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- PDB-1a6y: REVERBA ORPHAN NUCLEAR RECEPTOR/DNA COMPLEX -

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Basic information

Entry
Database: PDB / ID: 1a6y
TitleREVERBA ORPHAN NUCLEAR RECEPTOR/DNA COMPLEX
Components
  • DNA (5'-D(*CP*AP*AP*CP*TP*AP*GP*GP*TP*CP*AP*CP*(5IT)P*AP*GP*GP*TP*CP*AP*G)-3')
  • DNA (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 REGULATION / 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 / intracellular glucose homeostasis / E-box binding / nuclear steroid receptor activity / regulation of lipid metabolic process / cellular response to interleukin-1 / proteasomal protein catabolic process / intracellular receptor signaling pathway / hormone-mediated signaling pathway / negative regulation of canonical NF-kappaB signal transduction / 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 / negative regulation of inflammatory response / DNA-binding transcription repressor activity, RNA polymerase II-specific / nuclear receptor activity / sequence-specific double-stranded DNA binding / cellular response to tumor necrosis factor / : / cellular response to lipopolysaccharide / dendritic spine / DNA-binding transcription factor activity, RNA polymerase II-specific / cell differentiation / 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: 2.3 Å
AuthorsZhao, Q. / Khorasanizadeh, S. / Rastinejad, F.
CitationJournal: Mol.Cell / Year: 1998
Title: Structural elements of an orphan nuclear receptor-DNA complex.
Authors: Zhao, Q. / Khorasanizadeh, S. / Miyoshi, Y. / Lazar, M.A. / Rastinejad, F.
History
DepositionMar 4, 1998Deposition site: NDB / Processing site: NDB
Revision 1.0Oct 21, 1998Provider: repository / Type: Initial release
Revision 1.1May 22, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 2, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: database_2 / diffrn_source ...database_2 / diffrn_source / pdbx_initial_refinement_model / struct_conn / struct_conn_type / 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 / _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_conn_type.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: DNA (5'-D(*CP*AP*AP*CP*TP*AP*GP*GP*TP*CP*AP*CP*(5IT)P*AP*GP*GP*TP*CP*AP*G)-3')
D: DNA (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)34,4458
Polymers34,1844
Non-polymers2624
Water4,216234
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)38.670, 45.690, 47.950
Angle α, β, γ (deg.)75.16, 80.64, 85.58
Int Tables number1
Cell settingtriclinic
Space group name H-MP1

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Components

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


Mass: 6254.863 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: DNA chain DNA (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
#3: Protein ORPHAN NUCLEAR RECEPTOR NR1D1 / THYROID HORMONE RECEPTOR-RELATED PROTEIN REV-ERBA-ALPHA / REVERB / REVERBA ORPHAN NUCLEAR RECEPTOR ...THYROID HORMONE RECEPTOR-RELATED PROTEIN REV-ERBA-ALPHA / REVERB / REVERBA ORPHAN NUCLEAR RECEPTOR / V-ERBA RELATED PROTEIN EAR-1


Mass: 10902.009 Da / Num. of mol.: 2
Fragment: DNA BINDING DOMAIN CONSISTS OF RESIDUES A 101 TO A 164, B 101 TO B 164
Mutation: H116L
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 (bacteria) / Strain (production host): BL21 / 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.: 234 / 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: 2.58 Å3/Da / Density % sol: 53.4 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 7.5
Details: PROTEIN AND DNA COMPLEX WAS CRYSTALLIZED FROM 25-30% PEG 8000, 5 MM MGCL2, 400 MM NACL2, 100 MM TRIS, PH 7.5., VAPOR DIFFUSION, HANGING DROP
Components of the solutions
IDNameCrystal-IDSol-ID
1NACL11
2MGCL211
3TRIS11
4PEG 800011
5PEG 800012
Crystal
*PLUS
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
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Dec 15, 1996 / Details: NONE
RadiationMonochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.3→19.4 Å / Num. obs: 13482 / % possible obs: 97.3 % / Observed criterion σ(I): 2 / Redundancy: 3.6 % / Rsym value: 0.088 / Net I/σ(I): 15.1
Reflection shellResolution: 2.3→2.38 Å / Mean I/σ(I) obs: 2.8 / Rsym value: 0.492 / % possible all: 94
Reflection
*PLUS
Rmerge(I) obs: 0.088
Reflection shell
*PLUS
% possible obs: 94 %

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Processing

Software
NameVersionClassification
AMoREphasing
X-PLOR3.84refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2NLL (TR PORTION)

2nll


Resolution: 2.3→6 Å / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Details: THERE IS AN INSERT GLN 133A IN BOTH CHAIN A AND B
RfactorNum. reflection% reflectionSelection details
Rfree0.288 674 5 %RANDOM
Rwork0.1921 ---
obs-10614 97.2 %-
Displacement parametersBiso mean: 31.1 Å2
Refinement stepCycle: LAST / Resolution: 2.3→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1282 813 5 234 2334
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.011
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.805
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d22.08
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d0.995
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
LS refinement shellResolution: 2.3→2.4 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.313 47 4.6 %
Rwork0.2864 966 -
obs--94.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARAMXX4.CPXTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAM11X.DNATOPH11I.DNA
X-RAY DIFFRACTION3PARHCSDX.PRO
Software
*PLUS
Name: X-PLOR / Version: 3.84 / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.1921 / Rfactor Rfree: 0.2882
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg22.08
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg0.995
LS refinement shell
*PLUS
Rfactor Rfree: 0.313

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