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PDB | 3L0L | Crystal structure of orphan nuclear receptor RORgamma in complex with natural ligand

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Internal ID
69040
PDB Entry ID
3L0L
Title
Crystal structure of orphan nuclear receptor RORgamma in complex with natural ligand
Authors
Martynowski, D.,Li, Y.
Primary Citation
AuthorsJin, L., Martynowski, D., Zheng, S., Wada, T., Xie, W., Li, Y.
TitleStructural basis for hydroxycholesterols as natural ligands of orphan nuclear receptor RORgamma.
JournalMol.Endocrinol., v.24, pp.923 - 929, 2010
AbstractView
Pubmed20203100
DOI10.1210/me.2009-0507
 
History
Deposition: 2009-12-10Release: 2010-03-16Last Modified: 2010-05-12
Experimental Method
TypeX-RAY DIFFRACTION
Parameters
Resolution [Å]R-Value (Obs.)R-Value (Work)R-FreeSpace Group
1.740.1890.1860.252P 21 21 21
Unit Cell
Length [Å]a66.78b86.26c91.94
Angles [°]alpha90.00beta90.00gamma90.00
Molecular Description
PolymerMoleculeMutationFragmentChainsEC NumberOther details
1Nuclear receptor ROR-gammaRORgammaA, B
2SCR2-2SRC2-2C, E
Functional Class
Source
PolymerScientific NameCommon NameExpression System
1Homo sapienshumanEscherichia coli
2Homo sapienshumanEscherichia coli
Related PDB Entries
IDDetails
3L0J
Chemical Component
IdentifierNameFormulaLigand StructureLigand Interaction
HC325-HYDROXYCHOLESTEROLC27H46O2[View][View]
SCOP Classification
CATH Classification
Structural Details
KeywordTRANSCRIPTION
Textnuclear receptor, RORgamma, DNA-binding, Metal-binding, Nucleus, Receptor, Transcription, Transcription regulation, Zinc-finger, Activator, Phosphoprotein
 
Polymeric Molecules
Chain A
DescriptionNuclear receptor ROR-gamma
FragmentRORgamma
Polymer typepolypeptide
Formula Weight28865.6
Source Methodgenetically manipulated
Entity NameRetinoid-related orphan receptor-gamma, Nuclear receptor RZR-gamma, Nuclear receptor subfamily 1 group F member 3
Entity Name Sysn/a
 
Chain B
DescriptionNuclear receptor ROR-gamma
FragmentRORgamma
Polymer typepolypeptide
Formula Weight28865.6
Source Methodgenetically manipulated
Entity NameRetinoid-related orphan receptor-gamma, Nuclear receptor RZR-gamma, Nuclear receptor subfamily 1 group F member 3
Entity Name Sysn/a
 
Chain C
DescriptionSCR2-2
FragmentSRC2-2
Polymer typepolypeptide
Formula Weight1621.9
Source Methodgenetically manipulated
Entity NameNCoA-2, Transcriptional intermediary factor 2, hTIF2
Entity Name Sysn/a
 
Chain E
DescriptionSCR2-2
FragmentSRC2-2
Polymer typepolypeptide
Formula Weight1621.9
Source Methodgenetically manipulated
Entity NameNCoA-2, Transcriptional intermediary factor 2, hTIF2
Entity Name Sysn/a
 
Entity Poly
EntityChiralityLinkageMonomer# Mon.StrandTypeDetails
1n/anonon/aA,Bpolypeptide(L)n/a
2n/anonon/aC,Epolypeptide(L)n/a
Ligands And Prosthetic Groups
IDNameFormulaWeightLigand Structure
HC325-HYDROXYCHOLESTEROLC27H46O2402.659View
Natural/Genetically Modified Source
Common Namehuman
Scientific NameHomo sapiens
Source Genusn/a
GeneRORC, NR1F3, RORG, RZRG
Host Common Namen/a
Host Scientific NameEscherichia coli
Host Genusn/a
Host Cell Linen/a
Host Strainn/a
Host Vector Typen/a
Host Plasmidn/a
 
Common Namehuman
Scientific NameHomo sapiens
Source Genusn/a
GeneNCOA2, TIF2
Host Common Namen/a
Host Scientific NameEscherichia coli
Host Genusn/a
Host Cell Linen/a
Host Strainn/a
Host Vector Typen/a
Host Plasmidn/a
 
Unit Cell
Length a (Å)Length b Å)Length c (Å)
66.7886.2691.94
Angle Alpha (°)Angle Beta (°)Angle Gamma (°)
90.0090.0090.00
Space Group
P 21 21 21
Diffraction Detector
Detectorn/a
Typen/a
Detailsn/a
Collection Daten/a
 
Diffraction Radiation
Monochromatorn/a
Diffraction ProtocolSINGLE WAVELENGTH
Wavelengthn/a
Wavelength Listn/a
 
