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- PDB-4n73: Crystal structure of the ligand binding domain (LBD) of REV-ERB b... -

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Basic information

Entry
Database: PDB / ID: 4n73
TitleCrystal structure of the ligand binding domain (LBD) of REV-ERB beta bound to Cobalt Protoporphyrin IX
ComponentsNuclear receptor subfamily 1 group D member 2
KeywordsTRANSCRIPTION / Transcriptional Regulator / Nuclear Receptor
Function / homology
Function and homology information


regulation of skeletal muscle cell differentiation / circadian behavior / lipid homeostasis / regulation of lipid metabolic process / energy homeostasis / hormone-mediated signaling pathway / regulation of circadian rhythm / DNA-binding transcription repressor activity, RNA polymerase II-specific / negative regulation of inflammatory response / Nuclear Receptor transcription pathway ...regulation of skeletal muscle cell differentiation / circadian behavior / lipid homeostasis / regulation of lipid metabolic process / energy homeostasis / hormone-mediated signaling pathway / regulation of circadian rhythm / 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 / regulation of inflammatory response / cell differentiation / 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 / regulation of DNA-templated transcription / 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
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 ...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
PROTOPORPHYRIN IX CONTAINING CO / Nuclear receptor subfamily 1 group D member 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8662 Å
AuthorsMatta-Camacho, E. / Kojetin, D.
CitationJournal: J.Biol.Chem. / Year: 2014
Title: Structure of REV-ERB beta Ligand-binding Domain Bound to a Porphyrin Antagonist.
Authors: Matta-Camacho, E. / Banerjee, S. / Hughes, T.S. / Solt, L.A. / Wang, Y. / Burris, T.P. / Kojetin, D.J.
History
DepositionOct 14, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 4, 2014Provider: repository / Type: Initial release
Revision 1.1Jul 2, 2014Group: Database references
Revision 1.2Jul 30, 2014Group: Database references
Revision 1.3Mar 14, 2018Group: Database references / Category: struct_ref_seq_dif / Item: _struct_ref_seq_dif.details
Revision 1.4Sep 20, 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 / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Nuclear receptor subfamily 1 group D member 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,0742
Polymers22,4551
Non-polymers6201
Water4,107228
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)73.660, 48.680, 69.750
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-774-

HOH

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Components

#1: Protein Nuclear receptor subfamily 1 group D member 2 / Orphan nuclear hormone receptor BD73 / Rev-erb-beta / V-erbA-related protein 1-related / EAR-1R


Mass: 22454.797 Da / Num. of mol.: 1 / Fragment: C-terminal fragment of the Rev-Erb LBD (381-578) / Mutation: L386M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NR1D2, R1D2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: Q14995
#2: Chemical ChemComp-COH / PROTOPORPHYRIN IX CONTAINING CO


Mass: 619.575 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32CoN4O4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 228 / 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: 2.78 Å3/Da / Density % sol: 55.83 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 1.7M ammonium sulfate, 4% Jeffamine and 0.1M Tris, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293.15K

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Sep 18, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.866→40.612 Å / Num. all: 39377 / Num. obs: 21145 / % possible obs: 85 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1
Reflection shell
Resolution (Å)Diffraction-ID% possible all
1.866-1.883194.7
4.61-40199.8

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
PHASERphasing
PHENIX(phenix.refine: 1.8_1069)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3CQV

3cqv


Resolution: 1.8662→40.612 Å / SU ML: 0.39 / σ(F): 1.2 / Phase error: 30.46 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2541 1955 4.97 %
Rwork0.2145 --
obs0.2165 39356 97.57 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.8662→40.612 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1561 0 43 228 1832
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0121651
X-RAY DIFFRACTIONf_angle_d1.3252246
X-RAY DIFFRACTIONf_dihedral_angle_d15.452605
X-RAY DIFFRACTIONf_chiral_restr0.05249
X-RAY DIFFRACTIONf_plane_restr0.006281
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8662-1.91290.42331240.48462564X-RAY DIFFRACTION93
1.9129-1.96460.49941320.47072569X-RAY DIFFRACTION94
1.9646-2.02240.26431740.24592707X-RAY DIFFRACTION100
2.0224-2.08770.37991290.27632732X-RAY DIFFRACTION100
2.0877-2.16230.23531440.21692738X-RAY DIFFRACTION100
2.1623-2.24880.28811190.22382498X-RAY DIFFRACTION91
2.2488-2.35120.35621100.29492465X-RAY DIFFRACTION90
2.3512-2.47510.28711550.19332715X-RAY DIFFRACTION100
2.4751-2.63020.21921390.18122741X-RAY DIFFRACTION100
2.6302-2.83320.23291510.18712756X-RAY DIFFRACTION100
2.8332-3.11820.22841480.17952717X-RAY DIFFRACTION100
3.1182-3.56920.23991380.17252732X-RAY DIFFRACTION100
3.5692-4.49590.22971430.17582733X-RAY DIFFRACTION99
4.4959-40.62210.19311490.19642734X-RAY DIFFRACTION100

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