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- PDB-5vb3: X-ray structure of nuclear receptor ROR-gammat Ligand Binding Dom... -

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Basic information

Entry
Database: PDB / ID: 5vb3
TitleX-ray structure of nuclear receptor ROR-gammat Ligand Binding Domain + SRC2 peptide
ComponentsNuclear receptor ROR-gamma, SRC2 chimera
KeywordsTRANSCRIPTION / NUCLEAR RECEPTOR / NUCLEAR HORMONE RECEPTOR
Function / homology
Function and homology information


cellular response to sterol / T-helper 17 cell differentiation / regulation of steroid metabolic process / ligand-activated transcription factor activity / Peyer's patch development / positive regulation of circadian rhythm / T-helper cell differentiation / oxysterol binding / RUNX3 Regulates Immune Response and Cell Migration / negative regulation of thymocyte apoptotic process ...cellular response to sterol / T-helper 17 cell differentiation / regulation of steroid metabolic process / ligand-activated transcription factor activity / Peyer's patch development / positive regulation of circadian rhythm / T-helper cell differentiation / 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 / DNA-binding transcription factor activity, RNA polymerase II-specific / nuclear body / DNA-binding transcription factor activity / RNA polymerase II cis-regulatory region sequence-specific DNA binding / 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
Nuclear receptor ROR-gamma
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsLi, X.
CitationJournal: J. Biol. Chem. / Year: 2017
Title: Structural studies unravel the active conformation of apo ROR gamma t nuclear receptor and a common inverse agonism of two diverse classes of ROR gamma t inhibitors.
Authors: Li, X. / Anderson, M. / Collin, D. / Muegge, I. / Wan, J. / Brennan, D. / Kugler, S. / Terenzio, D. / Kennedy, C. / Lin, S. / Labadia, M.E. / Cook, B. / Hughes, R. / Farrow, N.A.
History
DepositionMar 28, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 7, 2017Provider: repository / Type: Initial release
Revision 1.1Jul 26, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Mar 6, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _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, SRC2 chimera
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,4652
Polymers32,4421
Non-polymers231
Water2,864159
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area140 Å2
ΔGint-10 kcal/mol
Surface area12720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.272, 61.272, 154.226
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, SRC2 chimera / 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: residues 260-507
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) / 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 159 / 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: 2.23 Å3/Da / Density % sol: 44.87 %
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: Nov 29, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.95→43.33 Å / Num. obs: 21942 / % possible obs: 98.5 % / Redundancy: 11.8 % / Rmerge(I) obs: 0.074 / Net I/σ(I): 14.4
Reflection shellResolution: 1.95→2.02 Å / Redundancy: 12.56 % / Rmerge(I) obs: 0.593 / Mean I/σ(I) obs: 3.2 / % possible all: 98

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Processing

Software
NameVersionClassification
PHENIX1.8.2_1309refinement
d*TREK9.9.9.4Ldata reduction
d*TREKdata scaling
PHENIX1.8.2_1309phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.95→43.326 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.02
RfactorNum. reflection% reflection
Rfree0.2298 1123 5.12 %
Rwork0.1957 --
obs0.1974 21934 98.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.95→43.326 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2099 0 1 159 2259
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0042195
X-RAY DIFFRACTIONf_angle_d0.7312965
X-RAY DIFFRACTIONf_dihedral_angle_d15.611818
X-RAY DIFFRACTIONf_chiral_restr0.063321
X-RAY DIFFRACTIONf_plane_restr0.004382
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9501-1.99540.29591490.23972506X-RAY DIFFRACTION98
1.9954-2.04530.26841440.25352563X-RAY DIFFRACTION98
2.0453-2.10060.31281330.25482550X-RAY DIFFRACTION98
2.1006-2.16250.2891410.23642520X-RAY DIFFRACTION98
2.1625-2.23230.35771520.22562520X-RAY DIFFRACTION98
2.2323-2.3120.24261280.20692569X-RAY DIFFRACTION99
2.312-2.40460.24961580.20942547X-RAY DIFFRACTION99
2.4046-2.5140.26181310.20372537X-RAY DIFFRACTION99
2.514-2.64650.28721140.21072595X-RAY DIFFRACTION99
2.6465-2.81230.25521580.21952569X-RAY DIFFRACTION99
2.8123-3.02940.26131430.2132553X-RAY DIFFRACTION99
3.0294-3.33420.21791430.2052577X-RAY DIFFRACTION100
3.3342-3.81640.21261350.17512551X-RAY DIFFRACTION99
3.8164-4.80730.17521280.15862583X-RAY DIFFRACTION99
4.8073-43.33620.19811260.19082580X-RAY DIFFRACTION99

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