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- PDB-5x8q: Crystal Structure of the mutant Human ROR gamma Ligand Binding Do... -

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Basic information

Entry
Database: PDB / ID: 5x8q
TitleCrystal Structure of the mutant Human ROR gamma Ligand Binding Domain With rockogenin.
Components
  • Nuclear receptor ROR-gamma
  • Nuclear receptor corepressor 2
KeywordsTRANSFERASE/IHIBITOR / Inhibitor / Ternary Complex / Nuclear Receptor / TRANSFERASE-IHIBITOR complex
Function / homology
Function and homology information


Loss of MECP2 binding ability to the NCoR/SMRT complex / negative regulation of androgen receptor signaling pathway / regulation of cellular ketone metabolic process / T-helper 17 cell differentiation / ligand-activated transcription factor activity / cellular response to sterol / regulation of steroid metabolic process / nuclear glucocorticoid receptor binding / Peyer's patch development / T-helper cell differentiation ...Loss of MECP2 binding ability to the NCoR/SMRT complex / negative regulation of androgen receptor signaling pathway / regulation of cellular ketone metabolic process / T-helper 17 cell differentiation / ligand-activated transcription factor activity / cellular response to sterol / regulation of steroid metabolic process / nuclear glucocorticoid receptor binding / Peyer's patch development / T-helper cell differentiation / positive regulation of circadian rhythm / oxysterol binding / RUNX3 Regulates Immune Response and Cell Migration / negative regulation of thymocyte apoptotic process / Notch binding / regulation of fat cell differentiation / NR1H2 & NR1H3 regulate gene expression to control bile acid homeostasis / Notch-HLH transcription pathway / Regulation of MECP2 expression and activity / regulation of glucose metabolic process / estrous cycle / lymph node development / adipose tissue development / nuclear retinoid X receptor binding / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / response to organonitrogen compound / lactation / transcription repressor complex / Regulation of lipid metabolism by PPARalpha / xenobiotic metabolic process / cerebellum development / negative regulation of miRNA transcription / SUMOylation of transcription cofactors / HDACs deacetylate histones / Downregulation of SMAD2/3:SMAD4 transcriptional activity / circadian regulation of gene expression / PPARA activates gene expression / NOTCH1 Intracellular Domain Regulates Transcription / Cytoprotection by HMOX1 / Constitutive Signaling by NOTCH1 PEST Domain Mutants / Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants / DNA-binding transcription repressor activity, RNA polymerase II-specific / nuclear matrix / histone deacetylase binding / Transcriptional regulation of white adipocyte differentiation / HCMV Early Events / Nuclear Receptor transcription pathway / transcription corepressor activity / nuclear receptor activity / sequence-specific double-stranded DNA binding / response to estradiol / Interleukin-4 and Interleukin-13 signaling / nuclear body / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / negative regulation of DNA-templated transcription / chromatin binding / chromatin / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / DNA binding / zinc ion binding / nucleoplasm / membrane / nucleus
Similarity search - Function
N-CoR, GPS2-interacting domain / G-protein pathway suppressor 2-interacting domain / Nuclear receptor ROR / Retinoid-related orphan receptors, DNA-binding 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 ...N-CoR, GPS2-interacting domain / G-protein pathway suppressor 2-interacting domain / Nuclear receptor ROR / Retinoid-related orphan receptors, DNA-binding 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
Chem-82R / Nuclear receptor ROR-gamma / Nuclear receptor corepressor 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsNoguchi, M. / Nomura, A. / Murase, K. / Doi, S. / Yamaguchi, K. / Adachi, T.
CitationJournal: Genes Cells / Year: 2017
Title: Ternary complex of human ROR gamma ligand-binding domain, inverse agonist and SMRT peptide shows a unique mechanism of corepressor recruitment
Authors: Noguchi, M. / Nomura, A. / Murase, K. / Doi, S. / Yamaguchi, K. / Hirata, K. / Shiozaki, M. / Hirashima, S. / Kotoku, M. / Yamaguchi, T. / Katsuda, Y. / Steensma, R. / Li, X. / Tao, H. / ...Authors: Noguchi, M. / Nomura, A. / Murase, K. / Doi, S. / Yamaguchi, K. / Hirata, K. / Shiozaki, M. / Hirashima, S. / Kotoku, M. / Yamaguchi, T. / Katsuda, Y. / Steensma, R. / Li, X. / Tao, H. / Tse, B. / Fenn, M. / Babine, R. / Bradley, E. / Crowe, P. / Thacher, S. / Adachi, T. / Kamada, M.
History
DepositionMar 3, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 7, 2017Provider: repository / Type: Initial release
Revision 1.1Jun 28, 2017Group: Database references / Category: citation
Item: _citation.country / _citation.journal_volume ..._citation.country / _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Nov 22, 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 ROR-gamma
B: Nuclear receptor corepressor 2
C: Nuclear receptor ROR-gamma
D: Nuclear receptor corepressor 2
E: Nuclear receptor ROR-gamma
F: Nuclear receptor corepressor 2
G: Nuclear receptor ROR-gamma
H: Nuclear receptor corepressor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)131,14812
Polymers129,4178
Non-polymers1,7314
Water5,765320
1
A: Nuclear receptor ROR-gamma
B: Nuclear receptor corepressor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,7873
Polymers32,3542
Non-polymers4331
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1420 Å2
ΔGint-9 kcal/mol
Surface area12580 Å2
MethodPISA
2
C: Nuclear receptor ROR-gamma
D: Nuclear receptor corepressor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,7873
Polymers32,3542
Non-polymers4331
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1390 Å2
ΔGint-10 kcal/mol
Surface area12690 Å2
MethodPISA
3
E: Nuclear receptor ROR-gamma
F: Nuclear receptor corepressor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,7873
Polymers32,3542
Non-polymers4331
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1380 Å2
ΔGint-9 kcal/mol
Surface area12650 Å2
MethodPISA
4
G: Nuclear receptor ROR-gamma
H: Nuclear receptor corepressor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,7873
Polymers32,3542
Non-polymers4331
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1440 Å2
ΔGint-11 kcal/mol
Surface area12550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.630, 71.940, 99.210
Angle α, β, γ (deg.)90.00, 90.06, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Nuclear receptor ROR-gamma / Nuclear receptor RZR-gamma / Nuclear receptor subfamily 1 group F member 3 / RAR-related orphan ...Nuclear receptor RZR-gamma / Nuclear receptor subfamily 1 group F member 3 / RAR-related orphan receptor C / Retinoid-related orphan receptor-gamma


