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- PDB-3n00: Crystal Structure of a deletion mutant of human Reverba ligand bi... -

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Basic information

Entry
Database: PDB / ID: 3n00
TitleCrystal Structure of a deletion mutant of human Reverba ligand binding domain bound with an NCoR ID1 peptide determined to 2.60A
Components
  • Nuclear receptor corepressor 1
  • Rev-erbA-alpha
KeywordsTranscription regulator / Reverba NCoRID1 / anti-parallel b-sheet
Function / homology
Function and homology information


regulation of circadian sleep/wake cycle / positive regulation of bile acid biosynthetic process / NR1D1 (REV-ERBA) represses gene expression / circadian temperature homeostasis / regulation of type B pancreatic cell proliferation / negative regulation of astrocyte activation / negative regulation of microglial cell activation / Loss of MECP2 binding ability to the NCoR/SMRT complex / response to leptin / negative regulation of neuroinflammatory response ...regulation of circadian sleep/wake cycle / positive regulation of bile acid biosynthetic process / NR1D1 (REV-ERBA) represses gene expression / circadian temperature homeostasis / regulation of type B pancreatic cell proliferation / negative regulation of astrocyte activation / negative regulation of microglial cell activation / Loss of MECP2 binding ability to the NCoR/SMRT complex / response to leptin / negative regulation of neuroinflammatory response / negative regulation of toll-like receptor 4 signaling pathway / negative regulation of androgen receptor signaling pathway / regulation of insulin secretion involved in cellular response to glucose stimulus / negative regulation of JNK cascade / glycogen biosynthetic process / negative regulation of glycolytic process / negative regulation of cold-induced thermogenesis / nuclear thyroid hormone receptor binding / regulation of fat cell differentiation / nuclear steroid receptor activity / negative regulation of fatty acid metabolic process / NR1H2 & NR1H3 regulate gene expression to control bile acid homeostasis / Notch-HLH transcription pathway / E-box binding / intracellular glucose homeostasis / locomotor rhythm / histone deacetylase complex / regulation of lipid metabolic process / Regulation of MECP2 expression and activity / spindle assembly / cellular response to interleukin-1 / negative regulation of canonical NF-kappaB signal transduction / 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 / proteasomal protein catabolic process / transcription corepressor binding / negative regulation of miRNA transcription / cholesterol homeostasis / HDACs deacetylate histones / nuclear receptor binding / Downregulation of SMAD2/3:SMAD4 transcriptional activity / RNA polymerase II transcription regulatory region sequence-specific DNA binding / circadian regulation of gene expression / Heme signaling / protein destabilization / 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 / histone deacetylase binding / 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 / transcription corepressor activity / nuclear receptor activity / sequence-specific double-stranded DNA binding / Circadian Clock / cellular response to tumor necrosis factor / chromatin organization / cellular response to lipopolysaccharide / RNA polymerase II-specific DNA-binding transcription factor binding / dendritic spine / cell differentiation / nuclear body / 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 / dendrite / heme binding / 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 / 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 / Retinoid X Receptor / Retinoid X 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 / Retinoid X Receptor / Retinoid X Receptor / 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 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Nuclear receptor corepressor 1 / Nuclear receptor subfamily 1 group D member 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsGampe, R. / Nolte, R.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2010
Title: Structure of Rev-erbalpha bound to N-CoR reveals a unique mechanism of nuclear receptor-co-repressor interaction.
Authors: Phelan, C.A. / Gampe, R.T. / Lambert, M.H. / Parks, D.J. / Montana, V. / Bynum, J. / Broderick, T.M. / Hu, X. / Williams, S.P. / Nolte, R.T. / Lazar, M.A.
History
DepositionMay 13, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 30, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 16, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 1.3Sep 6, 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Rev-erbA-alpha
B: Nuclear receptor corepressor 1