Diffraction Source
SourceSYNCHROTRON
TypeAPS BEAMLINE 21-ID-F
SiteAPS
Beamline21-ID-F
 
Reflection Details
Observed Criterion Sigma (F)n/a
Observed Criterion Sigma (I)n/a
Resolution (High)1.74
Resolution (Low)37.87
Number Reflections (All) n/a
Number Reflections (Observed)52446
Percent Possible (Observed)n/a
R Merge I (Observed)n/a
Net I Over Average Sigma (I)n/a
B (Isotropic) From Wilson Plotn/a
Redundancyn/a
 
Refinement Statistics
Structure Solution MethodMOLECULAR REPLACEMENT
Resolution (High)1.74
Resolution (Low)40.56
Cut-off Sigma (F)n/a
Cut-off Sigma (I)n/a
Number of Reflections (All)n/a
Number of Reflections (Observed)49707
Number of Reflections (R-Free) 2669
Percent Reflections (Observed)95.40
R-Factor (All)n/a
R-Factor (Observed)0.18948
R-Work0.18625
R-Free0.25164
R-Free Selection DetailsRANDOM
 
Temperature Factor Modeling
Isotropic Thermal Modeln/a
Mean Isotropic B Value19.105
Anisotropic B[1][1]0.00
Anisotropic B[1][2]0.00
Anisotropic B[1][3]0.00
Anisotropic B[2][2]-0.02
Anisotropic B[2][3]0.00
Anisotropic B[3][3]0.02
 
Resolution Shells
Shell Resol (High)1.74
Shell Resolution (Low)n/a
Number of Reflections (Observed)n/a
Number of Reflections (R-Free)131
Number of Reflections (R-Work)2236
R-Factor (R-Work)0.265
R-Factor (R-Free)0.408
R-Free Errorn/a
Percent Reflections (Observed)59.23
 
RMS Deviations
First|Previous|1 of 2|Next|Last|
Parameter TypeDeviation From Ideal
r_bond_refined_d0.015
r_bond_other_dn/a
r_angle_refined_deg1.681
r_angle_other_degn/a
r_dihedral_angle_1_deg4.845
r_dihedral_angle_2_deg35.618
r_dihedral_angle_3_deg16.149
r_dihedral_angle_4_deg19.840
r_chiral_restr0.109
r_gen_planes_refined0.007
r_gen_planes_othern/a
r_nbd_refined0.217
r_nbd_othern/a
r_nbtor_refined0.307
r_nbtor_othern/a
r_xyhbond_nbd_refined0.196
r_xyhbond_nbd_othern/a
r_metal_ion_refinedn/a
r_metal_ion_othern/a
r_symmetry_vdw_refined0.254
First|Previous|1 of 2|Next|Last|
Number of Non-Hydrogen Atoms Used in Refinement
Protein Atoms4243
Nucleic Acid Atoms0
Heterogen Atoms58
Solvent Atoms727
 
Programs
Data Collectionn/a
Data Reduction (intensity integration)n/a
Data Reduction (data scaling)n/a
Structure Solutionn/a
Structure RefinementREFMAC 5.2.0019
 
Software
Classificationrefinement
Software NameREFMAC
Software Version 5.2.0019
 
Sequence Chain
A
Sequence
  1   PEAPYASLTE  IEHLVQSVCK  SYRETCQLRL  EDLLRQRSNI  FSREEVTGYQ  RKSMWEMWER

 61   CAHHLTEAIQ  YVVEFAKRLS  GFMELCQNDQ  IVLLKAGAME  VVLVRMCRAY  NADNRTVFFE

121   GKYGGMELFR  ALGCSELISS  IFDFSHSLSA  LHFSEDEIAL  YTALVLINAH  RPGLQEKRKV

181   EQLQYNLELA  FHHHLCKTHR  QSILAKLPPK  GKLRSLCSQH  VERLQIFQHL  HPIVVQAAFP

241   PLYKELFS  

Sequence Chain
B
Sequence
  1   PEAPYASLTE  IEHLVQSVCK  SYRETCQLRL  EDLLRQRSNI  FSREEVTGYQ  RKSMWEMWER

 61   CAHHLTEAIQ  YVVEFAKRLS  GFMELCQNDQ  IVLLKAGAME  VVLVRMCRAY  NADNRTVFFE

121   GKYGGMELFR  ALGCSELISS  IFDFSHSLSA  LHFSEDEIAL  YTALVLINAH  RPGLQEKRKV

181   EQLQYNLELA  FHHHLCKTHR  QSILAKLPPK  GKLRSLCSQH  VERLQIFQHL  HPIVVQAAFP

241   PLYKELFS  

Sequence Chain
C
Sequence
 1   EKHKILHRLL  QDS  

Sequence Chain
E
Sequence
 1   EKHKILHRLL  QDS