
Baniso -1Baniso -2Baniso -3
1--39.691 Å2-1.626 Å2-2.807 Å2
2--10.855 Å2-10.126 Å2
3---28.836 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.56 Å0.52 Å
Luzzati d res low-5 Å
Luzzati sigma a1.1 Å1.06 Å
Refinement stepCycle: LAST / Resolution: 2.8→18.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1160 814 4 9 1987
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0165
X-RAY DIFFRACTIONc_angle_deg3.8266
X-RAY DIFFRACTIONc_dihedral_angle_d23.271
X-RAY DIFFRACTIONc_improper_angle_d1.8505
LS refinement shellResolution: 2.8→2.9 Å
RfactorNum. reflection% reflection
Rfree0.5721 83 -
Rwork0.5517 --
obs--97 %
Software
*PLUS
Name: CNS / Version: 0.9 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.8 Å / Lowest resolution: 18.6 Å / σ(F): 0
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg2.3
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.271
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.8505
LS refinement shell
*PLUS
Highest resolution: 2.7 Å / Lowest resolution: 2.8 Å

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