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- PDB-2v0v: Crystal Structure of Rev-Erb beta -

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Basic information

Entry
Database: PDB / ID: 2v0v
TitleCrystal Structure of Rev-Erb beta
ComponentsORPHAN NUCLEAR RECEPTOR NR1D2
KeywordsTRANSCRIPTION / ZINC / RECEPTOR / REPRESSOR / ZINC-FINGER / DNA-BINDING / CONSTITUTIVE REPRESSION / TRANSCRIPTION REGULATION / ORPHAN RECEPTOR / A-HELICAL SANDWICH / METAL-BINDING / NUCLEAR PROTEIN
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. / Jun Kim, S. / Eon Ryu, S.
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. / Jun Kim, S. / Kim, K.-J. / Yoon, S.-M. / Park, B.-C. / Eon Ryu, S.
History
DepositionMay 19, 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 1.3Oct 24, 2018Group: Data collection / Refinement description / Source and taxonomy
Category: entity_src_gen / software
Item: _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name ..._entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain / _software.name
Revision 1.4May 22, 2019Group: Data collection / Refinement description / Category: refine / Item: _refine.pdbx_ls_cross_valid_method
Revision 1.5May 8, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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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
C: ORPHAN NUCLEAR RECEPTOR NR1D2
D: ORPHAN NUCLEAR RECEPTOR NR1D2


Theoretical massNumber of molelcules
Total (without water)87,7774
Polymers87,7774
Non-polymers00
Water1,72996
1
A: ORPHAN NUCLEAR RECEPTOR NR1D2


Theoretical massNumber of molelcules
Total (without water)21,9441
Polymers21,9441
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: ORPHAN NUCLEAR RECEPTOR NR1D2


Theoretical massNumber of molelcules
Total (without water)21,9441
Polymers21,9441
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
3
C: ORPHAN NUCLEAR RECEPTOR NR1D2


Theoretical massNumber of molelcules
Total (without water)21,9441
Polymers21,9441
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
4
D: ORPHAN NUCLEAR RECEPTOR NR1D2


Theoretical massNumber of molelcules
Total (without water)21,9441
Polymers21,9441
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)102.456, 102.456, 143.964
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number80
Space group name H-MI41
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.99868, -0.04858, 0.01665), (-0.04847, 0.9988, 0.00699), (-0.01697, 0.00617, -0.99984)-1.30339, 0.91793, 18.78336
2given(-0.08449, 0.99569, 0.03837), (0.99641, 0.08425, 0.00776), (0.00449, 0.03889, -0.99923)-3.50674, 51.04293, -17.22289
3given(0.06159, 0.9957, 0.0692), (-0.99801, 0.06048, 0.01809), (0.01383, -0.07017, 0.99744)-47.98832, -6.59137, 38.27809

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Components

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


Mass: 21944.166 Da / Num. of mol.: 4 / 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 BL21(DE3) (bacteria) / References: UniProt: Q14995
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 96 / 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 Å3/Da / Density % sol: 39 % / Description: NONE
Crystal growpH: 7.5 / Details: PEG 4000 18%, ISOPROPANOL 10%, 100 MM HEPES PH 7.5

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 1
DetectorType: ADSC CCD / Detector: CCD / Date: Apr 25, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→30 Å / Num. obs: 29048 / % possible obs: 99.4 % / Redundancy: 5 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 17.6
Reflection shellResolution: 2.4→2.49 Å / Rmerge(I) obs: 0.32 / Mean I/σ(I) obs: 4.7 / % possible all: 99.1

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Processing

Software
NameClassification
SHELXL-97refinement
HKL-2000data reduction
HKL-2000data scaling
SHELXDEphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 2.4→99 Å / Num. parameters: 23276 / Num. restraintsaints: 23794 / Cross valid method: FREE R-VALUE / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.2195 1357 5 %RANDOM
all0.1376 27157 --
obs0.1765 -93.6 %-
Refine analyzeNum. disordered residues: 0 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 5818
Refinement stepCycle: LAST / Resolution: 2.4→99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5714 0 0 96 5810
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.005
X-RAY DIFFRACTIONs_angle_d0.021
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.0229
X-RAY DIFFRACTIONs_zero_chiral_vol0.023
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.031
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.023
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.112
X-RAY DIFFRACTIONs_approx_iso_adps0

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