4O9R

Human Smoothened Receptor structure in complex with cyclopamine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.204 Å
  • R-Value Free: 0.278 
  • R-Value Work: 0.232 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Lipidic cubic phase injector facilitates membrane protein serial femtosecond crystallography.

Weierstall, U.James, D.Wang, C.White, T.A.Wang, D.Liu, W.Spence, J.C.Bruce Doak, R.Nelson, G.Fromme, P.Fromme, R.Grotjohann, I.Kupitz, C.Zatsepin, N.A.Liu, H.Basu, S.Wacker, D.Han, G.W.Katritch, V.Boutet, S.Messerschmidt, M.Williams, G.J.Koglin, J.E.Marvin Seibert, M.Klinker, M.Gati, C.Shoeman, R.L.Barty, A.Chapman, H.N.Kirian, R.A.Beyerlein, K.R.Stevens, R.C.Li, D.Shah, S.T.Howe, N.Caffrey, M.Cherezov, V.

(2014) Nat Commun 5: 3309-3309

  • DOI: 10.1038/ncomms4309

  • PubMed Abstract: 
  • Lipidic cubic phase (LCP) crystallization has proven successful for high-resolution structure determination of challenging membrane proteins. Here we present a technique for extruding gel-like LCP with embedded membrane protein microcrystals, providi ...

    Lipidic cubic phase (LCP) crystallization has proven successful for high-resolution structure determination of challenging membrane proteins. Here we present a technique for extruding gel-like LCP with embedded membrane protein microcrystals, providing a continuously renewed source of material for serial femtosecond crystallography. Data collected from sub-10-μm-sized crystals produced with less than 0.5 mg of purified protein yield structural insights regarding cyclopamine binding to the Smoothened receptor.


    Organizational Affiliation

    Department of Physics, Arizona State University, Tempe, Arizona 85287, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Smoothened homolog/Soluble cytochrome b562 chimeric protein
A
468Homo sapiensEscherichia coli
This entity is chimeric
Gene Names: SMO (SMOH), cybC
Find proteins for Q99835 (Homo sapiens)
Go to Gene View: SMO
Go to UniProtKB:  Q99835
Find proteins for P0ABE7 (Escherichia coli)
Go to UniProtKB:  P0ABE7
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CY8
Query on CY8

Download SDF File 
Download CCD File 
A
Cyclopamine
(3alpha,8alpha,14beta,22S,23R)-17,23-epoxyveratraman-3-ol
C27 H41 N O2
QASFUMOKHFSJGL-LAFRSMQTSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
CY8IC50: 64 - 1900 nM (98) BINDINGDB
CY8Kd: 12.4 nM (98) BINDINGDB
CY8Ki: 12.7 nM (98) BINDINGDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.204 Å
  • R-Value Free: 0.278 
  • R-Value Work: 0.232 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 40.500α = 90.00
b = 157.300β = 97.00
c = 52.400γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
PHASERphasing
CrystFELdata reduction
CrystFELdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Revision History 

  • Version 1.0: 2014-03-05
    Type: Initial release
  • Version 1.1: 2017-08-02
    Type: Refinement description, Source and taxonomy
  • Version 1.2: 2018-02-14
    Type: Data collection