Mass: 29754.301 Da / Num. of mol.: 4 / Fragment: UNP residues 261-518 / Mutation: K469A,R473A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RORC, NR1F3, RORG, RZRG / Production host: Escherichia coli (E. coli) / References: UniProt: P51449
#2: Protein/peptide
Nuclear receptor corepressor 2 / N-CoR2 / CTG repeat protein 26 / SMAP270 / Silencing mediator of retinoic acid and thyroid hormone ...N-CoR2 / CTG repeat protein 26 / SMAP270 / Silencing mediator of retinoic acid and thyroid hormone receptor / SMRT / T3 receptor-associating factor / TRAC / Thyroid- / retinoic-acid-receptor-associated corepressor


Mass: 2599.999 Da / Num. of mol.: 4 / Fragment: UNP residues 2346-2367
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NCOR2, CTG26 / Production host: synthetic construct (others) / References: UniProt: Q9Y618
#3: Chemical
ChemComp-82R / (1R,2S,4S,5'R,6R,7S,8R,9S,10R,12S,13S,16S,18S)-5',7,9,13-tetramethylspiro[5-oxapentacyclo[10.8.0.0^{2,9}.0^{4,8}.0^{13,18}]icosane-6,2'-oxane]-10,16-diol / rockogenin


Mass: 432.636 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C27H44O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 320 / 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: 2.2 Å3/Da / Density % sol: 43.98 %
Crystal growTemperature: 299 K / Method: vapor diffusion, sitting drop / pH: 6.9
Details: 0.1M MES pH6.0, 10% PEG6000, Sitting DROP, temperature 299K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97949 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: May 21, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.61
11-h,-k,l20.39
ReflectionResolution: 2.2→79.63 Å / Num. obs: 57108 / % possible obs: 99.9 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.049 / Net I/σ(I): 12.5
Reflection shellResolution: 2.2→2.26 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.486 / Mean I/σ(I) obs: 1.5 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0155refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3L0L

3l0l


Resolution: 2.2→79.63 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.937 / SU B: 5.625 / SU ML: 0.151 / Cross valid method: THROUGHOUT / ESU R: 0.057 / ESU R Free: 0.045
RfactorNum. reflection% reflectionSelection details
Rfree0.2411 2971 5.2 %RANDOM
Rwork0.19052 ---
obs0.19317 54120 99.55 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 51.757 Å2
Baniso -1Baniso -2Baniso -3
1--38.12 Å2-0 Å2-0.47 Å2
2--51.05 Å20 Å2
3----12.93 Å2
Refinement stepCycle: 1 / Resolution: 2.2→79.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7843 0 124 320 8287
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0198202
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6021.97211085
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1325976
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.94423.106396
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.731151503
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.2191570
X-RAY DIFFRACTIONr_chiral_restr0.1130.21199
X-RAY DIFFRACTIONr_gen_planes_refined0.010.026020
X-RAY DIFFRACTIONr_gen_planes_other
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_it5.8084.9053907
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it7.5137.3294882
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it6.8255.3154295
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined12.2291.90733501
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.198→2.255 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.413 226 -
Rwork0.403 3844 -
obs--96.01 %

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