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- PDB-2v7c: Crystal Structure of Rev-Erb beta -

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Basic information

Entry
Database: PDB / ID: 2v7c
TitleCrystal Structure of Rev-Erb beta
ComponentsORPHAN NUCLEAR RECEPTOR NR1D2
KeywordsRECEPTOR / DNA-BINDING / TRANSCRIPTION / METAL-BINDING / ZINC / NUCLEUS / REPRESSOR / ZINC-FINGER / CONSTITUTIVE REPRESSION / TRANSCRIPTION REGULATION / ORPHAN RECEPTOR / A-HELICAL SANDWICH
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 ...: / 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
Nuclear receptor subfamily 1 group D member 2
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.4 Å
AuthorsWoo, E.-J. / Jeong, D.G. / Lim, M.-Y. / Kim, S.J. / Ryu, S.E.
CitationJournal: J.Mol.Biol. / Year: 2007
Title: Structural Insight Into the Constitutive Repression Function of the Nuclear Receptor Rev-Erbbeta
Authors: Woo, E.-J. / Jeong, D.G. / Lim, M.-Y. / Kim, S.J. / Kim, K.-J. / Yoon, S.-M. / Park, B.-C. / Ryu, S.E.
History
DepositionJul 29, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 23, 2007Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ORPHAN NUCLEAR RECEPTOR NR1D2
B: ORPHAN NUCLEAR RECEPTOR NR1D2


Theoretical massNumber of molelcules
Total (without water)44,6392
Polymers44,6392
Non-polymers00
Water1,06359
1
A: ORPHAN NUCLEAR RECEPTOR NR1D2


Theoretical massNumber of molelcules
Total (without water)22,3191
Polymers22,3191
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: ORPHAN NUCLEAR RECEPTOR NR1D2


Theoretical massNumber of molelcules
Total (without water)22,3191
Polymers22,3191
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)71.677, 71.677, 145.566
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein ORPHAN NUCLEAR RECEPTOR NR1D2 / REV-ERB-BETA / EAR-1R / ORPHAN NUCLEAR HORMONE RECEPTOR BD73


Mass: 22319.328 Da / Num. of mol.: 2 / Fragment: LIGAND-BINDING DOMAIN, RESIDUES 386-579
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PET28 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q14995
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 59 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.12 Å3/Da / Density % sol: 43 % / Description: NONE
Crystal growpH: 7.5
Details: 14% POLYETHYLENE GLYCOL 4000, 10% ISOPROPANOL, 100MM HEPES (PH 7.5)

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 6C1 / Wavelength: 0.97935
DetectorType: ADSC CCD / Detector: CCD / Date: Apr 21, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97935 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 74212 / % possible obs: 99 % / Observed criterion σ(I): 0 / Redundancy: 8.4 % / Biso Wilson estimate: 31.5 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 13.1
Reflection shellResolution: 1.89→1.96 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.74 / Mean I/σ(I) obs: 1.5 / % possible all: 95.2

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Processing

Software
NameVersionClassification
CNS1.1refinement
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 2.4→29.56 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 213935.5 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: DISORDERED REGION CHAIN A 471-480
RfactorNum. reflection% reflectionSelection details
Rfree0.28 1323 4.9 %RANDOM
Rwork0.223 ---
obs0.223 26828 94.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 46.0598 Å2 / ksol: 0.350549 e/Å3
Displacement parametersBiso mean: 45.7 Å2
Baniso -1Baniso -2Baniso -3
1-4.45 Å20 Å20 Å2
2--4.45 Å20 Å2
3----8.89 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.39 Å0.3 Å
Luzzati d res low-5 Å
Luzzati sigma a0.35 Å0.25 Å
Refinement stepCycle: LAST / Resolution: 2.4→29.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2690 0 0 59 2749
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d19.6
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.85
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.4→2.55 Å / Rfactor Rfree error: 0.023 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.346 234 5.6 %
Rwork0.276 3958 -
obs--88.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP

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