Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Standalone Viewers  
Protein Workshop | Ligand Explorer

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 52806.82 
• Atom Count: 3419 
• Residue Count: 468 
• Unique protein chains: 1

4O9R

Human Smoothened Receptor structure in complex with cyclopamine

• DOI: 10.2210/pdb4O9R/pdb

• Classification: SIGNALING PROTEIN
• Organism(s): Homo sapiens, Escherichia coli
• Expression System: Spodoptera frugiperda
• Mutation(s): 3 


• Deposited: 2014-01-02 Released: 2014-03-05 
• Deposition Author(s): Wang, C., Weierstall, U., James, D., White, T.A., Wang, D., Liu, W., Spence, J.C.H., Doak, R.B., 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., Willams, G.J., Koglin, J.E., Seibert, M.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.A., Howe, N., Caffrey, M., Cherezov, V., GPCR Network (GPCR)

---

Experimental Data Snapshot

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

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

• PubMed: 24525480 
• 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, 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.,School of Medicine and School of Biochemistry and Immunology, Trinity College Dublin, Dublin 2, Ireland.,1] Center for Free-Electron Laser Science, DESY, Notkestrasse 85, Hamburg 22607, Germany [2] Departamento de Química, Universidad Autónoma de Madrid, Ciudad Universitaria de Cantoblanco, Madrid 28049, Spain.,Department of Chemistry and Biochemistry, Arizona State University, Tempe, Arizona 85287, USA.,SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California 94025, USA.,The Scripps Research Institute, Department of Integrative Structural and Computational Biology, La Jolla, California 92037, USA.,1] Center for Free-Electron Laser Science, DESY, Notkestrasse 85, Hamburg 22607, Germany [2] Department of Physics, University of Hamburg, Hamburg 22761, Germany [3] Center for Ultrafast Imaging, Hamburg 22607, Germany.,Center for Free-Electron Laser Science, DESY, Notkestrasse 85, Hamburg 22607, Germany.,Department of Physics, Arizona State University, Tempe, Arizona 85287, USA.,1] Department of Physics, Arizona State University, Tempe, Arizona 85287, USA [2] Center for Free-Electron Laser Science, DESY, Notkestrasse 85, Hamburg 22607, Germany.,1] SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California 94025, USA [2] Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), Uppsala SE-751 24, Sweden.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Smoothened homolog/Soluble cytochrome b562 chimeric protein	A	468	Homo sapiens, Escherichia coli This entity is chimeric	Mutation(s): 3  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
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
CY8	A	Cyclopamine (3alpha,8alpha,14beta,22S,23R)-17,23-epoxyveratraman-3-ol C27 H41 N O2 QASFUMOKHFSJGL-LAFRSMQTSA-N

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
CY8	IC50: 64 - 1900 nM (98) BINDINGDB
CY8	Kd: 12.4 nM (98) BINDINGDB
CY8	Ki: 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 = 40.500	α = 90.00
b = 157.300	β = 97.00
c = 52.400	γ = 90.00

Software Package:

Software Name	Purpose
CrystFEL	data reduction
PHASER	phasing
CrystFEL	data scaling
PHENIX	refinement

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2014-01-02 
• Released Date: 2014-03-05 
• Deposition Author(s): Wang, C., Weierstall, U., James, D., White, T.A., Wang, D., Liu, W., Spence, J.C.H., Doak, R.B., 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., Willams, G.J., Koglin, J.E., Seibert, M.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.A., Howe, N., Caffrey, M., Cherezov, V., GPCR Network (GPCR)

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