Theoretical massNumber of molelcules
Total (without water)30,0822
Polymers30,0822
Non-polymers00
Water1,11762
1
A: Rev-erbA-alpha
B: Nuclear receptor corepressor 1

A: Rev-erbA-alpha
B: Nuclear receptor corepressor 1


Theoretical massNumber of molelcules
Total (without water)60,1654
Polymers60,1654
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_676x-y+1,-y+2,-z+11
Buried area5470 Å2
ΔGint-48 kcal/mol
Surface area18680 Å2
MethodPISA
2


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2040 Å2
ΔGint-17 kcal/mol
Surface area10030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)112.550, 112.550, 103.833
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32

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Components

#1: Protein Rev-erbA-alpha / Nuclear receptor subfamily 1 group D member 1 / V-erbA-related protein 1 / EAR-1


Mass: 27612.463 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NR1D1, EAR1, HREV, THRAL / Production host: Escherichia coli (E. coli) / Strain (production host): BL21DE3 / References: UniProt: P20393
#2: Protein/peptide Nuclear receptor corepressor 1 / N-CoR1 / N-CoR


Mass: 2469.860 Da / Num. of mol.: 1 / Fragment: CORNR box 2 residues 2045-2065 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: O75376
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 62 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsRESIDUES 324-422 WERE DELETED IN THIS CONSTRUCT.

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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: 2.1 Å3/Da / Density % sol: 41.53 %
Crystal growTemperature: 295 K / Method: vapor diffusion / pH: 7.5
Details: 1ul of precipitant composed of 6-9% of PEG 3350, 8% glycerol, 200mM proline, 80mM HEPES was mixed with 1uL of the Rev-erba NCoR complex at 5-6 mG/Lit to obtain diffraction grade crystals, pH ...Details: 1ul of precipitant composed of 6-9% of PEG 3350, 8% glycerol, 200mM proline, 80mM HEPES was mixed with 1uL of the Rev-erba NCoR complex at 5-6 mG/Lit to obtain diffraction grade crystals, pH 7.5, VAPOR DIFFUSION, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: MAR CCD 165 mm / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. all: 7931 / Num. obs: 7921 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 10.9 % / Biso Wilson estimate: 32 Å2 / Rmerge(I) obs: 0.049 / Net I/σ(I): 50.5
Reflection shellResolution: 2.6→2.69 Å / Redundancy: 9.8 % / Rmerge(I) obs: 0.296 / Mean I/σ(I) obs: 7.3 / Num. unique all: 783 / % possible all: 99.4

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Processing

Software
NameVersionClassification
JDirectordata collection
AMoREphasing
REFMAC6.0.2refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1db1

1db1


Resolution: 2.6→30.04 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.918 / SU B: 10.17 / SU ML: 0.206 / Cross valid method: THROUGHOUT / ESU R Free: 0.32 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26633 225 2.8 %RANDOM
Rwork0.19861 ---
obs0.20035 7693 99.86 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 39.146 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å20 Å2
2---0.01 Å20 Å2
3---0.01 Å2
Refinement stepCycle: LAST / Resolution: 2.6→30.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1549 0 0 62 1611
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0221570
X-RAY DIFFRACTIONr_bond_other_d0.0010.021055
X-RAY DIFFRACTIONr_angle_refined_deg1.1261.9672116
X-RAY DIFFRACTIONr_angle_other_deg0.83732564
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4335201
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.15623.17563
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.11515274
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.9341512
X-RAY DIFFRACTIONr_chiral_restr0.0550.2255
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.021730
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02318
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6041.51012
X-RAY DIFFRACTIONr_mcbond_other0.0671.5417
X-RAY DIFFRACTIONr_mcangle_it1.18421610
X-RAY DIFFRACTIONr_scbond_it1.5913558
X-RAY DIFFRACTIONr_scangle_it2.94.5506
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.602→2.669 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.262 16 -
Rwork0.264 554 -
obs--98.79 %

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