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- PDB-4ymq: X-ray co-structure of nuclear receptor ROR-GAMMAT + SRC2 peptide ... -

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Basic information

Entry
Database: PDB / ID: 4ymq
TitleX-ray co-structure of nuclear receptor ROR-GAMMAT + SRC2 peptide with a benzothiadiazole dioxide inverse agonist
ComponentsNuclear receptor ROR-gamma
KeywordsNUCLEAR HORMONE RECEPTOR / RORGT / BENZOTHIADIAZOLE DIOXIDE / INVERSE AGONIST
Function / homology
Function and homology information


T-helper 17 cell differentiation / ligand-activated transcription factor activity / cellular response to sterol / regulation of steroid metabolic process / 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 ...T-helper 17 cell differentiation / ligand-activated transcription factor activity / cellular response to sterol / regulation of steroid metabolic process / 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 / regulation of fat cell differentiation / regulation of glucose metabolic process / lymph node development / adipose tissue development / xenobiotic metabolic process / circadian regulation of gene expression / DNA-binding transcription repressor activity, RNA polymerase II-specific / Nuclear Receptor transcription pathway / nuclear receptor activity / sequence-specific double-stranded DNA binding / 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 / chromatin / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / zinc ion binding / nucleoplasm / nucleus
Similarity search - Function
Nuclear receptor ROR / Retinoid-related orphan receptors, DNA-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 receptor ROR / Retinoid-related orphan receptors, DNA-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
Chem-ZBD / Nuclear receptor ROR-gamma
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
Authorsli, X.
CitationJournal: Bioorg.Med.Chem.Lett. / Year: 2015
Title: Discovery of 1,3-dihydro-2,1,3-benzothiadiazole 2,2-dioxide analogs as new RORC modulators.
Authors: Muegge, I. / Collin, D. / Cook, B. / Hill-Drzewi, M. / Horan, J. / Kugler, S. / Labadia, M. / Li, X. / Smith, L. / Zhang, Y.
History
DepositionMar 7, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 22, 2015Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2015Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Source and taxonomy
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / entity_src_gen / pdbx_struct_assembly / pdbx_struct_conn_angle / pdbx_struct_oper_list / struct_conn
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_src_gen.pdbx_alt_source_flag / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Nuclear receptor ROR-gamma
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,1554
Polymers32,4421
Non-polymers7133
Water2,000111
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)61.909, 61.909, 156.965
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 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: 32442.436 Da / Num. of mol.: 1 / Fragment: UNP residues 260-507
Source method: isolated from a genetically manipulated source
Details: Human RORgt ligand binding domain with N-terminal His6-Thrombin tag and a C-terminal linked SRC2 peptide via a GGG linker
Source: (gene. exp.) Homo sapiens (human) / Fragment: RORgt-LBD 260-507 / Gene: RORC, NR1F3, RORG, RZRG / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P51449
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-ZBD / 4-{3-[4-(1,1,1,3,3,3-hexafluoro-2-hydroxypropan-2-yl)benzyl]-2,2-dioxido-2,1,3-benzothiadiazol-1(3H)-yl}-N-[(2R)-4-hydroxybutan-2-yl]-N-methylbutanamide


Mass: 597.570 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C25H29F6N3O5S
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 111 / Source method: isolated from a natural source / Formula: H2O
Compound detailsThe C-terminal tag is composed of GGG linker and SRC2 peptide.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.32 Å3/Da / Density % sol: 46.94 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: PEG 4000 (2-8%), NaCl 0.5M, PIPES (0.1M) / PH range: 6.9 - 7.2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Apr 7, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→43.78 Å / Num. all: 21390 / Num. obs: 21380 / % possible obs: 99.7 % / Redundancy: 11.62 % / Biso Wilson estimate: 46.94 Å2 / Rmerge(I) obs: 0.074 / Rsym value: 0.078 / Net I/σ(I): 13.7
Reflection shellResolution: 2→2.07 Å / Redundancy: 11.82 % / Rmerge(I) obs: 0.729 / Mean I/σ(I) obs: 2.2 / % possible all: 99.5

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.8.2_1309)refinement
d*TREKdata reduction
d*TREKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→30.955 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.17 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2385 1098 5.14 %Random selection
Rwork0.1981 ---
obs0.2001 21380 99.67 %-
Solvent computationShrinkage radii: 1 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2→30.955 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2071 0 47 111 2229
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0042176
X-RAY DIFFRACTIONf_angle_d0.5862948
X-RAY DIFFRACTIONf_dihedral_angle_d16.392822
X-RAY DIFFRACTIONf_chiral_restr0.053322
X-RAY DIFFRACTIONf_plane_restr0.003369
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.0910.30131300.25832471X-RAY DIFFRACTION100
2.091-2.20120.25191220.22952489X-RAY DIFFRACTION100
2.2012-2.33910.27411500.2212458X-RAY DIFFRACTION100
2.3391-2.51960.26211340.23082512X-RAY DIFFRACTION100
2.5196-2.77310.27651400.23292515X-RAY DIFFRACTION100
2.7731-3.1740.2461550.21462517X-RAY DIFFRACTION100
3.174-3.99750.23011330.18762588X-RAY DIFFRACTION100
3.9975-30.95840.2171340.17862732X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: -1.763 Å / Origin y: 19.5881 Å / Origin z: 19.7694 Å
111213212223313233
T0.2881 Å2-0.026 Å20.0288 Å2-0.2882 Å20.0129 Å2--0.3009 Å2
L2.3795 °2-0.7973 °21.3738 °2-1.5023 °2-0.5219 °2--2.865 °2
S-0.0316 Å °0.0261 Å °0.1025 Å °-0.0023 Å °-0.0188 Å °-0.0802 Å °-0.0247 Å °0.0775 Å °-0.0047 Å °
Refinement TLS groupSelection details: chain A

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