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- PDB-6wmq: Crystal Structure of Human REV-ERBbeta Ligand Binding Domain Co-B... -

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Basic information

Entry
Database: PDB / ID: 6wmq
TitleCrystal Structure of Human REV-ERBbeta Ligand Binding Domain Co-Bound to Heme and NCoR ID1 Peptide
Components
  • Nuclear receptor Rev-ErbA beta variant 1
  • Nuclear receptor corepressor 1
KeywordsTRANSCRIPTION / Nuclear receptor / heme-binding protein
Function / homology
Function and homology information


regulation of skeletal muscle cell differentiation / NR1D1 (REV-ERBA) represses gene expression / Loss of MECP2 binding ability to the NCoR/SMRT complex / negative regulation of androgen receptor signaling pathway / negative regulation of JNK cascade / negative regulation of glycolytic process / circadian behavior / nuclear thyroid hormone receptor binding / NR1H2 & NR1H3 regulate gene expression to control bile acid homeostasis / negative regulation of fatty acid metabolic process ...regulation of skeletal muscle cell differentiation / NR1D1 (REV-ERBA) represses gene expression / Loss of MECP2 binding ability to the NCoR/SMRT complex / negative regulation of androgen receptor signaling pathway / negative regulation of JNK cascade / negative regulation of glycolytic process / circadian behavior / nuclear thyroid hormone receptor binding / NR1H2 & NR1H3 regulate gene expression to control bile acid homeostasis / negative regulation of fatty acid metabolic process / Notch-HLH transcription pathway / lipid homeostasis / locomotor rhythm / histone deacetylase complex / regulation of lipid metabolic process / Regulation of MECP2 expression and activity / spindle assembly / energy homeostasis / Nuclear signaling by ERBB4 / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / transcription repressor complex / Regulation of lipid metabolism by PPARalpha / hormone-mediated signaling pathway / negative regulation of miRNA transcription / HDACs deacetylate histones / nuclear receptor binding / Downregulation of SMAD2/3:SMAD4 transcriptional activity / Heme signaling / Transcriptional activation of mitochondrial biogenesis / regulation of circadian rhythm / PPARA activates gene expression / Cytoprotection by HMOX1 / NOTCH1 Intracellular Domain Regulates Transcription / mitotic spindle / Constitutive Signaling by NOTCH1 PEST Domain Mutants / Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants / DNA-binding transcription repressor activity, RNA polymerase II-specific / negative regulation of inflammatory response / Transcriptional regulation of white adipocyte differentiation / Activation of anterior HOX genes in hindbrain development during early embryogenesis / HCMV Early Events / Nuclear Receptor transcription pathway / histone deacetylase binding / transcription corepressor activity / nuclear receptor activity / Circadian Clock / sequence-specific double-stranded DNA binding / chromatin organization / regulation of inflammatory response / RNA polymerase II-specific DNA-binding transcription factor binding / cell differentiation / 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 / chromatin / regulation of DNA-templated transcription / 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 / membrane / nucleus / cytosol / cytoplasm
Similarity search - Function
N-CoR, GPS2-interacting domain / G-protein pathway suppressor 2-interacting domain / SANT domain profile. / SANT domain / Myb domain / Myb-like DNA-binding domain / SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains / SANT/Myb domain / Homeobox-like domain superfamily / Nuclear hormone receptor ...N-CoR, GPS2-interacting domain / G-protein pathway suppressor 2-interacting domain / SANT domain profile. / SANT domain / Myb domain / Myb-like DNA-binding domain / SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains / SANT/Myb domain / Homeobox-like domain superfamily / 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
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / Nuclear receptor Rev-ErbA beta variant 1 / Nuclear receptor corepressor 1 / Nuclear receptor subfamily 1 group D member 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.55 Å
AuthorsMosure, S.A. / Shang, J. / Kojetin, D.J.
CitationJournal: Sci Adv / Year: 2021
Title: Structural basis for heme-dependent NCoR binding to the transcriptional repressor REV-ERB beta.
Authors: Mosure, S.A. / Strutzenberg, T.S. / Shang, J. / Munoz-Tello, P. / Solt, L.A. / Griffin, P.R. / Kojetin, D.J.
History
DepositionApr 21, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 17, 2021Provider: repository / Type: Initial release
Revision 1.1Feb 24, 2021Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Nuclear receptor Rev-ErbA beta variant 1
B: Nuclear receptor Rev-ErbA beta variant 1
E: Nuclear receptor corepressor 1
F: Nuclear receptor corepressor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,7056
Polymers50,4724
Non-polymers1,2332
Water1,04558
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, monomer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7570 Å2
ΔGint-83 kcal/mol
Surface area19610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)164.570, 48.500, 58.620
Angle α, β, γ (deg.)90.000, 105.300, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Nuclear receptor Rev-ErbA beta variant 1


Mass: 22494.861 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NR1D2 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: F1D8P2, UniProt: Q14995*PLUS
#2: Protein/peptide Nuclear receptor corepressor 1 / N-CoR1


Mass: 2741.156 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: O75376
#3: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 58 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.24 Å3/Da / Density % sol: 44.98 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop
Details: 2.0 M ammonium sulfate, 0.1 M Na HEPES, pH 7.5, 2% PEG 400

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 0.97741 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Sep 9, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97741 Å / Relative weight: 1
ReflectionResolution: 2.55→54 Å / Num. obs: 14814 / % possible obs: 99.91 % / Redundancy: 2 % / CC1/2: 1 / Rmerge(I) obs: 0.095 / Net I/σ(I): 6.83
Reflection shellResolution: 2.55→2.64 Å / Rmerge(I) obs: 0.366 / Mean I/σ(I) obs: 2.26 / Num. unique obs: 14814 / CC1/2: 0.727 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
SCALAdata scaling
PDB_EXTRACT3.25data extraction
MOSFLMdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3CQV

3cqv


Resolution: 2.55→53.154 Å / SU ML: 0.34 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 27.25 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2704 1482 10.01 %
Rwork0.1993 13326 -
obs0.2065 14808 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 117.54 Å2 / Biso mean: 30.4957 Å2 / Biso min: 8.11 Å2
Refinement stepCycle: final / Resolution: 2.55→53.154 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3354 0 86 58 3498
Biso mean--19.04 33.1 -
Num. residues----423
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083533
X-RAY DIFFRACTIONf_angle_d1.0994800
X-RAY DIFFRACTIONf_chiral_restr0.054539
X-RAY DIFFRACTIONf_plane_restr0.006604
X-RAY DIFFRACTIONf_dihedral_angle_d4.7582494
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
2.5501-2.63240.30811330.21971198
2.6324-2.72640.28591330.22121194
2.7264-2.83560.30191350.21961212
2.8356-2.96460.31771330.21451191
2.9646-3.12090.30691320.22621199
3.1209-3.31640.28881340.21141203
3.3164-3.57240.29171340.18561208
3.5724-3.93190.25621360.18151220
3.9319-4.50050.2251360.1631222
4.5005-5.66920.25851350.19471212
5.6692-53.150.2391410.21281267

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