4WG0

Crystal structure of a tridecameric superhelix


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.82 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.187 

Starting Model: in silico
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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Structure of a 13-fold superhelix (almost) determined from first principles.

Schoch, G.A.Sammito, M.Millan, C.Uson, I.Rudolph, M.G.

(2015) IUCrJ 2: 177-187

  • DOI: https://doi.org/10.1107/S2052252515000238
  • Primary Citation of Related Structures:  
    4WG0

  • PubMed Abstract: 

    Nuclear hormone receptors are cytoplasm-based transcription factors that bind a ligand, translate to the nucleus and initiate gene transcription in complex with a co-activator such as TIF2 (transcriptional intermediary factor 2). For structural studies the co-activator is usually mimicked by a peptide of circa 13 residues, which for the largest part forms an α-helix when bound to the receptor. The aim was to co-crystallize the glucocorticoid receptor in complex with a ligand and the TIF2 co-activator peptide. The 1.82 Å resolution diffraction data obtained from the crystal could not be phased by molecular replacement using the known receptor structures. HPLC analysis of the crystals revealed the absence of the receptor and indicated that only the co-activator peptide was present. The self-rotation function displayed 13-fold rotational symmetry, which initiated an exhaustive but unsuccessful molecular-replacement approach using motifs of 13-fold symmetry such as α- and β-barrels in various geometries. The structure was ultimately determined by using a single α-helix and the software ARCIMBOLDO, which assembles fragments placed by PHASER before using them as seeds for density modification model building in SHELXE. Systematic variation of the helix length revealed upper and lower size limits for successful structure determination. A beautiful but unanticipated structure was obtained that forms superhelices with left-handed twist throughout the crystal, stabilized by ligand interactions. Together with the increasing diversity of structural elements in the Protein Data Bank the results from TIF2 confirm the potential of fragment-based molecular replacement to significantly accelerate the phasing step for native diffraction data at around 2 Å resolution.


  • Organizational Affiliation

    Molecular Design and Chemical Biology, F. Hoffmann-La Roche Ltd , Grenzacherstrasse 124, 4070 Basel, Switzerland.


Macromolecules

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Nuclear receptor coactivator 2
A, B, C, D, E
A, B, C, D, E, F, G, H, I, J, K, L, M
15Homo sapiensMutation(s): 2 
UniProt & NIH Common Fund Data Resources
Find proteins for Q15596 (Homo sapiens)
Explore Q15596 
Go to UniProtKB:  Q15596
PHAROS:  Q15596
GTEx:  ENSG00000140396 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ15596
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CHD
Query on CHD

Download Ideal Coordinates CCD File 
CA [auth F]
FA [auth G]
IA [auth H]
LA [auth I]
OA [auth J]
CA [auth F],
FA [auth G],
IA [auth H],
LA [auth I],
OA [auth J],
P [auth A],
R [auth B],
RA [auth K],
T [auth C],
UA [auth L],
V [auth D],
XA [auth M],
Z [auth E]
CHOLIC ACID
C24 H40 O5
BHQCQFFYRZLCQQ-OELDTZBJSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
AA [auth F]
BA [auth F]
DA [auth G]
EA [auth G]
GA [auth H]
AA [auth F],
BA [auth F],
DA [auth G],
EA [auth G],
GA [auth H],
HA [auth H],
JA [auth I],
KA [auth I],
MA [auth J],
N [auth A],
NA [auth J],
O [auth A],
PA [auth K],
Q [auth B],
QA [auth K],
S [auth C],
SA [auth L],
TA [auth L],
U [auth D],
VA [auth M],
W [auth E],
WA [auth M],
X [auth E],
Y [auth E]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.82 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.187 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 95.869α = 90
b = 37.784β = 96.84
c = 101.43γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
PHENIXrefinement
Cootmodel building
Arcimboldophasing
SADABSdata scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-01-21
    Type: Initial release
  • Version 1.1: 2015-03-11
    Changes: Database references
  • Version 1.2: 2015-04-22
    Changes: Database references
  • Version 1.3: 2024-05-01
    Changes: Data collection, Database references, Derived calculations, Refinement description