4O9R

Human Smoothened Receptor structure in complex with cyclopamine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 0.278 
  • R-Value Work: 0.232 
  • R-Value Observed: 0.234 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.4 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: https://doi.org/10.1038/ncomms4309
  • Primary Citation of Related Structures:  
    4O9R

  • 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, 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

    Max-Planck-Institut für medizinische Forschung, Jahnstrasse 29, Heidelberg 69120, Germany.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Smoothened homolog/Soluble cytochrome b562 chimeric protein468Homo sapiensEscherichia coliMutation(s): 3 
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for P0ABE7 (Escherichia coli)
Explore P0ABE7 
Go to UniProtKB:  P0ABE7
Find proteins for Q99835 (Homo sapiens)
Explore Q99835 
Go to UniProtKB:  Q99835
GTEx:  ENSG00000128602 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsP0ABE7Q99835
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CY8
Query on CY8

Download Ideal Coordinates CCD File 
B [auth A]Cyclopamine
C27 H41 N O2
QASFUMOKHFSJGL-LAFRSMQTSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
CY8 BindingDB:  4O9R Ki: 12.7 (nM) from 1 assay(s)
Kd: 12.4 (nM) from 1 assay(s)
IC50: min: 64, max: 1900 (nM) from 7 assay(s)
Experimental Data & Validation

Experimental Data

Unit Cell:
Length ( Å )Angle ( ˚ )
a = 40.5α = 90
b = 157.3β = 97
c = 52.4γ = 90
Software Package:
Software NamePurpose
PHASERphasing
PHENIXrefinement
CrystFELdata reduction
CrystFELdata scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2014-03-05
    Type: Initial release
  • Version 1.1: 2017-08-02
    Changes: Refinement description, Source and taxonomy
  • Version 1.2: 2018-02-14
    Changes: Data collection
  • Version 1.3: 2023-08-16
    Changes: Data collection, Database references, Derived calculations
  • Version 1.4: 2023-09-20
    Changes: Refinement description